# refs

id: PMID:32265131
data:
  {"abstract":"The N- and O-linked oligosaccharides from fission yeast Schizosaccharomyces pombe not only contain large amounts of d-mannose (Man) but also contain large amounts of d-galactose (Gal). Although the galactomannans of S. pombe are mainly composed of α1,2- or α1,3-linked Gals, some of the terminal α1,2-linked Gals are found to be linked to pyruvylated β1,3-linked galactose (PvGal). We have determined the structural characteristics of the N-glycans and O-glycans in three Schizosaccharomyces species (S. japonicus, S. octosporus, and S. cryophilus) using lectin blot,  1 H NMR spectroscopy, and size-fractionation high performance liquid chromatography (HPLC), and found that the galactosylation of oligosaccharides was a common feature in fission yeasts. In addition, each of the terminal Galα1,2-, Galβ1,3- and non-substituted Man residues exhibited distinct characteristics. A BLAST search of gene databases in Schizosaccharomyces identified genes homologous to pvg1 encoding pyruvyltransferase of S. pombe. These genes, when expressed in an S. pombe pvg1Δ strains, led to the pyruvylation of non-reducing terminal β-linked Gal, suggesting the biosynthetic pathway of PvGal-containing oligosaccharides is highly conserved in fission yeasts.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Fukunaga T, Tanaka N, Furumoto T, Nakakita S, Ohashi T, Higuchi Y, Maekawa H, Takegawa K","authors_abbrev":"Fukunaga T et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"J Biosci Bioeng 2020 Aug;130(2):128-136","cv_annotations":{},"doi":"10.1016/j.jbiosc.2020.03.008","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2020","pubmed_entrez_date":"2020-04-09","pubmed_publication_date":"Aug 2020","terms_by_termid":{},"title":"Characterization of N- and O-linked galactosylated oligosaccharides from fission yeast species.","uniquename":"PMID:32265131"}


id: GO_REF:0000111
data:
  {"abstract":"The Gene Ontology Consortium uses the IC (Inferred by Curator; ECO:0000305) evidence code when assignment of a GO term cannot be supported by direct experimental or sequence-based evidence, but can, based on a curator’s biological knowledge, be reasonably inferred from existing GO annotations to the same gene/gene product.  Use of the IC evidence code with GO_REF:0000111 indicates that a curator inferred the GO term based on at least one supporting annotation with an 'Inferred from Sequence Similarity' (ISS; ECO:0000250) evidence code.  Note that additional supporting annotations may be experimentally evidenced. When using GO_REF:0000111, the 'with/from' field must contain all GO identifiers used as supporting annotations.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"TBD","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotations Inferred by Curator (IC) using at least one Inferred by Sequence Similarity (ISS) annotation to support the inference","uniquename":"GO_REF:0000111"}


id: GO_REF:0000104
data:
  {"abstract":"GO terms are manually assigned to each rule in UniRule. These rules are prepared manually by UniProt curators based on the annotations present in reviewed UniProtKB/Swiss-Prot records that share sequence features, sequence similarity and taxonomy. The assigned GO terms are then transferred to all unreviewed UniProtKB/TrEMBL proteins that meet the conditions given in the UniRule rule. GO annotations using this technique receive the evidence code Inferred from Electronic Annotation (IEA; ECO:0000501). These annotations are updated regularly by UniProt and are available for download on both the GO and GOA EBI ftp sites. To report an annotation error or inconsistency, or for further information, please contact the UniProt Automated Annotation team at automated_annotation@ebi.ac.uk. UniRule is a collaboration between the European Bioinformatics Institute (EMBL-EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource at Georgetown University (PIR). For further information, please see UniProt: a hub for protein information Nucleic Acids Res. 2015, 43, D204, doi: 10.1093/nar/gku989 or www.uniprot.org.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"UniProt curators","canto_curator_role":"JaponicusDB","cv_annotations":{"biological_process":[{"annotations":[64160],"is_not":false,"summary":null,"term":"GO:0030041"},{"annotations":[61874],"is_not":false,"summary":null,"term":"GO:0006308"},{"annotations":[58449,65387,67692],"is_not":false,"summary":null,"term":"GO:0006281"},{"annotations":[63970],"is_not":false,"summary":null,"term":"GO:0071788"},{"annotations":[56879,60327,62130,62808,63680,66540,66748,67723],"is_not":false,"summary":null,"term":"GO:0006541"},{"annotations":[64897],"is_not":false,"summary":null,"term":"GO:0006071"},{"annotations":[67047],"is_not":false,"summary":null,"term":"GO:0043647"},{"annotations":[67690],"is_not":false,"summary":null,"term":"GO:0016226"},{"annotations":[58121],"is_not":false,"summary":null,"term":"GO:0016042"},{"annotations":[61106],"is_not":false,"summary":null,"term":"GO:0051321"},{"annotations":[58879],"is_not":false,"summary":null,"term":"GO:0045292"},{"annotations":[61047,63432,64117],"is_not":false,"summary":null,"term":"GO:0006397"},{"annotations":[57984,63921],"is_not":false,"summary":null,"term":"GO:0051028"},{"annotations":[61003],"is_not":false,"summary":null,"term":"GO:0016095"},{"annotations":[68039],"is_not":false,"summary":null,"term":"GO:1903599"},{"annotations":[63969],"is_not":false,"summary":null,"term":"GO:1903373"},{"annotations":[65819,67586],"is_not":false,"summary":null,"term":"GO:0045901"},{"annotations":[65820,67587],"is_not":false,"summary":null,"term":"GO:0045905"},{"annotations":[60718,67020],"is_not":false,"summary":null,"term":"GO:0097354"},{"annotations":[59846],"is_not":false,"summary":null,"term":"GO:0006612"},{"annotations":[60839,64355],"is_not":false,"summary":null,"term":"GO:0015031"},{"annotations":[68158],"is_not":false,"summary":null,"term":"GO:0042176"},{"annotations":[65274],"is_not":false,"summary":null,"term":"GO:0042254"},{"annotations":[59255],"is_not":false,"summary":null,"term":"GO:0031167"}],"cellular_component":[{"annotations":[64357,66895],"is_not":false,"summary":null,"term":"GO:0005737"},{"annotations":[58962],"is_not":false,"summary":null,"term":"GO:0030659"},{"annotations":[59453,61665,62797,66969],"is_not":false,"summary":null,"term":"GO:0005783"},{"annotations":[58961,59647,60962,62173,67332],"is_not":false,"summary":null,"term":"GO:0005789"},{"annotations":[63967],"is_not":false,"summary":null,"term":"GO:0098826"},{"annotations":[60368],"is_not":false,"summary":null,"term":"GO:0010008"},{"annotations":[58018,59159,60852,65201,65896],"is_not":false,"summary":null,"term":"GO:0000139"},{"annotations":[57013,57392,57711,64634],"is_not":false,"summary":null,"term":"GO:0016020"},{"annotations":[57844,62954,67493],"is_not":false,"summary":null,"term":"GO:0005743"},{"annotations":[66149,66677],"is_not":false,"summary":null,"term":"GO:0005759"},{"annotations":[67897],"is_not":false,"summary":null,"term":"GO:0031533"},{"annotations":[60103],"is_not":false,"summary":null,"term":"GO:0031965"},{"annotations":[67729],"is_not":false,"summary":null,"term":"GO:0005730"},{"annotations":[56905,59657,60222,61240],"is_not":false,"summary":null,"term":"GO:0005634"},{"annotations":[58694],"is_not":false,"summary":null,"term":"GO:0005681"}],"molecular_function":[{"annotations":[61005],"is_not":false,"summary":null,"term":"GO:0003865"},{"annotations":[67334],"is_not":false,"summary":null,"term":"GO:0030246"},{"annotations":[60223,60374,63446,64067],"is_not":false,"summary":null,"term":"GO:0003677"},{"annotations":[60392,68160],"is_not":false,"summary":null,"term":"GO:0030234"},{"annotations":[60512],"is_not":false,"summary":null,"term":"GO:0005525"},{"annotations":[60265,67186],"is_not":false,"summary":null,"term":"GO:0016829"},{"annotations":[56812,57447,59248,59893,60149,60279,60549,61027,61212,61682,61871,62402,62845,62897,63441,63652,64069,64929,66099,66500,67045,67970,68450,68650],"is_not":false,"summary":null,"term":"GO:0046872"},{"annotations":[61320,65147],"is_not":false,"summary":null,"term":"GO:0008509"},{"annotations":[64602],"is_not":false,"summary":null,"term":"GO:0045131"},{"annotations":[56967,57057,58558,59256,59756,61275,66252,66921,66923,67231,67545],"is_not":false,"summary":null,"term":"GO:0003723"},{"annotations":[59257],"is_not":false,"summary":null,"term":"GO:0000179"},{"annotations":[57900],"is_not":false,"summary":null,"term":"GO:0008270"}]},"gene_count":111,"genes_by_uniquename":{"SJAG_00054":null,"SJAG_00083":null,"SJAG_00097":null,"SJAG_00159":null,"SJAG_00231":null,"SJAG_00249":null,"SJAG_00261":null,"SJAG_00328":null,"SJAG_00339":null,"SJAG_00396":null,"SJAG_00471":null,"SJAG_00473":null,"SJAG_00525":null,"SJAG_00530":null,"SJAG_00537":null,"SJAG_00583":null,"SJAG_00616":null,"SJAG_00634":null,"SJAG_00645":null,"SJAG_00691":null,"SJAG_00811":null,"SJAG_00887":null,"SJAG_01004":null,"SJAG_01044":null,"SJAG_01075":null,"SJAG_01184":null,"SJAG_01260":null,"SJAG_01355":null,"SJAG_01375":null,"SJAG_01385":null,"SJAG_01409":null,"SJAG_01415":null,"SJAG_01455":null,"SJAG_01542":null,"SJAG_01574":null,"SJAG_01630":null,"SJAG_01672":null,"SJAG_01677":null,"SJAG_01702":null,"SJAG_01720":null,"SJAG_01811":null,"SJAG_01941":null,"SJAG_01949":null,"SJAG_02019":null,"SJAG_02189":null,"SJAG_02203":null,"SJAG_02245":null,"SJAG_02261":null,"SJAG_02275":null,"SJAG_02287":null,"SJAG_02320":null,"SJAG_02345":null,"SJAG_02408":null,"SJAG_02416":null,"SJAG_02425":null,"SJAG_02463":null,"SJAG_02524":null,"SJAG_02532":null,"SJAG_02557":null,"SJAG_02583":null,"SJAG_02627":null,"SJAG_02655":null,"SJAG_02720":null,"SJAG_02794":null,"SJAG_02812":null,"SJAG_02821":null,"SJAG_02866":null,"SJAG_02907":null,"SJAG_03038":null,"SJAG_03070":null,"SJAG_03158":null,"SJAG_03250":null,"SJAG_03289":null,"SJAG_03328":null,"SJAG_03355":null,"SJAG_03396":null,"SJAG_03479":null,"SJAG_03539":null,"SJAG_03574":null,"SJAG_03588":null,"SJAG_03593":null,"SJAG_03594":null,"SJAG_03609":null,"SJAG_03638":null,"SJAG_03650":null,"SJAG_03775":null,"SJAG_03810":null,"SJAG_03812":null,"SJAG_03866":null,"SJAG_03877":null,"SJAG_03997":null,"SJAG_04021":null,"SJAG_04088":null,"SJAG_04096":null,"SJAG_04111":null,"SJAG_04183":null,"SJAG_04208":null,"SJAG_04217":null,"SJAG_04233":null,"SJAG_04350":null,"SJAG_04368":null,"SJAG_04474":null,"SJAG_04488":null,"SJAG_04502":null,"SJAG_04634":null,"SJAG_04757":null,"SJAG_04837":null,"SJAG_04880":null,"SJAG_04954":null,"SJAG_05024":null,"SJAG_05323":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0000139":null,"GO:0000179":null,"GO:0003677":null,"GO:0003723":null,"GO:0003865":null,"GO:0005525":null,"GO:0005634":null,"GO:0005681":null,"GO:0005730":null,"GO:0005737":null,"GO:0005743":null,"GO:0005759":null,"GO:0005783":null,"GO:0005789":null,"GO:0006071":null,"GO:0006281":null,"GO:0006308":null,"GO:0006397":null,"GO:0006541":null,"GO:0006612":null,"GO:0008270":null,"GO:0008509":null,"GO:0010008":null,"GO:0015031":null,"GO:0016020":null,"GO:0016042":null,"GO:0016095":null,"GO:0016226":null,"GO:0016829":null,"GO:0030041":null,"GO:0030234":null,"GO:0030246":null,"GO:0030659":null,"GO:0031167":null,"GO:0031533":null,"GO:0031965":null,"GO:0042176":null,"GO:0042254":null,"GO:0043647":null,"GO:0045131":null,"GO:0045292":null,"GO:0045901":null,"GO:0045905":null,"GO:0046872":null,"GO:0051028":null,"GO:0051321":null,"GO:0071788":null,"GO:0097354":null,"GO:0098826":null,"GO:1903373":null,"GO:1903599":null},"title":"Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features.","uniquename":"GO_REF:0000104"}


id: GO_REF:0000062
data:
  {"abstract":"We have created a standard template for classes describing processes occurring in parts of the cell. The underlying equivalence axiom template is \"P and 'occurs in' some C\", where P is a biological process and C is a cellular component.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of processes occurring in parts of the cell in the Gene Ontology","uniquename":"GO_REF:0000062"}


id: PMID:29191091
data:
  {"abstract":"Coenzyme Q (CoQ) is essential for mitochondrial respiration and as a cofactor for sulfide quinone reductase. Schizosaccharomyces pombe produces a human-type CoQ 10 . Here, we analyzed CoQ in other fission yeast species. S. cryophilus and S. octosporus produce CoQ 9 . S. japonicus produces low levels of CoQ 10 , although all necessary genes for CoQ synthesis have been identified in its genome. We expressed three genes (dps1, dlp1, and ppt1) for CoQ synthesis from S. japonicus in the corresponding S. pombe mutants, and confirmed that they were functional. S. japonicus had very low levels of oxygen consumption and was essentially respiration defective, probably due to mitochondrial dysfunction. S. japonicus grows well on minimal medium during anaerobic culture, indicating that it acquires sufficient energy by fermentation. S. japonicus produces comparable levels of ethanol under both normal and elevated temperature (42 °C) conditions, at which S. pombe is not able to grow.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":4,"community_curator":true,"file_name":null,"file_type":null,"name":"Makoto Kawamukai","orcid":null},{"annotation_count":3,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-15","authors":"Kaino T, Tonoko K, Mochizuki S, Takashima Y, Kawamukai M","authors_abbrev":"Kaino T et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-01 07:29:31","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Makoto Kawamukai","canto_curator_role":"community","canto_first_approved_date":"2021-07-15 11:51:14","canto_session_key":"53ebb2b64b3102f9","canto_session_submitted_date":"2021-07-15 08:22:11","canto_triage_status":"Curatable","citation":"Biosci Biotechnol Biochem 2018 Jun;82(6):1031-1042","cv_annotations":{"biological_process":[{"annotations":[115223,115224],"is_not":false,"summary":null,"term":"GO:0006744"},{"annotations":[115222],"is_not":false,"summary":null,"term":"GO:0006743"}],"molecular_function":[{"annotations":[115220,115221],"is_not":false,"summary":null,"term":"GO:0097269"}]},"doi":"10.1080/09168451.2017.1401914","gene_count":3,"genes_by_uniquename":{"SJAG_01865":null,"SJAG_04568":null,"SJAG_06603":null},"genetic_interactions":[[{"gene_a_uniquename":"SJAG_01865","gene_b_uniquename":"SJAG_04568","interaction_type":"Synthetic Rescue"},[{"reference_uniquename":"PMID:29191091","throughput":"low"}]]],"genotypes_by_uniquename":{},"ltp_gene_count":3,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2018","pubmed_entrez_date":"2017-12-02","pubmed_publication_date":"Jun 2018","terms_by_termid":{"GO:0006743":null,"GO:0006744":null,"GO:0097269":null},"title":"Schizosaccharomyces japonicus has low levels of CoQ 10  synthesis, respiration deficiency, and efficient ethanol production.","uniquename":"PMID:29191091"}


id: PMID:23873862
data:
  {"abstract":"Many fungi respond to light and regulate fungal development and behavior. A blue light-activated complex has been identified in Neurospora crassa as the product of the wc-1 and wc-2 genes. Orthologs of WC-1 and WC-2 have hitherto been found only in filamentous fungi and not in yeast, with the exception of the basidiomycete pathogenic yeast Cryptococcus. Here, we report that the fission yeast Schizosaccharomyces japonicus responds to blue light depending on Wcs1 and Wcs2, orthologs of components of the WC complex. Surprisingly, those of ascomycete S. japonicus are more closely related to those of the basidiomycete. S. japonicus reversibly changes from yeast to hyphae in response to environmental stresses. After incubation at 30°C, a colony of yeast was formed, and then hyphal cells extended from the periphery of the colony. When light cycles were applied, distinct dark- and bright-colored hyphal cell stripes were formed because the growing hyphal cells had synchronously activated cytokinesis. In addition, temperature cycles of 30°C for 12 h and 35°C for 12 h or of 25°C for 12 h and 30°C for 12 h during incubation in the dark induced a response in the hyphal cells similar to that of light. The stripe formation of the temperature cycles was independent of the wcs genes. Both light and temperature, which are daily external cues, have the same effect on growing hyphal cells. A dual sensing mechanism of external cues allows organisms to adapt to daily changes of environmental alteration. ","alleles_by_uniquename":{"SJAG_02860:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02860","name":"wcs1delta","uniquename":"SJAG_02860:allele-1"},"SJAG_05242:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_05242","name":"wcs2delta","uniquename":"SJAG_05242:allele-1"}},"annotation_curators":[{"annotation_count":7,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-12-01","authors":"Okamoto S, Furuya K, Nozaki S, Aoki K, Niki H","authors_abbrev":"Okamoto S et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-12-01 10:29:08","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-12-01 10:29:08","canto_session_key":"0e71b7054e7d7754","canto_session_submitted_date":"2022-12-01 10:28:58","canto_triage_status":"Curatable","citation":"Eukaryot Cell 2013 Sep;12(9):1235-43","cv_annotations":{"biological_process":[{"annotations":[115564,115565],"is_not":false,"summary":null,"term":"GO:0071483"}],"molecular_function":[{"annotations":[115563],"is_not":false,"summary":null,"term":"GO:0009882"}],"single_locus_phenotype":[{"annotations":[115566,115567],"is_not":false,"summary":null,"term":"FYPO:0008031"},{"annotations":[115568,115569],"is_not":false,"summary":null,"term":"FYPO:0008046"}]},"doi":"10.1128/EC.00109-13","gene_count":2,"genes_by_uniquename":{"SJAG_02860":null,"SJAG_05242":null},"genotypes_by_uniquename":{"wcs1delta":{"display_name":"wcs1delta","display_uniquename":"wcs1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02860:allele-1","expression":"Null"}]}]},"wcs2delta":{"display_name":"wcs2delta","display_uniquename":"wcs2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_05242:allele-1","expression":"Null"}]}]}},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2013","pubmed_entrez_date":"2013-07-23","pubmed_publication_date":"Sep 2013","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000126":null,"FYPO:0008031":null,"FYPO:0008046":null,"FYPO_EXT:0000001":null,"GO:0009882":null,"GO:0071483":null},"title":"Synchronous activation of cell division by light or temperature stimuli in the dimorphic yeast Schizosaccharomyces japonicus.","uniquename":"PMID:23873862"}


id: PMID:26457121
data:
  {"abstract":"Transposable elements (TEs) are common constituents of centromeres. However, it is not known what causes this relationship. Schizosaccharomyces japonicus contains 10 families of Long Terminal Repeat (LTR)-retrotransposons and these elements cluster in centromeres and telomeres. In the related yeast, Schizosaccharomyces pombe LTR-retrotransposons Tf1 and Tf2 are distributed in the promoter regions of RNA pol II transcribed genes. Sequence analysis of TEs indicates that Tj1 of S. japonicus is related to Tf1 and Tf2, and uses the same mechanism of self-primed reverse transcription. Thus, we wondered why these related retrotransposons localized in different regions of the genome.\nTo characterize the integration behavior of Tj1 we expressed it in S. pombe. We found Tj1 was active and capable of generating de novo integration in the chromosomes of S. pombe. The expression of Tj1 is similar to Type C retroviruses in that a stop codon at the end of Gag must be present for efficient integration. 17 inserts were sequenced, 13 occurred within 12 bp upstream of tRNA genes and 3 occurred at other RNA pol III transcribed genes. The link between Tj1 integration and RNA pol III transcription is reminiscent of Ty3, an LTR-retrotransposon of Saccharomyces cerevisiae that interacts with TFIIIB and integrates upstream of tRNA genes.\nThe integration of Tj1 upstream of tRNA genes and the centromeric clustering of tRNA genes in S. japonicus demonstrate that the clustering of this TE in centromere sequences is due to a unique pattern of integration.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Guo Y, Singh PK, Levin HL","authors_abbrev":"Guo Y et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Mob DNA 2015;6:19","cv_annotations":{},"doi":"10.1186/s13100-015-0048-2","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2015","pubmed_entrez_date":"2015-10-13","pubmed_publication_date":"2015","terms_by_termid":{},"title":"A long terminal repeat retrotransposon of Schizosaccharomyces japonicus integrates upstream of RNA pol III transcribed genes.","uniquename":"PMID:26457121"}


id: PMID:37664581
data:
  {"abstract":"Non-muscle myosin II activation by regulatory light chain (Rlc1 Sp ) phosphorylation at Ser35 is crucial for cytokinesis during respiration in the fission yeast  Schizosaccharomyces pombe.  We show that in the early divergent and dimorphic fission yeast  S. japonicus  non-phosphorylated Rlc1 Sj  regulates the activity of Myo2 Sj  and Myp2 Sj  heavy chains during cytokinesis. Intriguingly, Rlc1 Sj -Myo2 Sj  nodes delay yeast to hyphae onset but are essential for mycelial development. Structure-function analysis revealed that phosphorylation-induced folding of Rlc1 Sp  α1 helix into an open conformation allows precise regulation of Myo2 Sp  during cytokinesis. Consistently, inclusion of bulky tryptophan residues in the adjacent α5 helix triggered Rlc1 Sp  shift and supported cytokinesis in absence of Ser35 phosphorylation. Remarkably, unphosphorylated Rlc1 Sj  lacking the α1 helix was competent to regulate  S. pombe  cytokinesis during respiration. Hence, early diversification resulted in two efficient phosphorylation-independent and -dependent modes of Rlc1 regulation of myosin II activity in fission yeasts, the latter being conserved through evolution.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Prieto-Ruiz F, Gómez-Gil E, Vicente-Soler J, Franco A, Soto T, Madrid M, Cansado J","authors_abbrev":"Prieto-Ruiz F et al.","canto_added_date":"2023-09-05 00:40:05","canto_curator_role":"JaponicusDB","canto_triage_status":"Curatable","citation":"iScience 2023 Sep 15;26(9):107611","cv_annotations":{},"doi":"10.1016/j.isci.2023.107611","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2023","pubmed_entrez_date":"2023-09-04","pubmed_publication_date":"15 Sep 2023","terms_by_termid":{},"title":"Divergence of cytokinesis and dimorphism control by myosin II regulatory light chain in fission yeasts.","uniquename":"PMID:37664581"}


id: PMID:26343758
data:
  {"abstract":"CENP-A is a centromere-specific histone H3 variant that is required for kinetochore assembly and accurate chromosome segregation. For it to function properly, CENP-A must be specifically localized to centromeres. In fission yeast, Scm3sp and the Mis18 complex, composed of Mis16, Eic1, and Mis18, function as a CENP-A(Cnp1)-specific chaperone and a recruiting factor, respectively, and together ensure accurate delivery of CENP-A(Cnp1) to centromeres. Although how Scm3sp specifically recognizes CENP-A(Cnp1) has been revealed recently, the recruiting mechanism of CENP-A(Cnp1) via the Mis18 complex remains unknown. In this study, we have determined crystal structures of Schizosaccharomyces japonicus Mis16 alone and in complex with the helix 1 of histone H4 (H4α1). Crystal structures followed by mutant analysis and affinity pull-downs have revealed that Mis16 recognizes both H4α1 and Scm3sp independently within the CENP-A(Cnp1)/H4:Scm3sp complex. This observation suggests that Mis16 gains CENP-A(Cnp1) specificity by recognizing both Scm3sp and histone H4. Our studies provide insights into the molecular mechanisms underlying specific recruitment of CENP-A(Cnp1)/H4:Scm3sp into centromeres. ","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":4,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-05-13","authors":"An S, Kim H, Cho US","authors_abbrev":"An S et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-05-13 14:11:41","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Val Wood","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-05-13 14:11:41","canto_session_key":"fb189c5ef542852c","canto_session_submitted_date":"2021-05-12 16:00:22","canto_triage_status":"Curatable","citation":"J Mol Biol 2015 Oct 09;427(20):3230-3240","cv_annotations":{"molecular_function":[{"annotations":[115555,115556,115557,115558],"is_not":false,"summary":null,"term":"GO:0042393"}]},"doi":"10.1016/j.jmb.2015.08.022","gene_count":4,"genes_by_uniquename":{"SJAG_00303":null,"SJAG_02513":null,"SJAG_03542":null,"SJAG_03867":null},"genotypes_by_uniquename":{},"ltp_gene_count":3,"ortholog_annotations":[],"paralog_annotations":[],"pdb_entries":[{"entry_authors":"An S,Kim H,Cho U-S","entry_authors_abbrev":"An S et al.","experimental_method":"X-ray","gene_chains":[{"chain":"A","gene_uniquename":"SJAG_03867","position":"1-427"}],"pdb_id":"4xyh","reference_uniquename":"PMID:26343758","resolution":"2.3","title":"Wild-type full length Mis16 in Schizosaccharomyces japonicus"},{"entry_authors":"An S,Kim H,Cho U-S","entry_authors_abbrev":"An S et al.","experimental_method":"X-ray","gene_chains":[{"chain":"B","gene_uniquename":"SJAG_03542","position":"1-103"},{"chain":"A","gene_uniquename":"SJAG_03867","position":"1-427"}],"pdb_id":"4xyi","reference_uniquename":"PMID:26343758","resolution":"3.0","title":"Mis16 with H4 peptide"}],"physical_interactions":[],"publication_year":"2015","pubmed_entrez_date":"2015-09-08","pubmed_publication_date":"09 Oct 2015","terms_by_termid":{"GO:0042393":null},"title":"Mis16 Independently Recognizes Histone H4 and the CENP-ACnp1-Specific Chaperone Scm3sp.","uniquename":"PMID:26343758"}


id: PMID:34427722
data:
  {"abstract":"Fungal pathogens, from phytopathogenic fungus to human pathogens, are able to alternate between the yeast-like form and filamentous forms. This morphological transition (dimorphism) is in close connection with their pathogenic lifestyles and with their responses to changing environmental conditions. The mechanisms governing these morphogenetic conversions are still not fully understood. Therefore, we studied the filamentous growth of the less-known, non-pathogenic dimorphic fission yeast, S. japonicus, which belongs to an ancient and early evolved branch of the Ascomycota. Its RNA sequencing revealed that several hundred genes were up- or down-regulated in the hyphae compared to the yeast-phase cells. These genes belonged to different GO categories, confirming that mycelial growth is a rather complex process. The genes of transport- and metabolic processes appeared especially in high numbers among them. High expression of genes involved in glycolysis and ethanol production was found in the hyphae, while other results pointed to the regulatory role of the protein kinase A (PKA) pathway. The homologues of 49 S. japonicus filament-associated genes were found by sequence alignments also in seven distantly related dimorphic and filamentous species. The comparative genomic analyses between S. japonicus and the closely related but non-dimorphic S. pombe shed some light on the differences in their genomes. All these data can contribute to a better understanding of hyphal growth and those genomic rearrangements that underlie it.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":2,"community_curator":true,"file_name":null,"file_type":null,"name":"Ida Miklos","orcid":"0000-0002-7074-4019"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-10-06","authors":"Papp LA, Ács-Szabó L, Batta G, Miklós I","authors_abbrev":"Papp LA et al.","canto_added_date":"2021-09-29 13:11:40","canto_annotation_status":"APPROVED","canto_approved_date":"2021-10-06 13:34:09","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Ida Miklos","canto_curator_role":"community","canto_first_approved_date":"2021-10-06 13:34:09","canto_session_key":"acb5c82405799ef1","canto_session_submitted_date":"2021-09-29 13:38:18","canto_triage_status":"Curatable","citation":"Curr Genet 2021 Dec;67(6):953-968","cv_annotations":{"biological_process":[{"annotations":[115415,115416],"is_not":false,"summary":null,"term":"GO:0030448"}]},"doi":"10.1007/s00294-021-01206-y","gene_count":2,"genes_by_uniquename":{"SJAG_00124":null,"SJAG_04312":null},"genotypes_by_uniquename":{},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-08-24","pubmed_publication_date":"Dec 2021","terms_by_termid":{"GO:0030448":null},"title":"Molecular and comparative genomic analyses reveal evolutionarily conserved and unique features of the Schizosaccharomyces japonicus mycelial growth and the underlying genomic changes.","uniquename":"PMID:34427722"}


id: PMID:9396147
data:
  {"abstract":"Both living and fixed cells of Schizosaccharomyces japonicus var. versatilis showed thread-like mitochondria when studied by phase-contrast and fluorescence microscopy. In the interphase cells, mitochondria extended from pole to pole and converged towards the growing tips. The mitochondrial threads did not disrupt but persisted during mitosis and, subsequently, their bundle was split between the two daughter cells by a concentrically growing septum. Mitochondria in the interphase cells were accompanied by cytoplasmic microtubules. These disappeared during mitosis and, instead, spindle microtubules were formed in the nucleus. The cytoplasmic microtubules reappeared after anaphase B, again in coaligment with mitochondria. Protoplasting as well as the action of microtubule inhibitors methyl-1-(butylcarbamoyl)-2-benzimidazolecarbamate (benomyl) and 2-methylbenzimidazole (MBC) resulted in rapid disintegration of microtubules and, suprisingly, also in disruption of mitochondria into small bodies. Removal of the inhibitors or a short regeneration of protoplasts allowed both the cytoplasmic microtubules and the thread-like mitochondria to reaggregate into the original pattern. Cytochalasin D treatment caused a complete disintegration of actin filaments, while the cytoplasmic microtubules and mitochondria remained intact. These findings of a transient close association of mitochondria and microtubules and their relative independence of the arrangement of actin filaments suggest that microtubules, but not actin cables, form supports for positioning or movement of mitochondria along the cylindrical cells. The persistence of mitochondria in the cell centre during mitosis may be accounted for by the fact that disrupted microtubules fail to provide support for mitochondrial movement towards the cell poles.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Svoboda A, Slaninová I","authors_abbrev":"Svoboda A et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Can J Microbiol 1997 Oct;43(10):945-53","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1997","pubmed_entrez_date":"1997-12-13","pubmed_publication_date":"Oct 1997","terms_by_termid":{},"title":"Colocalization of microtubules and mitochondria in the yeast Schizosaccharomyces japonicus var. versatilis.","uniquename":"PMID:9396147"}


id: GO_REF:0000022
data:
  {"abstract":"GO terms describing processes, functions, and cellular components related to the immune system have existed in the GO from its beginning and been used extensively in the annotation of gene products. However, particularly in the biological process ontology, the initial set of terms relating to immunology failed to cover the breadth of known immunological processes, and in many cases diverged from current usage and understanding in their names, definitions, and ontological placement. As part of a larger effort to improve the representation of immunology in the GO, a GO Content Meeting was held November 15-16, 2005, at The Institute for Genomic Research, to discuss improvements to representation of immunology in the biological process ontology of the GO. As a result of the meeting, a number of high level terms for immunological processes were created, an overall structure for immunologically related terms was established, and certain existing terms were renamed or redefined as well to bring them in line with current usage.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Alison Deckhut Augustine (1), Alan Collmer (2), Judith A. Blake (3, 4), Candace W. Collmer (2, 3), Shane C. Burgess (5), Lindsay Grey Cowell (6), Jennifer I. Clark (3, 7), Bernard de Bono (7), Russell T. Collins (8), Alexander D. Diehl (3, 4), Michelle Gwinn Giglio (3, 9), Jamie A. Lee (10), Linda Hannick (3, 9), Jane Lomax (3, 7), Midori A. Harris (3, 7), Christopher J. Mungall (3, 11), David P. Hill (3, 4), Richard H. Scheuermann (10), Amelia Ireland (3, 7), Alessandro Sette (12) (1. NIAID, 2. Cornell University, 3. The GO Consortium, 4. Mouse Genome Informatics, 5. Mississippi State University, 6. Duke University, 7. EMBL-EBI, 8. University of Cambridge, 9. The Institute for Genomic Research, 10. U.T. Southwestern Medical Center, 11. HHMI, 12. La Jolla Institute for Allergy and Immunology)","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Improving the representation of immunology in the biological process Ontology","uniquename":"GO_REF:0000022"}


id: GO_REF:0000096
data:
  {"abstract":"Mouse Genome Database (MGD), The HUGO Gene Nomenclature Committee (HGNC), and Rat Genome Database (RGD) have extensive procedures in place, overseen by expert curation, to establish orthology relationships between their genes. The Experimentally based annotations annotated by each group (IDA, IMP IPI, IGI, and EXP) are used to provide annotations  to the respective mouse and rat orthologs, and given the ISO evidence code and an entry in the inferred_from field to indicate the orthologous entity. ","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Mouse Genome Informatics scientific curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Automated transfer of experimentally-verified manual GO annotation data to close orthologs.","uniquename":"GO_REF:0000096"}


id: GO_REF:0000079
data:
  {"abstract":"We have created a standard template for classes describing the assembly or disassembly of a cellular component as a biological process. The underlying equivalence axiom templates are \"GO:0022607 and 'results_in_assembly_of' some C\" (assembly) and \"GO:0022411 and 'results_in_disassembly_of' some C\" (disassembly), where C is a cellular component.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of assembly or disassembly of a cell component as biological process in the Gene Ontology","uniquename":"GO_REF:0000079"}


id: PMID:30726171
data:
  {"abstract":"Many fungal species are dimorphic, exhibiting both unicellular yeast-like and filamentous forms. Schizosaccharomyces japonicus, a member of the fission yeast clade, is one such dimorphic fungus. Here, we first identify fruit extracts as natural, stress-free, starvation-independent inducers of filamentation, which we use to describe the properties of the dimorphic switch. During the yeast-to-hypha transition, the cell evolves from a bipolar to a unipolar system with 10-fold accelerated polarized growth but constant width, vacuoles segregated to the nongrowing half of the cell, and hyper-lengthening of the cell. We demonstrate unusual features of S. japonicus hyphae: these cells lack a Spitzenkörper, a vesicle distribution center at the hyphal tip, but display more rapid cytoskeleton-based transport than the yeast form, with actin cables being essential for the transition. S. japonicus hyphae also remain mononuclear and undergo complete cell divisions, which are highly asymmetric: one daughter cell inherits the vacuole, the other the growing tip. We show that these elongated cells scale their nuclear size, spindle length, and elongation rates, but display altered division size controls. This establishes S. japonicus as a unique system that switches between symmetric and asymmetric modes of growth and division.","alleles_by_uniquename":{"SJAG_02392:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02392","name":"pom1delta","uniquename":"SJAG_02392:allele-1"},"SJAG_02695:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02695","name":"tip1delta","uniquename":"SJAG_02695:allele-1"},"SJAG_04703:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04703","name":"for3delta","uniquename":"SJAG_04703:allele-1"}},"annotation_curators":[{"annotation_count":21,"community_curator":true,"file_name":null,"file_type":null,"name":"Sophie Martin","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-06-16","authors":"Kinnaer C, Dudin O, Martin SG","authors_abbrev":"Kinnaer C et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-06-16 18:49:31","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sophie Martin","canto_curator_role":"community","canto_first_approved_date":"2021-06-16 18:49:31","canto_session_key":"bf05a60cb09b4cdb","canto_session_submitted_date":"2021-06-04 10:25:08","canto_triage_status":"Curatable","citation":"Mol Biol Cell 2019 04 01;30(8):975-991","cv_annotations":{"cellular_component":[{"annotations":[115493],"is_not":false,"summary":null,"term":"GO:0051286"},{"annotations":[115475,115477,115479,115481,115483,115485],"is_not":false,"summary":null,"term":"GO:0035838"},{"annotations":[115494],"is_not":false,"summary":null,"term":"GO:0085039"},{"annotations":[115476,115478,115480,115482,115484,115486],"is_not":false,"summary":null,"term":"GO:0001411"},{"annotations":[115487],"is_not":false,"summary":null,"term":"GO:0035371"},{"annotations":[115488],"is_not":false,"summary":null,"term":"GO:0030133"}],"single_locus_phenotype":[{"annotations":[115490],"is_not":false,"summary":null,"term":"FYPO:0003315"},{"annotations":[115491],"is_not":false,"summary":null,"term":"FYPO:0001355"},{"annotations":[115495],"is_not":false,"summary":null,"term":"FYPO:0007801"},{"annotations":[115492],"is_not":false,"summary":null,"term":"FYPO:0004293"},{"annotations":[115489],"is_not":false,"summary":null,"term":"FYPO:0001956"}]},"doi":"10.1091/mbc.E18-12-0774","gene_count":9,"genes_by_uniquename":{"SJAG_01196":null,"SJAG_02392":null,"SJAG_02695":null,"SJAG_03011":null,"SJAG_03625":null,"SJAG_03915":null,"SJAG_04624":null,"SJAG_04703":null,"SJAG_04960":null},"genotypes_by_uniquename":{"for3delta":{"display_name":"for3delta","display_uniquename":"for3delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04703:allele-1","expression":"Null"}]}]},"pom1delta":{"display_name":"pom1delta","display_uniquename":"pom1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02392:allele-1","expression":"Null"}]}]},"tip1delta":{"display_name":"tip1delta","display_uniquename":"tip1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02695:allele-1","expression":"Null"}]}]}},"ltp_gene_count":9,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2019","pubmed_entrez_date":"2019-02-07","pubmed_publication_date":"01 04 2019","terms_by_termid":{"FYPO:0001355":null,"FYPO:0001956":null,"FYPO:0003315":null,"FYPO:0004293":null,"FYPO:0007801":null,"GO:0001411":null,"GO:0030133":null,"GO:0035371":null,"GO:0035838":null,"GO:0051286":null,"GO:0085039":null},"title":"Yeast-to-hypha transition of Schizosaccharomyces japonicus in response to environmental stimuli.","uniquename":"PMID:30726171"}


id: PMID:20618870
data:
  {"abstract":"The genus Schizosaccharomyces is presently comprised of three species, namely Schizosaccharomyces pombe, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus. Here, we describe a hitherto unknown species, Schizosaccharomyces cryophilus, named for its preference for growth at lower temperatures than the other fission yeast species. Although morphologically similar to S. octosporus, analysis of several rapidly evolving sequences, including the D1/D2 divergent domain of the large subunit (LSU) rRNA gene, the RNA subunit of RNAse P and the internal transcribed spacer elements, revealed significant divergence from any previously characterized Schizosaccharomyces strain. Based on phylogenetic analysis of the D1/D2 domain of the LSU rRNA gene, S. octosporus is the closest known relative of S. cryophilus, with the sequences of the two species differing by 25 nucleotide substitutions (>4%). Sequencing of the S. cryophilus genome and phylogenetic analysis of all 1 : 1 protein orthologs confirmed this observation, and together with morphological and physiological characterization, supports the assignment of S. cryophilus as a new species within the genus Schizosaccharomyces. The type strain of the new species is NRRL Y-48691(T) (=NBRC 106824(T)=CBS 11777(T)).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Helston RM, Box JA, Tang W, Baumann P","authors_abbrev":"Helston RM et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Phylogeny and evolutionary studies","citation":"FEMS Yeast Res 2010 Sep;10(6):779-86","cv_annotations":{},"doi":"10.1111/j.1567-1364.2010.00657.x","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2010","pubmed_entrez_date":"2010-07-13","pubmed_publication_date":"Sep 2010","terms_by_termid":{},"title":"Schizosaccharomyces cryophilus sp. nov., a new species of fission yeast.","uniquename":"PMID:20618870"}


id: GO_REF:0000011
data:
  {"abstract":"A Hidden Markov Model (HMM) is a statistical representation of patterns found in a data set. When using HMMs with proteins, the HMM is a statistical model of the patterns of the amino acids found in a multiple alignment of a set of proteins called the \"seed\". Seed proteins are chosen based on sequence similarity to each other. Seed members can be chosen with different levels of relationship to each other. They can be members of a superfamily (ex. ABC transporter, ATP-binding proteins), they can all share the same exact specific function (ex. biotin synthase) or they could share another type of relationship of intermediate specificity (ex. subfamily, domain). New proteins can be scored against the model generated from the seed according to how closely the patterns of amino acids in the new proteins match those in the seed. There are two scores assigned to the HMM which allow annotators to judge how well any new protein scores to the model. Proteins scoring above the \"trusted cutoff\" score can be assumed to be part of the group defined by the seed. Proteins scoring below the \"noise cutoff\" score can be assumed to NOT be a part of the group. Proteins scoring between the trusted and noise cutoffs may be part of the group but may not. One of the important features of HMMs is that they are built from a multiple alignment of protein sequences, not a pairwise alignment. This is significant, since shared similarity between many proteins is much more likely to indicate shared functional relationship than sequence similarity between just two proteins. The usefulness of an HMM is directly related to the amount of care that is taken in chosing the seed members, building a good multiple alignment of the seed members, assessing the level of specificity of the model, and choosing the cutoff scores correctly. In order to properly assess what functional relevance an above-trusted scoring HMM match has to a query, one must carefully determine what the functional scope of the HMM is. If the HMM models proteins that all share the same function then it is likely possible to assign a specific function to high-scoring match proteins based on the HMM. If the HMM models proteins that have a wide variety of functions, then it will not be possible to assign a specific function to the query based on the HMM match, however, depending on the nature of the HMM in question, it may be possible to assign a more general (family or subfamily level) function. In order to determine the functional scope of an HMM, one must carefully read the documentation associated with the HMM. The annotator must also consider whether the function attributed to the proteins in the HMM makes sense for the query based on what is known about the organism in which the query protein resides and in light of any other information that might be available about the query protein. After carefully considering all of these issues the annotator makes an annotation.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Michelle Gwinn, TIGR curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Hidden Markov Models (TIGR)","uniquename":"GO_REF:0000011"}


id: GO_REF:0000078
data:
  {"abstract":"We have created a standard template for classes describing the transport or vesicle-mediated transport of a chemical entity (ChEBI) from and/or to a cellular component as a biological process. The underlying equivalence axiom templates are \"GO:0006810 and 'transports or maintains localization of' some X [ and 'has_target_start_location' some F] [ and 'has_target_end_location' some T]\" (transport) and \"GO:0016192 and 'transports or maintains localization of' some X [ and 'has_target_start_location' some F] [ and 'has_target_end_location' some T]\" (vesicle-mediated transport), where F and T are cellular components and X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation for the transport or vesicle-mediated transport of a chemical from and/or to a cell component as biological process in the Gene Ontology","uniquename":"GO_REF:0000078"}


id: GO_REF:0000101
data:
  {"abstract":"This reference is used to describe functional annotations transferred from one or more reference (\"source\") organisms to a newly annotated (\"target\") organism on the basis of ortholog cluster membership. In detail, predicted (e.g. by AUGUSTUS, see doi:10.1186/1471-2105-7-62) or transferred (e.g. via RATT, see doi:10:1093/nar/gkg1268) gene models in the target genome are translated and processed by OrthoMCL 1.4 together with reference protein sequences to produce clusters of gene products derived from orthologous genes. For each cluster, GO terms are automatically transferred from source products to the target gene products if they are experimentally verified (IDA (ECO:0000314), IMP (ECO:0000315), IPI (ECO:0000353), IGI (ECO:0000316), (EXP ECO:0000269). They are tagged with the ISO evidence code and the \"with/from\" is populated with the source feature references (e.g. \"GeneDB:LmjF.28.0960\"). OrthoMCL runs are done using the parameterization suggested in the OrthoMCL algorithm document (blastall -F 'm S' -e 1e-5).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Sascha Steinbiss, GeneDB curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Automated transfer of experimentally-verified GO annotation data to close orthologs","uniquename":"GO_REF:0000101"}


id: PMID:37457408
data:
  {"abstract":"The online version contains supplementary material available at 10.1007/s10068-023-01265-6.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Choi J, Park SY, Park MK, Kim YS, Ahn C, Kim YJ, Park CS","authors_abbrev":"Choi J et al.","canto_added_date":"2023-07-18 00:40:02","canto_curator_role":"JaponicusDB","canto_triage_status":"Biotech","citation":"Food Sci Biotechnol 2023 Sep;32(10):1383-1393","cv_annotations":{},"doi":"10.1007/s10068-023-01265-6","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2023","pubmed_entrez_date":"2023-07-17","pubmed_publication_date":"Sep 2023","terms_by_termid":{},"title":"Application of  Schizosaccharomyces japonicus  in  makgeolli  fermentation and its brewing characteristics.","uniquename":"PMID:37457408"}


id: PMID:32140970
data:
  {"abstract":"In eukaryotes, chromosome ends (telomeres) are tethered to the inner nuclear membrane. During the early stages of meiosis, telomeres move along the nuclear membrane and gather near the spindle-pole body, resulting in a bouquet-like arrangement of chromosomes. This chromosomal configuration appears to be widely conserved among eukaryotes, and is assumed to play an important role in the normal progression of meiosis, by mediating the proper pairing of homologous chromosomes. In fission yeast, the Bqt1-Bqt2 protein complex plays a key role in tethering the telomere to the inner nuclear membrane. However, the structural details of the complex required to clarify how telomeres are gathered near the spindle-pole body remain enigmatic. Previously, we devised a preparation procedure for the Schizosaccharomyces japonicus Bqt1-Bqt2 complex, in which a SUMO tag was fused to the N-terminus of the Bqt1 protein. This allowed us to purify the Bqt1-Bqt2 complex from the soluble fraction. In the present study, we found that a maltose-binding protein homolog, Athe_0614, served as a better fusion partner than the SUMO protein, resulting in the marked increase in the solubility of the Bqt1-Bqt2 complex. The Athe_0614 fusion partner may open up new avenues for X-ray crystallographic analyses of the structure of the Bqt1-Bqt2 complex.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Yuzurihara H, Aizawa Y, Saotome M, Ichikawa Y, Yokoyama H, Chikashige Y, Haraguchi T, Hiraoka Y, Kurumizaka H, Kagawa W","authors_abbrev":"Yuzurihara H et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Protein J 2020 04;39(2):174-181","cv_annotations":{},"doi":"10.1007/s10930-020-09887-z","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2020","pubmed_entrez_date":"2020-03-07","pubmed_publication_date":"04 2020","terms_by_termid":{},"title":"Improved Methods for Preparing the Telomere Tethering Complex Bqt1-Bqt2 for Structural Studies.","uniquename":"PMID:32140970"}


id: GO_REF:0000113
data:
  {"abstract":"The TFClass (http://tfclass.bioinf.med.uni-goettingen.de/index.jsf) database provides a comprehensive classification of mammalian DNA binding transcription factors (DbTFs) based on their DNA binding domains (DBDs) (PMID:29087517). TFClass classifies mammalian DbTFs by a five-level classification in which the four highest levels represent groups defined by structural and sequence similarities (superclass, class, family, subfamily, and genera) (more details at http://www.edgar-wingender.de/TFClass_schema.html). This classification is based on the combination of background knowledge of the molecular structural features of DBDs (PMID:9340487, PMID:23427989) and phylogenetic trees constructed via multiple sequence alignment with hierarchical clustering of manually validated DBDs and/or full-length protein sequences retrieved from UniProt (PMID:23427989, PMID:23180794, PMID:23427989). ","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Marcio Luis Acencio (1), George Georghiou (2), Sandra Orchard (2), Liv Thommensen (1), Martin Kuiper (1) and Astrid Lægreid (1). (1) Norwegian University of Science and Technology (NTNU), Trondheim, Norway; (2) European Bioinformatics Institute (EBI), Hinxton, Cambridgeshire, United Kingdom","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotation of human sequence-specific DNA binding transcription factors (DbTFs) based on the TFClass database","uniquename":"GO_REF:0000113"}


id: GO_REF:0000105
data:
  {"abstract":"Gene Ontology annotation based on predicted cytoplasmic tRNAs using tRNAscan-SE analysis (doi: 10.1093/nar/25.5.0955) of the Drosophila melanogaster genome (2002). Annotations have been reviewed by FlyBase (2015) and found to be consistent when compared with the most recent tRNAscan-SE analysis of the genome (http://gtrnadb.ucsc.edu/genomes/eukaryota/Dmela6/).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"FlyBase","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotation of transfer RNAs based on tRNAscan-SE analysis of the Drosophila melanogaster genome (2002).","uniquename":"GO_REF:0000105"}


id: GO_REF:0000063
data:
  {"abstract":"We have created a standard template for classes describing processes regulated by other regulating processes. The underlying equivalence axiom template is \"R and 'results_in' some P\", where R is a biological process and P is a regulation of biological process subclass.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of processes regulated by other regulating processes in the Gene Ontology","uniquename":"GO_REF:0000063"}


id: GO_REF:0000025
data:
  {"abstract":"Genes in prokaryotic organisms are often arranged in operons. Genes in an operon are all transcribed into one mRNA. Generally the genes in the operons code for proteins that all have related functions. For example, they may be the steps in a biochemical pathway, or they may be the subunits of a protein complex. Often the genes in operons shared between organisms are syntenic; that is, the same genes are in the same order in the operon in different species. When assessing sequence-comparison-based evidence during the process of manual annotation of a genome, it is often the case that some of the genes in the operon will have strong sequence-based evidence while others will have weak evidence. If seen alone, not in the presence of an operon, the weak evidence in question may not be sufficient to make a functional annotation. However, in the presence of an operon in which there is strong evidence for some of the genes, the very presence of the gene in the operon is a strong indication that the gene shares in the process carried out by the operon. If the putative function is one expected to exist for the process in question and particularly if that function has been observed in the same operon in another species, then the annotation should be made. This type of evidence is inferred from the context of the gene in an operon, and therefore the evidence code is IGC \"inferred from genomic context.\"","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Michelle Gwinn, TIGR curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Operon structure as IGC evidence","uniquename":"GO_REF:0000025"}


id: PMID:32109380
data:
  {"abstract":"Eukaryotic genomes are organized within the nucleus through interactions with inner nuclear membrane (INM) proteins. How chromatin tethering to the INM is controlled in interphase and how this process contributes to subsequent mitotic nuclear envelope (NE) remodeling remains unclear. We have probed these fundamental questions using the fission yeast Schizosaccharomyces japonicus, which breaks and reforms the NE during mitosis. We show that attachments between heterochromatin and the transmembrane Lem2-Nur1 complex at the INM are remodeled in interphase by the ESCRT-III/Vps4 machinery. Failure of ESCRT-III/Vps4 to release Lem2-Nur1 from heterochromatin leads to persistent association of chromosomes with the INM throughout mitosis. At mitotic exit, such trapping of Lem2-Nur1 on heterochromatin prevents it from re-establishing nucleocytoplasmic compartmentalization. Our work identifies the Lem2-Nur1 complex as a substrate for the nuclear ESCRT machinery and explains how the dynamic tethering of chromosomes to the INM is linked to the establishment of nuclear compartmentalization.","alleles_by_uniquename":{"SJAG_01050:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01050","name":"nur1delta","uniquename":"SJAG_01050:allele-1"},"SJAG_01242:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01242","name":"vps32delta","uniquename":"SJAG_01242:allele-1"},"SJAG_01330:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01330","name":"mad2delta","uniquename":"SJAG_01330:allele-1"},"SJAG_01745:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01745","name":"lem2delta","uniquename":"SJAG_01745:allele-1"},"SJAG_03250:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03250","name":"sst4delta","uniquename":"SJAG_03250:allele-1"},"SJAG_03783:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03783","name":"vps24delta","uniquename":"SJAG_03783:allele-1"},"SJAG_03892:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03892","name":"vps4delta","uniquename":"SJAG_03892:allele-1"},"SJAG_03892:allele-2":{"allele_type":"amino_acid_mutation","description":"E233Q","gene_uniquename":"SJAG_03892","name":"Vps4-EQ","uniquename":"SJAG_03892:allele-2"},"SJAG_03892:allele-3":{"allele_type":"amino_acid_mutation","description":"I307T L327S","gene_uniquename":"SJAG_03892","name":"vps4-ts","uniquename":"SJAG_03892:allele-3"},"SJAG_04349:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04349","name":"vps28delta","uniquename":"SJAG_04349:allele-1"},"SJAG_04489:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04489","name":"did4delta","uniquename":"SJAG_04489:allele-1"},"SJAG_04912:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04912","name":"vps25delta","uniquename":"SJAG_04912:allele-1"},"SJAG_05207:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_05207","name":"cmp7delta","uniquename":"SJAG_05207:allele-1"}},"annotation_curators":[{"annotation_count":53,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-06-17","authors":"Pieper GH, Sprenger S, Teis D, Oliferenko S","authors_abbrev":"Pieper GH et al.","canto_added_date":"2021-05-10 02:37:07","canto_annotation_status":"APPROVED","canto_approved_date":"2021-06-17 17:46:25","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-06-17 17:46:25","canto_session_key":"89c611dbc0229af1","canto_session_submitted_date":"2021-06-17 17:46:16","canto_triage_status":"Curatable","citation":"Dev Cell 2020 04 06;53(1):27-41.e6","cv_annotations":{"cellular_component":[{"annotations":[115244],"is_not":false,"summary":null,"term":"GO:0000781"},{"annotations":[115242],"is_not":false,"summary":null,"term":"GO:0005783"},{"annotations":[115264],"is_not":false,"summary":null,"term":"GO:0000792"},{"annotations":[115269],"is_not":false,"summary":null,"term":"GO:1990343"},{"annotations":[115226],"is_not":false,"summary":null,"term":"GO:0000776"},{"annotations":[115246],"is_not":false,"summary":null,"term":"GO:0005771"},{"annotations":[115248],"is_not":false,"summary":null,"term":"GO:0032585"},{"annotations":[115247,115249],"is_not":false,"summary":null,"term":"GO:0031965"},{"annotations":[115270],"is_not":false,"summary":null,"term":"GO:0005643"},{"annotations":[115227,115232,115250],"is_not":false,"summary":null,"term":"GO:0005816"}],"molecular_function":[{"annotations":[115225],"is_not":false,"summary":null,"term":"GO:0043515"}],"multi_locus_phenotype":[{"annotations":[115255],"is_not":false,"summary":null,"term":"FYPO:0007771"},{"annotations":[115266],"is_not":false,"summary":null,"term":"FYPO:0001132"}],"single_locus_phenotype":[{"annotations":[115251,115252,115253],"is_not":false,"summary":null,"term":"FYPO:0001440"},{"annotations":[115262,115263],"is_not":false,"summary":null,"term":"FYPO:0001370"},{"annotations":[115265],"is_not":false,"summary":null,"term":"FYPO:0004718"},{"annotations":[115230,115231,115237,115238,115240,115241,115254,115256,115257,115258,115259,115260,115261],"is_not":false,"summary":null,"term":"FYPO:0007771"},{"annotations":[115243],"is_not":false,"summary":null,"term":"FYPO:0004318"},{"annotations":[115234],"is_not":false,"summary":null,"term":"FYPO:0007073"},{"annotations":[115228,115229,115235,115236],"is_not":false,"summary":null,"term":"FYPO:0007772"},{"annotations":[115239],"is_not":false,"summary":null,"term":"FYPO:0007770"},{"annotations":[115245],"is_not":false,"summary":null,"term":"FYPO:0003780"},{"annotations":[115233],"is_not":false,"summary":null,"term":"FYPO:0003657"},{"annotations":[115267,115268],"is_not":false,"summary":null,"term":"FYPO:0001234"}]},"doi":"10.1016/j.devcel.2020.01.028","gene_count":15,"genes_by_uniquename":{"SJAG_00684":null,"SJAG_01050":null,"SJAG_01242":null,"SJAG_01330":null,"SJAG_01601":null,"SJAG_01745":null,"SJAG_01777":null,"SJAG_03250":null,"SJAG_03299":null,"SJAG_03783":null,"SJAG_03892":null,"SJAG_04349":null,"SJAG_04489":null,"SJAG_04912":null,"SJAG_05207":null},"genotypes_by_uniquename":{"Vps4-EQ-E233Q-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"Vps4-EQ(E233Q aa)","display_uniquename":"Vps4-EQ-E233Q-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03892:allele-2","expression":"Not assayed or wild type"}]}]},"cmp7delta":{"display_name":"cmp7delta","display_uniquename":"cmp7delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_05207:allele-1","expression":"Null"}]}]},"cmp7delta__vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cmp7delta vps4-ts(I307T L327S aa)","display_uniquename":"cmp7delta__vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_05207:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03892:allele-3","expression":"Not assayed or wild type"}]}]},"did4delta":{"display_name":"did4delta","display_uniquename":"did4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04489:allele-1","expression":"Null"}]}]},"lem2delta":{"display_name":"lem2delta","display_uniquename":"lem2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01745:allele-1","expression":"Null"}]}]},"mad2delta":{"display_name":"mad2delta","display_uniquename":"mad2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01330:allele-1","expression":"Null"}]}]},"nur1delta":{"display_name":"nur1delta","display_uniquename":"nur1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01050:allele-1","expression":"Null"}]}]},"nur1delta__vps4delta":{"display_name":"nur1delta vps4delta","display_uniquename":"nur1delta__vps4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01050:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03892:allele-1","expression":"Null"}]}]},"sst4delta":{"display_name":"sst4delta","display_uniquename":"sst4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03250:allele-1","expression":"Null"}]}]},"vps24delta":{"display_name":"vps24delta","display_uniquename":"vps24delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03783:allele-1","expression":"Null"}]}]},"vps25delta":{"display_name":"vps25delta","display_uniquename":"vps25delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04912:allele-1","expression":"Null"}]}]},"vps28delta":{"display_name":"vps28delta","display_uniquename":"vps28delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04349:allele-1","expression":"Null"}]}]},"vps32delta":{"display_name":"vps32delta","display_uniquename":"vps32delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01242:allele-1","expression":"Null"}]}]},"vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"vps4-ts(I307T L327S aa)","display_uniquename":"vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03892:allele-3","expression":"Not assayed or wild type"}]}]},"vps4delta":{"display_name":"vps4delta","display_uniquename":"vps4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03892:allele-1","expression":"Null"}]}]}},"ltp_gene_count":15,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_01242","interactor_uniquename":"SJAG_03892","reference_uniquename":"PMID:32109380","throughput":"low"},{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_04489","interactor_uniquename":"SJAG_03892","reference_uniquename":"PMID:32109380","throughput":"low"},{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_05207","interactor_uniquename":"SJAG_01242","reference_uniquename":"PMID:32109380","throughput":"low"},{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_05207","interactor_uniquename":"SJAG_01745","reference_uniquename":"PMID:32109380","throughput":"low"},{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_05207","interactor_uniquename":"SJAG_03892","reference_uniquename":"PMID:32109380","throughput":"low"}],"publication_year":"2020","pubmed_entrez_date":"2020-02-29","pubmed_publication_date":"06 04 2020","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000137":null,"FYPO:0001132":null,"FYPO:0001234":null,"FYPO:0001370":null,"FYPO:0001440":null,"FYPO:0003657":null,"FYPO:0003780":null,"FYPO:0004318":null,"FYPO:0004718":null,"FYPO:0007073":null,"FYPO:0007770":null,"FYPO:0007771":null,"FYPO:0007772":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"GO:0000093":null,"GO:0000776":null,"GO:0000781":null,"GO:0000792":null,"GO:0000815":null,"GO:0005643":null,"GO:0005771":null,"GO:0005783":null,"GO:0005816":null,"GO:0031965":null,"GO:0032585":null,"GO:0043515":null,"GO:1990343":null},"title":"ESCRT-III/Vps4 Controls Heterochromatin-Nuclear Envelope Attachments.","uniquename":"PMID:32109380"}


id: GO_REF:0000072
data:
  {"abstract":"We have created a standard template for classes describing the homeostasis and cellular homeostasis for a chemical entity (ChEBI) as a biological process. The underlying equivalence axiom templates are \"GO:0048878 and 'regulates level of' some X\" (homeostasis) and \"GO:0055082 and 'regulates level of' some X\" (cellular homeostasis), where X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of chemical homeostasis and cellular chemical homeostasisl as biological process in the Gene Ontology","uniquename":"GO_REF:0000072"}


id: GO_REF:0000060
data:
  {"abstract":"We have created a standard template for classes describing processes involved in other processes. The underlying equivalence axiom template is \"P and 'part_of' some W\", where P and W are biological processes.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of processes involved in other process in the Gene Ontology","uniquename":"GO_REF:0000060"}


id: PMID:35940784
data:
  {"abstract":"Schizosaccharomyces japonicus have been found as dominant yeast species coexisting with Saccharomyces cerevisiae during late stages of spontaneous fermentation of local grapes in Guizhou, China. Therefore, this study further investigated the impacts of the two indigenous yeast species on typicality of crystal grape (Niagara) wine. Five indigenous and one commercial S. cerevisiae strains were firstly selected based on their genotypes and fermentation traits in synthetic medium. All the six S. cerevisiae exhibited high tolerance to glucose, temperature, and SO 2 . The two killer active strains FBKL2.996 and FBKL2.9126 showed relative higher tolerance capacity of ethanol, pH and osmotic pressure than the other four S. cerevisiae strains. Further pure fermentation of six strains using crystal grape must exhibited different contents of volatile compounds, with commercial strain CECA producing the highest levels of acetate esters (phenethyl acetate), ethyl esters (ethyl caprylate, ethyl hexanoate), n-caprylic acid isobutyl ester, and terpenes (linalool) whereas being ranked the last in the sensory analysis. The co-inoculation of indigenous S. japonicus with each of the six S. cerevisiae strains increased the acetate esters (mainly isoamyl acetate) by 2-3 times in crystal grape wine. The indigenous S. cerevisiae FBKL2.9128 showed the most obvious variation of volatile compounds between pure and mixed fermentation, exhibiting the significant increase of isoamyl acetate, ethyl decanoate, ethyl caprylate, ethyl hexanoate, methyl decanoate, and dodecanal when co-inoculated with S. japonicus. Sugar addition in immature crystal grape juice increased the ethanol, glycerol, and some volatile compounds such as ethyl butyrate, but decreased the volatile compounds with floral and animal odors. The aroma sensory analysis confirmed the decrease of varietal aroma in wines with sugar addition when comparing with wines made from immature crystal grape. The results of this study provide basic information on the impact of indigenous S. cerevisaie and S. japonicus, and sugar addition on typicality of crystal grape wine, which would help to improve the wine flavor made from crystal grape in southwest China.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Wang C, Liang S, Yang J, Wu C, Qiu S","authors_abbrev":"Wang C et al.","canto_added_date":"2023-05-04 00:40:03","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Food Res Int 2022 Sep;159:111580","cv_annotations":{},"doi":"10.1016/j.foodres.2022.111580","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2022","pubmed_entrez_date":"2022-08-08","pubmed_publication_date":"Sep 2022","terms_by_termid":{},"title":"The impact of indigenous Saccharomyces cerevisiae and Schizosaccharomyces japonicus on typicality of crystal grape (Niagara) wine.","uniquename":"PMID:35940784"}


id: PMID:36148799
data:
  {"abstract":"Tropomyosins are structurally conserved α-helical coiled-coil proteins that bind along the length of filamentous actin (F-actin) in fungi and animals. Tropomyosins play essential roles in the stability of actin filaments and in regulating myosin II contractility. Despite the crucial role of tropomyosin in actin cytoskeletal regulation, in vivo investigations of tropomyosin are limited, mainly due to the suboptimal live-cell imaging tools currently available. Here, we report on an mNeonGreen (mNG)-tagged tropomyosin, with native promoter and linker length configuration, that clearly reports tropomyosin dynamics in Schizosaccharomyces pombe (Cdc8), Schizosaccharomyces japonicus (Cdc8) and Saccharomyces cerevisiae (Tpm1 and Tpm2). We also describe a fluorescent probe to visualize mammalian tropomyosin (TPM2 isoform). Finally, we generated a camelid nanobody against S. pombe Cdc8, which mimics the localization of mNG-Cdc8 in vivo. Using these tools, we report the presence of tropomyosin in previously unappreciated patch-like structures in fission and budding yeasts, show flow of tropomyosin (F-actin) cables to the cytokinetic actomyosin ring and identify rearrangements of the actin cytoskeleton during mating. These powerful tools and strategies will aid better analyses of tropomyosin and F-actin cables in vivo.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":3,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-25","authors":"Hatano T, Lim TC, Billault-Chaumartin I, Dhar A, Gu Y, Massam-Wu T, Scott W, Adishesha S, Chapa-Y-Lazo B, Springall L, Sivashanmugam L, Mishima M, Martin SG, Oliferenko S, Palani S, Balasubramanian MK","authors_abbrev":"Hatano T et al.","canto_added_date":"2022-11-25 12:03:53","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-25 12:11:22","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2022-11-25 12:11:22","canto_session_key":"d572e8fc7f8a7a38","canto_session_submitted_date":"2022-11-25 12:11:07","canto_triage_status":"Curatable","citation":"J Cell Sci 2022 Sep 15;135(18)","cv_annotations":{"cellular_component":[{"annotations":[115315],"is_not":false,"summary":null,"term":"GO:0070648"},{"annotations":[115317],"is_not":false,"summary":null,"term":"GO:1990819"},{"annotations":[115316],"is_not":false,"summary":null,"term":"GO:0110085"}]},"doi":"10.1242/jcs.260288","gene_count":1,"genes_by_uniquename":{"SJAG_04887":null},"genotypes_by_uniquename":{},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2022","pubmed_entrez_date":"2022-09-23","pubmed_publication_date":"15 Sep 2022","terms_by_termid":{"GO:0070648":null,"GO:0110085":null,"GO:1990819":null},"title":"mNG-tagged fusion proteins and nanobodies to visualize tropomyosins in yeast and mammalian cells.","uniquename":"PMID:36148799"}


id: GO_REF:0000028
data:
  {"abstract":"This GO reference describes the criteria used in assigning the evidence codes of IDA (ECO:0000314), IEP (ECO:0000270), ISS (ECO:0000250), IGC (ECO_0000317), RCA (ECO:0000245) and IEA (ECO:0000501) to annotate gene products from PAMGO_MGG. Standard BLASTP from NCBI was used (http://www.ncbi.nih.gov/blast) to iteratively search reciprocal best hits and thus identify orthologs between predicted proteins of Magnaporthe grisea and GO proteins from multiple organisms with published association to GO terms. The alignments were manually reviewed for those hits with e-value equal to zero and with 80% or better coverage of both query and subject sequences, and for those hits with e<=10^-20, pid >=35 and sequence coverage >=80%. Furthermore, experimental or reviewed data from literature and other sources were incorporated into the GO annotation. IDA was assigned to an annotation if normal function of its gene was determined through transfections into a cell line and overexpression. IEP was assigned to an annotation if according to microarray experiments, its gene was upregulated in a biological process and the fold change was equal to or bigger than 10, or if according to Massively Parallel Signature Sequencing (MPSS), its gene was upregulated only in a certain biological process and the fold change was equal to or bigger than 10. ISS was assigned to an annotation if the entry at the With_column was experimentally characterized and the pairwise alignments were manually reviewed. IGC was assigned to an annotation if it based on comparison and analysis of gene location and structure, clustering of genes, and phylogenetic reconstruction of these genes. RCA was assigned to an annotation if it based on integrated computational analysis of whole genome microarray data, and matches to InterPro, pfam, and COG etc. IEA was assigned to an annotation if its function assignment based on computational work, and no manual review was done.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"PAMGO_MGG curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Criteria for IDA, IEP, ISS, IGC, RCA, and IEA assignment in PAMGO_MGG","uniquename":"GO_REF:0000028"}


id: PMID:36695178
data:
  {"abstract":"Nuclear envelope (NE) expansion must be controlled to maintain nuclear shape and function. The nuclear membrane expands massively during closed mitosis, enabling chromosome segregation within an intact NE. Phosphatidic acid (PA) and diacylglycerol (DG) can both serve as biosynthetic precursors for membrane lipid synthesis. How they are regulated in time and space and what the implications are of changes in their flux for mitotic fidelity are largely unknown. Using genetically encoded PA and DG probes, we show that DG is depleted from the inner nuclear membrane during mitosis in the fission yeast Schizosaccharomyces pombe, but PA does not accumulate, indicating that it is rerouted to membrane synthesis. We demonstrate that DG-to-PA conversion catalyzed by the diacylglycerol kinase Dgk1 (also known as Ptp4) and direct glycerophospholipid synthesis from DG by diacylglycerol cholinephosphotransferase/ethanolaminephosphotransferase Ept1 reinforce NE expansion. We conclude that DG consumption through both the de novo pathway and the Kennedy pathway fuels a spike in glycerophospholipid biosynthesis, controlling NE expansion and, ultimately, mitotic fidelity.","alleles_by_uniquename":{"SJAG_04883:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04883","name":"ptp4delta","uniquename":"SJAG_04883:allele-1"}},"annotation_curators":[{"annotation_count":1,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2023-03-02","authors":"Foo S, Cazenave-Gassiot A, Wenk MR, Oliferenko S","authors_abbrev":"Foo S et al.","canto_added_date":"2023-03-02 10:54:59","canto_annotation_status":"APPROVED","canto_approved_date":"2023-03-02 10:59:33","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2023-03-02 10:59:33","canto_session_key":"d8cda300a89f71aa","canto_session_submitted_date":"2023-03-02 10:59:20","canto_triage_status":"Curatable","citation":"J Cell Sci 2023 Feb 01;136(3)","cv_annotations":{"single_locus_phenotype":[{"annotations":[115182],"is_not":false,"summary":null,"term":"FYPO:0001007"}]},"doi":"10.1242/jcs.260568","gene_count":1,"genes_by_uniquename":{"SJAG_04883":null},"genotypes_by_uniquename":{"ptp4delta":{"display_name":"ptp4delta","display_uniquename":"ptp4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04883:allele-1","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2023","pubmed_entrez_date":"2023-01-25","pubmed_publication_date":"01 Feb 2023","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYPO:0001007":null},"title":"Diacylglycerol at the inner nuclear membrane fuels nuclear envelope expansion in closed mitosis.","uniquename":"PMID:36695178"}


id: PMID:28228545
data:
  {"abstract":"Inactivation of retrotransposons is accompanied by the emergence of centromere-binding protein-B (CENPB) in  Schizosaccharomyces , as well as in metazoans. The RNA interference (RNAi)-induced transcriptional silencing (RITS) complex, comprising chromodomain protein-1 (Chp1), Tas3 (protein with unknown function), and Argonaute (Ago1), plays an important role in RNAi-mediated heterochromatinization. We find that whereas the Ago1 subunit of the RITS complex is highly conserved, Tas3 is lost and Chp1 is truncated in  Schizosaccharomyces cryophilus  and  Schizosaccharomyces octosporus  We show that truncated Chp1 loses the property of heterochromatin localization and silencing when transformed in  Schizosaccharomyces pombe  Furthermore, multiple copies of CENPB, related to  Tc1/mariner and Tc5  transposons, occur in all  Schizosaccharomyces  species, as well as in humans, but with loss of transposase function (except  Schizosaccharomyces japonicus ). We propose that acquisition of  Tc1/mariner and Tc5  elements by horizontal transfer in  S. pombe  (and humans) is accompanied by alteration of their function from a transposase/endonuclease to a heterochromatin protein, designed to suppress transposon expression and recombination. The resulting redundancy of RITS may have eased the selection pressure, resulting in progressive loss or truncation of  tas3  and  chp1  genes in  S. octosporus  and  S. cryophilus  and triggered similar evolutionary dynamics in the metazoan orthologues.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Upadhyay U, Srivastava S, Khatri I, Nanda JS, Subramanian S, Arora A, Singh J","authors_abbrev":"Upadhyay U et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Phylogeny and evolutionary studies","citation":"Mol Biol Cell 2017 Apr 15;28(8):1132-1146","cv_annotations":{},"doi":"10.1091/mbc.E16-07-0485","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2017","pubmed_entrez_date":"2017-02-24","pubmed_publication_date":"15 Apr 2017","terms_by_termid":{},"title":"Ablation of RNA interference and retrotransposons accompany acquisition and evolution of transposases to heterochromatin protein CENPB.","uniquename":"PMID:28228545"}


id: GO_REF:0000094
data:
  {"abstract":"We have created a standard template for classes describing the development of a metazoan structure as a biological process. The underlying equivalence axiom template is \"'anatomical structure development' and 'results in development of' some E\", where E is a anatomical entity (UBERON:0001062).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of metazoan development as biological process in the Gene Ontology","uniquename":"GO_REF:0000094"}


id: GO_REF:0000061
data:
  {"abstract":"We have created a standard template for classes describing molecular function involved in other biological processes. The underlying equivalence axiom template is \"P and 'part_of' some W\", where P is a molecular function and W is a biological processes.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of a molecular function involved in a biological process in the Gene Ontology","uniquename":"GO_REF:0000061"}


id: PMID:28733412
data:
  {"abstract":"Genomic sequencing data and morphological properties demonstrate evolutionary relationships among groups of the fission yeast,  Schizosaccharomyces  Phylogenetically,  S. japonicus  is the furthest removed from other species of fission yeast. The basic characteristics of cell proliferation are shared among all fission yeast, including the process of binary fission during vegetative growth, conjugation and karyogamy with horsetail movement, mating-type switching, and sporulation. However,  S. japonicus  also exhibits characteristics that are unique to filamentous fungi.  S. japonicus  is a nonpathogenic yeast that exhibits dimorphism. Depending on the environmental conditions,  S. japonicus  transforms from yeast cells into filamentous cells (hyphae), and blue light triggers synchronous septation of hyphal cells. A rough version of the whole-genome sequence is now available, facilitating genetic manipulation of  S. japonicus.  Furthermore, the extensive genetic knowledge available for  S. pombe  is aiding the development of genetic tools for analyzing  S. japonicus. S. japonicus  will help shed light on the evolutionary relationships among the fission yeast.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Aoki K, Furuya K, Niki H","authors_abbrev":"Aoki K et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Cold Spring Harb Protoc 2017 Dec 01;2017(12):pdb.top082651","cv_annotations":{},"doi":"10.1101/pdb.top082651","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2017","pubmed_entrez_date":"2017-07-23","pubmed_publication_date":"01 Dec 2017","terms_by_termid":{},"title":" Schizosaccharomyces japonicus : A Distinct Dimorphic Yeast among the Fission Yeasts.","uniquename":"PMID:28733412"}


id: PMID:34251689
data:
  {"abstract":"The polymerase chain reaction (PCR)-based gene targeting method, which can delete a specific gene or introduce tags, has been widely utilized to study gene function in fission yeast. One of the critical steps in this method is to design primers for amplifying DNA fragments of deletion or tagging modules and for checking the integration of those DNA fragments at designated loci. Although the primer design tool Pombe PCR Primer Program (PPPP) is available for Schizosaccharomyces pombe, there is no such publicly available application for the other three fission yeast species, S. cryophilus, S. japonicus, and S. octosporus. Likewise, no application enabling DNA/protein sequence retrieval for these three fission yeast species is available either. Therefore, access to such functionality would substantially assist in retrieval of gene sequences of interest and primer design in these fission yeast species. In this report, we describe two applications for fission yeast study: Yesprit and Yeaseq. Yesprit is a primer design tool for strain construction using the PCR-based method, and Yeaseq is a sequence viewer that can acquire the DNA/protein sequences of specific genes. Both tools can be run on the Windows, macOS, and Linux platforms. We believe that the Yesprit and Yeaseq will facilitate research using the four fission yeast species.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Wang X, Xu R, Wang Y, Liu Z, Lou R, Sugiyama T","authors_abbrev":"Wang X et al.","canto_added_date":"2023-05-04 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Yeast 2021 Nov;38(11):583-591","cv_annotations":{},"doi":"10.1002/yea.3660","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-07-12","pubmed_publication_date":"Nov 2021","terms_by_termid":{},"title":"Yesprit and Yeaseq: Applications for designing primers and browsing sequences for research using the four Schizosaccharomyces species.","uniquename":"PMID:34251689"}


id: GO_REF:0000109
data:
  {"abstract":"Trypanosomes are exquisitely structured cells in which protein localisation can be extremely informative for likely function. TrypTag is a project using expression of N- and C-terminal mNeonGreen fusion proteins from the endogenous loci to determine the subcellular localisation of every gene in the Trypanosoma brucei genome. GO Cellular Component terms are manually assigned by curators studying fluorescence microscope images of the resulting cells labelled with mNeonGreen fusion proteins. As trypanosomes are a pathogenic basal eukaryote, this will indicate likely function of both highly conserved eukaryote genes and parasite-specific genes. Resource URL: http://www.tryptag.org Protein subcellular localisation images can be viewed on the Tryptag website, e.g. http://www.tryptag.org?id=Tb927.8.1550","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"TrypTag","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotation based on curation of genome-wide subcellular localisation of proteins using fluorescent protein tagging in Trypanosoma brucei","uniquename":"GO_REF:0000109"}


id: GO_REF:0000075
data:
  {"abstract":"We have created a standard template for classes describing the transport of a chemical entity (ChEBI) into a cellular component as a biological process. The underlying equivalence axiom template is \"GO:0006810 and 'has_target_end_location' some T and 'imports' some S\", where T is a cellular component and S is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of transport of a chemical into a cellular component as biological process in the Gene Ontology","uniquename":"GO_REF:0000075"}


id: PMID:2197287
data:
  {"abstract":"Changes in the distribution of microtubules and F-actin through the cell division cycle of the fission yeast Schizosaccharomyces japonicus var. versatilis were investigated by fluorescence microscopy. The fluorescence images obtained with S. japonicus were markedly superior to those previously reported for S. pombe and revealed new details of cytoskeletal organization in this important genus. As in S. pombe, F-actin in S. japonicus was present as a concentration of 'dots' at the growing poles of interphase cells and as a filamentous equatorial ring directing the deposition of the cytokinetic septum. The transition between these two states occurred at late anaphase, in contrast to the situation in S. pombe where the appearance of the equatorial actin ring is tightly coupled to the early events of mitosis. During the course of cytokinesis in S. japonicus the actin ring constricted and broadened, suggesting that it is contractile. Microtubule organization in S. japonicus also revealed interesting differences from S. pombe. Whereas in S. pombe cytoplasmic microtubules are reinitiated from a pair of microtubule organizing centres (MTOCs) at the cell equator, in S. japonicus they arise by extensive microtubule growth from the spindle poles. Western blots of cell extracts enriched for tubulin by DEAE-Sephadex chromatography showed that, like S. pombe, S. japonicus contains two alpha-tubulins and a single beta-tubulin. Whilst the alpha 1- and beta-tubulins from the two species comigrated on one-dimensional polyacrylamide gels, the alpha 2 species were electrophoretically distinct. Although fundamental differences clearly exist between the two species, S. japonicus could prove to be a useful tool in basic studies of fission yeast cell biology.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Alfa CE, Hyams JS","authors_abbrev":"Alfa CE et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"J Cell Sci 1990 May;96 ( Pt 1):71-7","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1990","pubmed_entrez_date":"1990-05-01","pubmed_publication_date":"May 1990","terms_by_termid":{},"title":"Distribution of tubulin and actin through the cell division cycle of the fission yeast Schizosaccharomyces japonicus var. versatilis: a comparison with Schizosaccharomyces pombe.","uniquename":"PMID:2197287"}


id: PMID:23090706
data:
  {"abstract":"DNA damage response includes DNA repair, nucleotide metabolism and even a control of cell fates including differentiation, cell death pathway or some combination of these. The responses to DNA damage differ from species to species. Here we aim to delineate the checkpoint pathway in the dimorphic fission yeast Schizosaccharomyces japonicus, where DNA damage can trigger a differentiation pathway that is a switch from a bidirectional yeast growth mode to an apical hyphal growth mode, and the switching is regulated via a checkpoint kinase, Chk1. This Chk1-dependent switch to hyphal growth is activated with even low doses of agents that damage DNA; therefore, we reasoned that this switch may depend on other genes orthologous to the components of the classical Sz. pombe Chk1-dependent DNA checkpoint pathway. As an initial test of this hypothesis, we assessed the effects of mutations in Sz. japonicus orthologs of Sz. pombe checkpoint genes on this switch from bidirectional to hyphal growth. The same set of DNA checkpoint genes was confirmed in Sz. japonicus. We tested the effect of each DNA checkpoint mutants on hyphal differentiation by DNA damage. We found that the Sz. japonicus hyphal differentiation pathway was dependent on Sz. japonicus orthologs of Sz. pombe checkpoint genes-(SP)rad3, (SP)rad26, (SP)rad9, (SP)rad1, (SP)rad24, (SP)rad25, (SP)crb2, and (SP)chk1-that function in the DNA damage checkpoint pathway, but was not dependent on orthologs of two Sz. pombe genes-(SP)cds1 or (SP)mrc1-that function in the DNA replication checkpoint pathway. These findings indicated that although the role of each component of the DNA damage checkpoint and DNA replication checkpoint is mostly same between the two fission yeasts, the DNA damage checkpoint was the only pathway that governed DNA damage-dependent hyphal growth. We also examined whether DNA damage checkpoint signaling engaged in functional crosstalk with other hyphal differentiation pathways because hyphal differentiation can also be triggered by nutritional stress. Here, we discovered genetic interactions that indicated that the cAMP pathway engaged in crosstalk with Chk1-dependent signaling.","alleles_by_uniquename":{"SJAG_00364:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00364","name":"rad3delta","uniquename":"SJAG_00364:allele-1"},"SJAG_00429:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00429","name":"rad26delta","uniquename":"SJAG_00429:allele-1"},"SJAG_01205:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01205","name":"crb2delta","uniquename":"SJAG_01205:allele-1"},"SJAG_01605:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01605","name":"rad9delta","uniquename":"SJAG_01605:allele-1"},"SJAG_01680:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01680","name":"chk1delta","uniquename":"SJAG_01680:allele-1"},"SJAG_01680:allele-2":{"allele_type":"amino_acid_mutation","description":"P470L","gene_uniquename":"SJAG_01680","name":"chk1-P470L","synonyms":[{"name":"chk1- hyperactive (chk1-hyp)","reference":"PMID:23090706","type":"exact"},{"name":"chk1-hyperactive (chk1-hyp)","reference":"PMID:20368354","type":"exact"}],"uniquename":"SJAG_01680:allele-2"},"SJAG_02266:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02266","name":"rad24delta","uniquename":"SJAG_02266:allele-1"},"SJAG_02576:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02576","name":"rad25delta","uniquename":"SJAG_02576:allele-1"},"SJAG_02771:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02771","name":"rad1delta","uniquename":"SJAG_02771:allele-1"},"SJAG_03720:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03720","name":"tel1delta","uniquename":"SJAG_03720:allele-1"},"SJAG_04287:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04287","name":"cds1delta","uniquename":"SJAG_04287:allele-1"},"SJAG_04671:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04671","name":"mrc1delta","uniquename":"SJAG_04671:allele-1"}},"annotation_curators":[{"annotation_count":28,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-21","authors":"Furuya K, Niki H","authors_abbrev":"Furuya K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-21 17:21:20","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-21 17:21:20","canto_session_key":"5f68f94ee65a99b7","canto_session_submitted_date":"2022-11-21 17:21:13","canto_triage_status":"Curatable","citation":"Curr Genet 2012 Dec;58(5-6):291-303","cv_annotations":{"multi_locus_phenotype":[{"annotations":[115093],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115099],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[115096],"is_not":false,"summary":null,"term":"FYPO:0000088"}],"single_locus_phenotype":[{"annotations":[115084,115085,115086,115087,115088,115089,115091,115092],"is_not":false,"summary":null,"term":"FYPO:0007782"},{"annotations":[115110],"is_not":false,"summary":null,"term":"FYPO:0007774"},{"annotations":[115109],"is_not":false,"summary":null,"term":"FYPO:0001690"},{"annotations":[115083,115090],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115108],"is_not":false,"summary":null,"term":"FYPO:0004693"},{"annotations":[115097,115098,115103,115104,115105],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[115094,115095,115100,115101,115102],"is_not":false,"summary":null,"term":"FYPO:0000088"},{"annotations":[115106,115107],"is_not":false,"summary":null,"term":"FYPO:0001234"}]},"doi":"10.1007/s00294-012-0384-4","gene_count":11,"genes_by_uniquename":{"SJAG_00364":null,"SJAG_00429":null,"SJAG_01205":null,"SJAG_01605":null,"SJAG_01680":null,"SJAG_02266":null,"SJAG_02576":null,"SJAG_02771":null,"SJAG_03720":null,"SJAG_04287":null,"SJAG_04671":null},"genotypes_by_uniquename":{"cds1delta":{"display_name":"cds1delta","display_uniquename":"cds1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04287:allele-1","expression":"Null"}]}]},"chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type__rad24delta":{"display_name":"chk1-P470L(aa) rad24delta","display_uniquename":"chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type__rad24delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-2","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_02266:allele-1","expression":"Null"}]}]},"chk1delta":{"display_name":"chk1delta","display_uniquename":"chk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-1","expression":"Null"}]}]},"chk1delta__crb2delta":{"display_name":"chk1delta crb2delta","display_uniquename":"chk1delta__crb2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_01205:allele-1","expression":"Null"}]}]},"crb2delta":{"display_name":"crb2delta","display_uniquename":"crb2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01205:allele-1","expression":"Null"}]}]},"mrc1delta":{"display_name":"mrc1delta","display_uniquename":"mrc1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04671:allele-1","expression":"Null"}]}]},"rad1delta":{"display_name":"rad1delta","display_uniquename":"rad1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02771:allele-1","expression":"Null"}]}]},"rad24delta":{"display_name":"rad24delta","display_uniquename":"rad24delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02266:allele-1","expression":"Null"}]}]},"rad25delta":{"display_name":"rad25delta","display_uniquename":"rad25delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02576:allele-1","expression":"Null"}]}]},"rad26delta":{"display_name":"rad26delta","display_uniquename":"rad26delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00429:allele-1","expression":"Null"}]}]},"rad3delta":{"display_name":"rad3delta","display_uniquename":"rad3delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00364:allele-1","expression":"Null"}]}]},"rad9delta":{"display_name":"rad9delta","display_uniquename":"rad9delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01605:allele-1","expression":"Null"}]}]},"tel1delta":{"display_name":"tel1delta","display_uniquename":"tel1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03720:allele-1","expression":"Null"}]}]}},"ltp_gene_count":11,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-10-24","pubmed_publication_date":"Dec 2012","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYECO:0000314":null,"FYPO:0000085":null,"FYPO:0000088":null,"FYPO:0001234":null,"FYPO:0001690":null,"FYPO:0004693":null,"FYPO:0007774":null,"FYPO:0007782":null,"FYPO:0007790":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"FYPO_EXT:0000003":null},"title":"Hyphal differentiation induced via a DNA damage checkpoint-dependent pathway engaged in crosstalk with nutrient stress signaling in Schizosaccharomyces japonicus.","uniquename":"PMID:23090706"}


id: GO_REF:0000012
data:
  {"abstract":"Pairwise alignments are generated by taking two sequences and aligning them so that the maximum number of amino acids in each protein match, or are similar to, each other. Tools such as BLAST work by comparing a protein-of-interest individually with every protein in a database of known protein sequences and retaining only those matches with a high probability of being significant. Basic BLAST generates local alignments between proteins for regions of high similarity. Other pairwise alignment tools attempt to generate global (full-length) protein alignments. A tool called Blast_Extend_repraze (BER, http://ber.sourceforge.net) has some benefits over basic BLAST. Input into the BER tool includes the underlying DNA sequence for each protein as well as 300 nucleotides upstream and downstream of the predicted boundaries of the protein coding sequence. This allows annotators to see the DNA sequence that underlies the query protein as part of the alignment. In addition, the BER tool is able to look for continuation of regions of similarity through frameshifts and in-frame stop codons.  If such regions are found the alignment is continued. BER searches are done in a two-step process: step one is a BLAST search against a non-redundant protein database, significant BLAST hits are stored in a mini-database for each query protein; step two is a modified Smith-Waterman alignment between the query and the proteins in its mini-database. In order to assess whether a given BER alignment is good enough to assert that the query shares the function of the match protein, one must look at a several factors. First of all, the match protein must itself be experimentally characterized in order to avoid transitive annotation errors. In addition, any residues or secondary structures known to be important for function in the match protein must be conserved in the query. The alignment should be visually inspected to look for any areas of lesser quality that might indicate the two proteins do not share the same function. Although it is impossible to set cutoff values for percent identity and length of match that will apply for every alignment, there are some guidelines. In general at least 40% identity that extends over the full lengths of both proteins is required in order to even consider functional equivalence. However, this percentage is highly dependent on the length and complexity of the proteins. 40% identity between two proteins 500 amino acids long is much more significant that 40% identity between two proteins that are only 100 amino acids long. Therefore, the annotator's experience and knowledge of what is considered significant for the organism and protein family in question is very important. Some sets of proteins are much more highly conserved than others and therefore tolerances for percent identity may have to be adjusted. Finally, the alignment must be considered in the context of what else is known about the query protein and the organism as a whole.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Michelle Gwinn, TIGR curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Pairwise alignment (TIGR)","uniquename":"GO_REF:0000012"}


id: PMID:30664646
data:
  {"abstract":"Cells of a specific cell type may divide within a certain size range. Yet, functionally optimal cellular organization is typically maintained across different cell sizes, a phenomenon known as scaling. The mechanisms underlying scaling and its physiological significance remain elusive. Here we approach this problem by interfering with scaling in the rod-shaped fission yeast Schizosaccharomyces japonicus that relies on cellular geometry cues to position the division site. We show that S. japonicus uses the Cdc42 polarity module to adjust its geometry to changes in the cell size. When scaling is prevented resulting in abnormal cellular length-to-width aspect ratio, cells exhibit severe division site placement defects. We further show that despite the generally accepted view, a similar scaling phenomenon can occur in the sister species, Schizosaccharomyces pombe. Our results demonstrate that scaling is required for normal cell function and delineate possible rules for cellular geometry maintenance in populations of proliferating cells.","alleles_by_uniquename":{"SJAG_00028:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00028","name":"rga6delta","uniquename":"SJAG_00028:allele-1"},"SJAG_00514:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00514","name":"scd1delta","uniquename":"SJAG_00514:allele-1"},"SJAG_03048:allele-1":{"allele_type":"amino_acid_mutation","description":"G146D","gene_uniquename":"SJAG_03048","name":"cdc2-1w","uniquename":"SJAG_03048:allele-1"},"SJAG_03581:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03581","name":"gef1delta","uniquename":"SJAG_03581:allele-1"},"SJAG_04280:allele-2":{"allele_type":"amino_acid_mutation","description":"T582G","gene_uniquename":"SJAG_04280","name":"wee1-as8","uniquename":"SJAG_04280:allele-2"},"SJAG_04280:allele-3":{"allele_type":"amino_acid_mutation","description":"G788E","gene_uniquename":"SJAG_04280","name":"wee1-G788E","uniquename":"SJAG_04280:allele-3"},"SJAG_04522:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04522","name":"rga4delta","uniquename":"SJAG_04522:allele-1"}},"annotation_curators":[{"annotation_count":3,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"},{"annotation_count":22,"community_curator":true,"file_name":null,"file_type":null,"name":"Ying Gu","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-02","authors":"Gu Y, Oliferenko S","authors_abbrev":"Gu Y et al.","canto_added_date":"2021-05-10 02:37:31","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-01 07:53:28","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Ying Gu","canto_curator_role":"community","canto_first_approved_date":"2021-07-02 12:32:27","canto_session_key":"0922e2a5229110bd","canto_session_submitted_date":"2021-06-30 22:18:13","canto_triage_status":"Curatable","citation":"Nat Commun 2019 01 21;10(1):268","cv_annotations":{"biological_process":[{"annotations":[115450],"is_not":false,"summary":null,"term":"GO:0061171"},{"annotations":[115451,115452],"is_not":false,"summary":null,"term":"GO:0008360"}],"multi_locus_phenotype":[{"annotations":[115438,115443],"is_not":false,"summary":null,"term":"FYPO:0007783"},{"annotations":[115449],"is_not":false,"summary":null,"term":"FYPO:0004105"},{"annotations":[115440],"is_not":false,"summary":null,"term":"FYPO:0001369"},{"annotations":[115442],"is_not":false,"summary":null,"term":"FYPO:0004293"}],"single_locus_phenotype":[{"annotations":[115444],"is_not":false,"summary":null,"term":"FYPO:0000198"},{"annotations":[115445,115446,115448],"is_not":false,"summary":null,"term":"FYPO:0005503"},{"annotations":[115439],"is_not":false,"summary":null,"term":"FYPO:0007783"},{"annotations":[115433],"is_not":false,"summary":null,"term":"FYPO:0004105"},{"annotations":[115447],"is_not":false,"summary":null,"term":"FYPO:0002870"},{"annotations":[115441],"is_not":false,"summary":null,"term":"FYPO:0001369"},{"annotations":[115434],"is_not":false,"summary":null,"term":"FYPO:0001234"},{"annotations":[115428,115429,115432],"is_not":false,"summary":null,"term":"FYPO:0000648"},{"annotations":[115430,115431,115437],"is_not":false,"summary":null,"term":"FYPO:0001877"},{"annotations":[115435,115436],"is_not":false,"summary":null,"term":"FYPO:0006616"}]},"doi":"10.1038/s41467-018-08218-2","gene_count":8,"genes_by_uniquename":{"SJAG_00028":null,"SJAG_00030":null,"SJAG_00514":null,"SJAG_01794":null,"SJAG_03048":null,"SJAG_03581":null,"SJAG_04280":null,"SJAG_04522":null},"genotypes_by_uniquename":{"cdc2-1w-G146D-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cdc2-1w(G146D aa)","display_uniquename":"cdc2-1w-G146D-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03048:allele-1","expression":"Not assayed or wild type"}]}]},"gef1delta":{"display_name":"gef1delta","display_uniquename":"gef1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03581:allele-1","expression":"Null"}]}]},"rga4delta":{"display_name":"rga4delta","display_uniquename":"rga4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04522:allele-1","expression":"Null"}]}]},"rga4delta__rga6delta":{"display_name":"rga4delta rga6delta","display_uniquename":"rga4delta__rga6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04522:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_00028:allele-1","expression":"Null"}]}]},"rga4delta__wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"rga4delta wee1-G788E(aa)","display_uniquename":"rga4delta__wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04522:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-3","expression":"Not assayed or wild type"}]}]},"rga4delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"rga4delta wee1-as8(T582G aa)","display_uniquename":"rga4delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04522:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-2","expression":"Not assayed or wild type"}]}]},"rga6delta":{"display_name":"rga6delta","display_uniquename":"rga6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00028:allele-1","expression":"Null"}]}]},"rga6delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"rga6delta wee1-as8(T582G aa)","display_uniquename":"rga6delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00028:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-2","expression":"Not assayed or wild type"}]}]},"scd1delta":{"display_name":"scd1delta","display_uniquename":"scd1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00514:allele-1","expression":"Null"}]}]},"wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"wee1-G788E(aa)","display_uniquename":"wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-3","expression":"Not assayed or wild type"}]}]},"wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"wee1-as8(T582G aa)","display_uniquename":"wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-2","expression":"Not assayed or wild type"}]}]}},"ltp_gene_count":6,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2019","pubmed_entrez_date":"2019-01-22","pubmed_publication_date":"21 01 2019","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000005":null,"FYECO:0000006":null,"FYECO:0000103":null,"FYECO:0000126":null,"FYECO:0000137":null,"FYECO:0000338":null,"FYPO:0000198":null,"FYPO:0000648":null,"FYPO:0001234":null,"FYPO:0001369":null,"FYPO:0001877":null,"FYPO:0002870":null,"FYPO:0004105":null,"FYPO:0004293":null,"FYPO:0005503":null,"FYPO:0006616":null,"FYPO:0007783":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"GO:0008360":null,"GO:0061171":null},"title":"Cellular geometry scaling ensures robust division site positioning.","uniquename":"PMID:30664646"}


id: GO_REF:0000008
data:
  {"abstract":"The sequence conservation that permits the establishment of orthology between mouse and rat or mouse and human genes is a strong predictor of the conservation of function for the gene product across these species. Therefore, in instances where a mouse gene product has not been functionally characterized, but its human or rat orthologs have, Mouse Genome Informatics (MGI) curators append the GO terms associated with the orthologous gene(s) to the mouse gene. Only those GO terms assigned by experimental determination to the ortholog of the mouse gene will be adopted by MGI. GO terms that are assigned to the ortholog of the mouse gene computationally (i.e. IEA), will not be transferred to the mouse ortholog. The evidence code represented by this citation is Inferred by Sequence Orthology (ISO).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Mouse Genome Informatics scientific curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotation by the MGI curatorial staff, curated orthology","uniquename":"GO_REF:0000008"}


id: GO_REF:0000093
data:
  {"abstract":"We have created a standard template for classes describing the degradation of a chemical entity to or via an other chemical entity as biological processes. The underlying equivalence axiom templates are \"GO:0009056 and 'has input' some S and 'has output' some T\" (catabolism to) and \"GO:0009056 and 'has input' some S and 'has intermediate' some I\" (catabolism via), where S,T, and I are chemical entities (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation for the degradation to or via a chemical as biological process in the Gene Ontology","uniquename":"GO_REF:0000093"}


id: GO_REF:0000064
data:
  {"abstract":"We have created a standard template for classes describing cell components as part of other cell components. The underlying equivalence axiom template is \"P and 'part_of' some W\", where P and W are cell components.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of cell components as part of other cell components in the Gene Ontology","uniquename":"GO_REF:0000064"}


id: PMID:8529460
data:
  {"abstract":"Meiotic prophase in Schizosaccharomyces pombe is characterized by striking nuclear movements and the formation of linear elements along chromosomes instead of tripartite synaptonemal complexes. We analysed the organization of nuclei and microtubules in cells of fission yeasts undergoing sexual differentiation. S. japonicus var. versatilis and S. pombe cells were studied in parallel, taking advantage of the better cytology in S. versatilis. During conjugation, microtubules were directed towards the mating projection. These microtubules seem to lead the haploid nuclei together in the zygote by interaction with the spindle pole bodies at the nuclear periphery. After karyogamy, arrays of microtubules emanating from the spindle pole body of the diploid nucleus extended to both cell poles. The same differentiated microtubule configuration was elaborated upon induction of azygotic meiosis in S. pombe. The cyclic movements of the elongated nuclei between the cell poles is reflected by a dynamic and coordinated shortening and lengthening of the two microtubule arrays. When the nucleus was at a cell end, one array was short while the other bridged the whole cell length. Experiments with inhibitors showed that microtubules are required for karyogamy and for the elongated shape and movement of nuclei during meiotic prophase. In both fission yeasts the SPBs and nucleoli are at the leading ends of the moving nuclei. Astral and cytoplasmic microtubules were also prominent during meiotic divisions and sporulation. We further show that in S. versatilis the linear elements formed during meiotic prophase are similar to those in S. pombe. Tripartite synaptonemal complexes were never detected. Taken together, these findings suggest that S. pombe and S. versatilis share basic characteristics in the organization of microtubules and the structure and behaviour of nuclei during their meiotic cell cycle. The prominent differentiations of microtubules and nuclei may be involved in the pairing, recombination, and segregation of meiotic chromosomes.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Svoboda A, Bähler J, Kohli J","authors_abbrev":"Svoboda A et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Chromosoma 1995 Nov;104(3):203-14","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1995","pubmed_entrez_date":"1995-11-01","pubmed_publication_date":"Nov 1995","terms_by_termid":{},"title":"Microtubule-driven nuclear movements and linear elements as meiosis-specific characteristics of the fission yeasts Schizosaccharomyces versatilis and Schizosaccharomyces pombe.","uniquename":"PMID:8529460"}


id: GO_REF:0000027
data:
  {"abstract":"This GO reference describes the criteria used in assigning the evidence code of ISS via BLAST searches to annotate gene products from PAMGO_GAT. Standard BLASTP from NCBI was used (http://www.ncbi.nih.gov/blast) to query the non-redundant (NR) database. Hits are considered to be significant if the E-value is at or less than 10^-4. All other parameters are default according to http://www.ncbi.nih.gov/blast.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"PAMGO_GAT curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"BLAST search criteria for ISS assignment in PAMGO_GAT","uniquename":"GO_REF:0000027"}


id: PMID:28342076
data:
  {"abstract":"Environmental glucose is an important regulator of biological processes, as it can launch different cell processes depending on its concentration. Thus, low glucose concentration can induce entry into quiescence, which ensures long-term viability for the cells or in other cases mycelial growth in the dimorphic species, which, in turn, provides the cells with fresh nutrients. Several genes, such as the genes of cAMP cascade, are involved in glucose sensing and response. Since this signal transduction pathway seemed to be an evolutionarily conserved process, we assumed that its genes were also conserved and preserved their functional homology. To obtain evidence, Schizosaccharomyces pombe rsv1 and its orthologous genes were investigated using in silico and experimental approaches. Our results supported that the Rsv1 zinc-finger transcription factors of Schizosaccharomyces japonicus and Schizosaccharomyces octosporus and the Candida albicans cas5p were really functional homologues of the S. pombe Rsv1. Namely, the homologous proteins were able to restore mutant phenotype of the S. pombe rsv1-deleted cells. Bioinformatic anaysis revealed that the most conserved parts of the proteins always contained the C2H2 domains and the complementation abilities of the counterpart genes were not uniform regarding the investigated features, which can be in connection with the conserved regions outside C2H2.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Pataki E, Sipiczki M, Miklos I","authors_abbrev":"Pataki E et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Curr Microbiol 2017 Jun;74(6):710-717","cv_annotations":{},"doi":"10.1007/s00284-017-1227-9","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2017","pubmed_entrez_date":"2017-03-26","pubmed_publication_date":"Jun 2017","terms_by_termid":{},"title":"Schizosaccharomyces pombe rsv1 Transcription Factor and its Putative Homologues Preserved their Functional Homology and are Evolutionarily Conserved.","uniquename":"PMID:28342076"}


id: GO_REF:0000043
data:
  {"abstract":"Transitive assignments using UniProtKB/Swiss-Prot keywords. The UniProtKB keyword controlled vocabulary contains 10 different categories of information to UniProtKB entries. Further information on the UniProtKB keyword resource can be found at https://www.uniprot.org/keywords/.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"UniProt-GOA","canto_curator_role":"JaponicusDB","cv_annotations":{"biological_process":[{"annotations":[66295],"is_not":false,"summary":null,"term":"GO:0000272"},{"annotations":[65015],"is_not":false,"summary":null,"term":"GO:0075523"}],"molecular_function":[{"annotations":[68331],"is_not":false,"summary":null,"term":"GO:0004812"},{"annotations":[57560],"is_not":false,"summary":null,"term":"GO:0005524"},{"annotations":[66293],"is_not":false,"summary":null,"term":"GO:0008061"},{"annotations":[57910,66538],"is_not":false,"summary":null,"term":"GO:0008483"}]},"gene_count":6,"genes_by_uniquename":{"SJAG_00620":null,"SJAG_00691":null,"SJAG_01595":null,"SJAG_02263":null,"SJAG_03856":null,"SJAG_04546":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0000272":null,"GO:0004812":null,"GO:0005524":null,"GO:0008061":null,"GO:0008483":null,"GO:0075523":null},"title":"Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping","uniquename":"GO_REF:0000043"}


id: PMID:34353908
data:
  {"abstract":"Biosynthesis of sterols, which are key constituents of canonical eukaryotic membranes, requires molecular oxygen. Anaerobic protists and deep-branching anaerobic fungi are the only eukaryotes in which a mechanism for sterol-independent growth has been elucidated. In these organisms, tetrahymanol, formed through oxygen-independent cyclization of squalene by a squalene-tetrahymanol cyclase, acts as a sterol surrogate. This study confirms an early report [C. J. E. A. Bulder,  Antonie Van Leeuwenhoek , 37, 353-358 (1971)] that  Schizosaccharomyces japonicus  is exceptional among yeasts in growing anaerobically on synthetic media lacking sterols and unsaturated fatty acids. Mass spectrometry of lipid fractions of anaerobically grown  Sch. japonicus  showed the presence of hopanoids, a class of cyclic triterpenoids not previously detected in yeasts, including hop-22(29)-ene, hop-17(21)-ene, hop-21(22)-ene, and hopan-22-ol. A putative gene in  Sch. japonicus  showed high similarity to bacterial squalene-hopene cyclase (SHC) genes and in particular to those of  Acetobacter  species. No orthologs of the putative  Sch. japonicus  SHC were found in other yeast species. Expression of the  Sch. japonicus  SHC gene ( Sjshc1 ) in  Saccharomyces cerevisiae  enabled hopanoid synthesis and stimulated anaerobic growth in sterol-free media, thus indicating that one or more of the hopanoids produced by SjShc1 could at least partially replace sterols. Use of hopanoids as sterol surrogates represents a previously unknown adaptation of eukaryotic cells to anaerobic growth. The fast anaerobic growth of  Sch. japonicus  in sterol-free media is an interesting trait for developing robust fungal cell factories for application in anaerobic industrial processes.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Bouwknegt J, Wiersma SJ, Ortiz-Merino RA, Doornenbal ESR, Buitenhuis P, Giera M, Müller C, Pronk JT","authors_abbrev":"Bouwknegt J et al.","canto_added_date":"2023-05-04 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Proc Natl Acad Sci U S A 2021 Aug 10;118(32)","cv_annotations":{},"doi":"10.1073/pnas.2105225118","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-08-06","pubmed_publication_date":"10 Aug 2021","terms_by_termid":{},"title":"A squalene-hopene cyclase in  Schizosaccharomyces japonicus  represents a eukaryotic adaptation to sterol-limited anaerobic environments.","uniquename":"PMID:34353908"}


id: PMID:27678009
data:
  {"abstract":"The cAMP cascade plays an important role in several biological processes. Thus, study of its molecular details can contribute to a better understanding of these processes, treatment of diseases, or even finding antifungal drug targets. To gain further information about the PKA pathway, and its evolutionarily conserved and species-specific features, the central regulator pka1 gene, which encodes the cAMP-dependent protein kinase catalytic subunit, was studied in the less known haplontic, dimorphic fission yeast Schizosaccharomyces japonicus. Namely, this species belongs to a highly divergent phylogenetic branch of fungi. Furthermore, S. japonicus had only a single copy pka1 gene in contrast to the budding yeasts. Therefore, the pka1 deleted mutant was created, whose RNA sequencing and phenotypic studies revealed that the Pka1 regulated at least 373 genes, among them further kinases, phosphatases and transcriptional regulators. It regulated elongation of hyphae, cell size, aging and stress response. Furthermore, half of the pka1 target genes seemed to be conserved in Schizosaccharomyces pombe and S. japonicus. However, there were oppositely regulated genes in the two closely related species. The target genes suggest that this single gene must be able to fulfill all the functions of TPK1-3 of Saccharomyces cerevisiae. Thus, our results shed light on certain similarities and differences of the PKA pathway of S. japonicus compared to the budding yeasts and confirmed the multifunctionality of the pka1 gene, but further experiments are needed to prove its involvement in the metabolic processes and transport.","alleles_by_uniquename":{"SJAG_04312:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04312","name":"pka1delta","uniquename":"SJAG_04312:allele-1"}},"annotation_curators":[{"annotation_count":6,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-07","authors":"Papp L, Sipiczki M, Miklós I","authors_abbrev":"Papp L et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-07 12:57:27","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-07 12:57:27","canto_session_key":"9dc3302039d46818","canto_session_submitted_date":"2021-07-07 12:56:39","canto_triage_status":"Curatable","citation":"Curr Genet 2017 Jun;63(3):487-497","cv_annotations":{"single_locus_phenotype":[{"annotations":[115112],"is_not":false,"summary":null,"term":"FYPO:0007773"},{"annotations":[115111],"is_not":false,"summary":null,"term":"FYPO:0001122"},{"annotations":[115113],"is_not":false,"summary":null,"term":"FYPO:0000245"},{"annotations":[115115],"is_not":false,"summary":null,"term":"FYPO:0000097"},{"annotations":[115114],"is_not":false,"summary":null,"term":"FYPO:0000087"},{"annotations":[115116],"is_not":false,"summary":null,"term":"FYPO:0001214"}]},"doi":"10.1007/s00294-016-0651-x","gene_count":1,"genes_by_uniquename":{"SJAG_04312":null},"genotypes_by_uniquename":{"pka1delta":{"display_name":"pka1delta","display_uniquename":"pka1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04312:allele-1","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2017","pubmed_entrez_date":"2016-09-29","pubmed_publication_date":"Jun 2017","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000005":null,"FYECO:0000102":null,"FYECO:0000137":null,"FYPO:0000087":null,"FYPO:0000097":null,"FYPO:0000245":null,"FYPO:0001122":null,"FYPO:0001214":null,"FYPO:0007773":null,"FYPO_EXT:0000002":null,"FYPO_EXT:0000003":null},"title":"Expression pattern and phenotypic characterization of the mutant strain reveals target genes and processes regulated by pka1 in the dimorphic fission yeast Schizosaccharomyces japonicus.","uniquename":"PMID:27678009"}


id: GO_REF:0000002
data:
  {"abstract":"Transitive assignment of GO terms based on InterPro classification. For any database entry (representing a protein or protein-coding gene) that has been annotated with one or more InterPro domains, the corresponding GO terms are obtained from a translation table of InterPro entries to GO terms (interpro2go) generated manually by the InterPro team at EBI. 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id: GO_REF:0000089
data:
  {"abstract":"We have created a standard template for classes describing the single-organism and multi-organism biological processes. The underlying equivalence axiom templates are \"P and 'bearer_of' some PATO:0002487\" (single-organism) and \"P and 'bearer_of' some PATO:0002486\" (multi-organism), where P is a biological process.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of single-organism and multi-organism biological processes in the Gene Ontology","uniquename":"GO_REF:0000089"}


id: GO_REF:0000068
data:
  {"abstract":"We have created a standard template for classes each describing the metabolism, catabolism, or biosynthesis of a chemical entity (ChEBI) as a process. The underlying equivalence axiom templates are \"GO:0008152 and 'has participant' some X\" (metabolism), \"GO:0009056 and 'has input' some X\" (catabolism), \"GO:0009058 and 'has output' some X\" and (biosynthesis),  where X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of metabolic triad (metabolism, catabolism, biosynthesis) as biological process in the Gene Ontology","uniquename":"GO_REF:0000068"}


id: PMID:22531001
data:
  {"abstract":"DNA replication initiates at distinct origins in eukaryotic genomes, but the genomic features that define these sites are not well understood.\nWe have taken a combined experimental and bioinformatic approach to identify and characterize origins of replication in three distantly related fission yeasts: Schizosaccharomyces pombe, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus. Using single-molecule deep sequencing to construct amplification-free high-resolution replication profiles, we located origins and identified sequence motifs that predict origin function. We then mapped nucleosome occupancy by deep sequencing of mononucleosomal DNA from the corresponding species, finding that origins tend to occupy nucleosome-depleted regions.\nThe sequences that specify origins are evolutionarily plastic, with low complexity nucleosome-excluding sequences functioning in S. pombe and S. octosporus, and binding sites for trans-acting nucleosome-excluding proteins functioning in S. japonicus. Furthermore, chromosome-scale variation in replication timing is conserved independently of origin location and via a mechanism distinct from known heterochromatic effects on origin function. These results are consistent with a model in which origins are simply the nucleosome-depleted regions of the genome with the highest affinity for the origin recognition complex. This approach provides a general strategy for understanding the mechanisms that define DNA replication origins in eukaryotes.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Xu J, Yanagisawa Y, Tsankov AM, Hart C, Aoki K, Kommajosyula N, Steinmann KE, Bochicchio J, Russ C, Regev A, Rando OJ, Nusbaum C, Niki H, Milos P, Weng Z, Rhind N","authors_abbrev":"Xu J et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Genome Biol 2012 Apr 24;13(4):R27","cv_annotations":{},"doi":"10.1186/gb-2012-13-4-r27","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-04-26","pubmed_publication_date":"24 Apr 2012","terms_by_termid":{},"title":"Genome-wide identification and characterization of replication origins by deep sequencing.","uniquename":"PMID:22531001"}


id: GO_REF:0000034
data:
  {"abstract":"Skeletal cell terms and relationships were added and revised at the Skeletal Anatomy Jamboree held by Phenoscape (NSF grant BDI-0641025) and hosted by the National Evolutionary Synthesis Center (NESCent), April 9-10, 2010.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Brian K. Hall (Dalhousie University), Matthew Vickaryous (Ontario Veterinary College, University of Guelph), David Blackburn, University of Kansas; Wasila Dahdul, University of South Dakota and NESCent; Alexander Diehl, Mouse Genome Informatics (MGI); Melissa Haendel, Oregon Health Sciences University; John G. Lundberg, Department of Ichthyology, Academy of Natural Sciences, Philadelphia; Paula Mabee, Department of Biology, University of South Dakota; Martin Ringwald, Mouse Genome Informatics (MGI); Erik Segerdell, Oregon Health Sciences University; Ceri Van Slyke, Zebrafish Information Network (ZFIN); Monte Westerfield, Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon.","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Phenoscape Skeletal Anatomy Jamboree","uniquename":"GO_REF:0000034"}


id: PMID:25318672
data:
  {"abstract":"Excess fatty acids and sterols are stored as triacylglycerols and sterol esters in specialized cellular organelles, called lipid droplets. Understanding what determines the cellular amount of neutral lipids and their packaging into lipid droplets is of fundamental and applied interest. Using two species of fission yeast, we show that cycling cells deficient in the function of the ER-resident CDP-DG synthase Cds1 exhibit markedly increased triacylglycerol content and assemble large lipid droplets closely associated with the ER membranes. We demonstrate that these unusual structures recruit the triacylglycerol synthesis machinery and grow by expansion rather than by fusion. Our results suggest that interfering with the CDP-DG route of phosphatidic acid utilization rewires cellular metabolism to adopt a triacylglycerol-rich lifestyle reliant on the Kennedy pathway. ","alleles_by_uniquename":{"SJAG_00426:allele-1":{"allele_type":"amino_acid_mutation","description":"P363S","gene_uniquename":"SJAG_00426","name":"bbl1-P363S","uniquename":"SJAG_00426:allele-1"}},"annotation_curators":[{"annotation_count":8,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-05-17","authors":"He Y, Yam C, Pomraning K, Chin JS, Yew JY, Freitag M, Oliferenko S","authors_abbrev":"He Y et al.","canto_added_date":"2021-05-10 02:38:06","canto_annotation_status":"APPROVED","canto_approved_date":"2021-05-17 12:42:41","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-05-17 12:42:41","canto_session_key":"f89ee2d26032c510","canto_session_submitted_date":"2021-05-17 12:42:28","canto_triage_status":"Curatable","citation":"Mol Biol Cell 2014 Dec 15;25(25):4083-95","cv_annotations":{"biological_process":[{"annotations":[115535],"is_not":false,"summary":null,"term":"GO:0016024"}],"cellular_component":[{"annotations":[115536],"is_not":false,"summary":null,"term":"GO:0005783"}],"molecular_function":[{"annotations":[115534],"is_not":false,"summary":null,"term":"GO:0004605"}],"single_locus_phenotype":[{"annotations":[115538],"is_not":false,"summary":null,"term":"FYPO:0000356"},{"annotations":[115537],"is_not":false,"summary":null,"term":"FYPO:0006433"},{"annotations":[115540],"is_not":false,"summary":null,"term":"FYPO:0004695"},{"annotations":[115539],"is_not":false,"summary":null,"term":"FYPO:0002227"},{"annotations":[115541],"is_not":false,"summary":null,"term":"FYPO:0001357"}]},"doi":"10.1091/mbc.E14-03-0832","gene_count":1,"genes_by_uniquename":{"SJAG_00426":null},"genotypes_by_uniquename":{"bbl1-P363S-P363S-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"bbl1-P363S(aa)","display_uniquename":"bbl1-P363S-P363S-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00426:allele-1","expression":"Not assayed or wild type"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2014","pubmed_entrez_date":"2014-10-17","pubmed_publication_date":"15 Dec 2014","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000006":null,"FYECO:0000162":null,"FYPO:0000356":null,"FYPO:0001357":null,"FYPO:0002227":null,"FYPO:0004695":null,"FYPO:0006433":null,"FYPO_EXT:0000001":null,"GO:0004605":null,"GO:0005783":null,"GO:0008654":null,"GO:0016024":null},"title":"Increase in cellular triacylglycerol content and emergence of large ER-associated lipid droplets in the absence of CDP-DG synthase function.","uniquename":"PMID:25318672"}


id: PMID:20368354
data:
  {"abstract":"Dimorphic yeasts change between unicellular growth and filamentous growth. Many dimorphic yeasts species are pathogenic for humans and plants, being infectious as invasive hypha. We have studied the determinants of the dimorphic switch in the nonpathogenic fission yeast Schizosaccharomyces japonicus, which is evolutionarily close to the well-characterized fission yeast S. pombe. We report that camptothecin, an inhibitor of topoisomerase I, reversibly induced the unicellular to hyphal transition in S. japonicus at low concentrations of camptothecin that did not induce checkpoint arrest and the transition required the DNA checkpoint kinase Chk1. Furthermore, a mutation of chk1 induced hyphal transition without camptothecin. Thus, we identify a second function for Chk1 distinct from its role in checkpoint arrest. Activation of the switch from single cell bipolar growth to monopolar filamentous growth may assist cells to evade the source of DNA damage.","alleles_by_uniquename":{"SJAG_01410:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01410","name":"rad51delta","uniquename":"SJAG_01410:allele-1"},"SJAG_01605:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01605","name":"rad9delta","uniquename":"SJAG_01605:allele-1"},"SJAG_01680:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01680","name":"chk1delta","uniquename":"SJAG_01680:allele-1"},"SJAG_01680:allele-2":{"allele_type":"amino_acid_mutation","description":"P470L","gene_uniquename":"SJAG_01680","name":"chk1-P470L","synonyms":[{"name":"chk1- hyperactive (chk1-hyp)","reference":"PMID:23090706","type":"exact"},{"name":"chk1-hyperactive (chk1-hyp)","reference":"PMID:20368354","type":"exact"}],"uniquename":"SJAG_01680:allele-2"}},"annotation_curators":[{"annotation_count":6,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-21","authors":"Furuya K, Niki H","authors_abbrev":"Furuya K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-21 16:35:04","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-21 16:35:04","canto_session_key":"f81a194894ea8808","canto_session_submitted_date":"2022-11-21 16:34:55","canto_triage_status":"Curatable","citation":"Mol Cell Biol 2010 Jun;30(12):2909-17","cv_annotations":{"single_locus_phenotype":[{"annotations":[115288,115292],"is_not":false,"summary":null,"term":"FYPO:0007782"},{"annotations":[115287],"is_not":false,"summary":null,"term":"FYPO:0007774"},{"annotations":[115289,115290,115291],"is_not":false,"summary":null,"term":"FYPO:0000085"}]},"doi":"10.1128/MCB.00049-10","gene_count":3,"genes_by_uniquename":{"SJAG_01410":null,"SJAG_01605":null,"SJAG_01680":null},"genotypes_by_uniquename":{"chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"chk1-P470L(aa)","display_uniquename":"chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-2","expression":"Not assayed or wild type"}]}]},"chk1delta":{"display_name":"chk1delta","display_uniquename":"chk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-1","expression":"Null"}]}]},"rad51delta":{"display_name":"rad51delta","display_uniquename":"rad51delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01410:allele-1","expression":"Null"}]}]},"rad9delta":{"display_name":"rad9delta","display_uniquename":"rad9delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01605:allele-1","expression":"Null"}]}]}},"ltp_gene_count":3,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2010","pubmed_entrez_date":"2010-04-07","pubmed_publication_date":"Jun 2010","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYECO:0000314":null,"FYPO:0000085":null,"FYPO:0007774":null,"FYPO:0007782":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null},"title":"The DNA damage checkpoint regulates a transition between yeast and hyphal growth in Schizosaccharomyces japonicus.","uniquename":"PMID:20368354"}


id: GO_REF:0000090
data:
  {"abstract":"We have created a rule-based approach to create relations between the branches of the Gene Ontology. The approach uses the equivalence axioms and a given pattern to create non-subClassOf relationships between the three different branches of the Gene Ontology (biological process, molecular function, cellular component). Currently, there are the following rules: \"'transporter activity' and 'transports_or_maintains_localization_of' some X' -part_of-> \"transport and 'transports_or_maintains_localization_of' some X\"; \"'transmembrane transporter activity' and 'transports_or_maintains_localization_of' some X -part_of-> 'transmembrane transport' and 'transports_or_maintains_localization_of' some X\"","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Automatic creation of relationships between ontology branches in the Gene Ontology","uniquename":"GO_REF:0000090"}


id: GO_REF:0000004
data:
  {"abstract":"Transitive assignments using UniProtKB keywords. The UniProtKB keyword controlled vocabulary has been created and used by the UniProt Knowledgebase (UniProtKB) to supply 10 different categories of information to UniProtKB entries. Further information on the UniProtKB keyword resource can be found at http://www.uniprot.org/docs/keywlist. <br>Further information on the UniProt annotation methods is available at  https://www.uniprot.org/help/manual_curation and https://www.uniprot.org/help/automatic_annotation.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GOA curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Comments","uniquename":"GO_REF:0000004"}


id: PMID:22572960
data:
  {"abstract":"The aim of mitosis is to produce two daughter nuclei, each containing a chromosome complement identical to that of the mother nucleus. This can be accomplished through a variety of strategies, with \"open\" and \"closed\" modes of mitosis positioned at the opposite ends of the spectrum and a range of intermediate patterns in between. In the \"closed\" mitosis, the nuclear envelope remains intact throughout the nuclear division. In the \"open\" division type, the envelope of the original nucleus breaks down early in mitosis and reassembles around the segregated daughter genomes. In any case, the nuclear membrane has to remodel to accommodate the mitotic spindle assembly, chromosome segregation and formation of the daughter nuclei. We have recently shown that within the fission yeast clade, the mitotic control of the nuclear surface area may determine the choice between the nuclear envelope breakdown and a fully \"closed\" division. Here we discuss our data and argue that comparative cell biology studies using two fission yeast species, Schizosaccharomyces pombe and Schizosaccharomyces japonicus, could provide unprecedented insights into physiology and evolution of mitosis.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Gu Y, Yam C, Oliferenko S","authors_abbrev":"Gu Y et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Nucleus 2012 May;3(3):220-5","cv_annotations":{},"doi":"10.4161/nucl.19514","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-05-11","pubmed_publication_date":"May 2012","terms_by_termid":{},"title":"Divergence of mitotic strategies in fission yeasts.","uniquename":"PMID:22572960"}


id: PMID:8546451
data:
  {"abstract":"The phylogenesis of fungi is controversial due to their simple morphology and poor fossilization. Traditional classification supported by morphological studies and physiological traits placed the fission yeasts in one group with ascomycetous yeasts. The rRNA sequence comparisons, however, revealed an enormous evolutionary gap between Saccharomyces and Schizosaccharomyces. As shown in this review, the protein sequences also show a large gap which is almost as large as that separating Schizosaccharomyces from higher animals. Since the two yeasts share features (both cytological and molecular) in common which are also characteristic of ascomycetous fungi, their separation must have taken place later than the sequence differences may suggest. Possible reasons for the paradox are discussed. The sequence data also suggest a slower evolutionary rate in the Schizosaccharomyces lineage than in the Saccharomyces branch. In the fission yeast lineage two ramifications can be supposed. First S. japonicus (Hasegawaea japonica) branched off, then S. octosporus (Octosporomyces octosporus) separated from S. pombe.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Sipiczki M","authors_abbrev":"Sipiczki M","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Phylogeny and evolutionary studies","citation":"Antonie Van Leeuwenhoek 1995 Aug;68(2):119-49","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1995","pubmed_entrez_date":"1995-08-01","pubmed_publication_date":"Aug 1995","terms_by_termid":{},"title":"Phylogenesis of fission yeasts. Contradictions surrounding the origin of a century old genus.","uniquename":"PMID:8546451"}


id: GO_REF:0000066
data:
  {"abstract":"We have created a standard template for classes describing the transport of a chemical entity (ChEBI) as a molecular function. The underlying equivalence axiom template is \"GO:0005215 and 'transports or maintains localization of' some X\", where X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of transport of a chemical entity as molecular function in the Gene Ontology","uniquename":"GO_REF:0000066"}


id: GO_REF:0000117
data:
  {"abstract":"Association-Rule-Based Annotator (ARBA) predicts Gene Ontology (GO) terms among other types of functional annotation such as Protein Description (DE), Keywords (KW), Enzyme Commission numbers (EC), subcellular LOcation (LO), etc. For all annotation types, reviewed UniProtKB/Swiss-Prot records having manual annotations as reference data are used to perform the machine learning phase and generate prediction models. For GO terms, ARBA has an additional feature to augment reference data using the relations between GO terms in the GO graph. The data augmentation is based on adding more general annotations into records containing manual GO terms, which will result in richer reference data. The predicted GO terms are then propagated to all unreviewed UniProtKB/TrEMBL proteins that meet the conditions of ARBA models. GO annotations using this technique receive the evidence code Inferred from Electronic Annotation (IEA; ECO:0000501).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"UniProt","canto_curator_role":"JaponicusDB","cv_annotations":{"biological_process":[{"annotations":[59096,64395,67517],"is_not":false,"summary":null,"term":"GO:0006338"},{"annotations":[59328],"is_not":false,"summary":null,"term":"GO:0006281"},{"annotations":[67607],"is_not":false,"summary":null,"term":"GO:0016197"},{"annotations":[63318],"is_not":false,"summary":null,"term":"GO:0051649"},{"annotations":[59095,64394,67516],"is_not":false,"summary":null,"term":"GO:0010468"},{"annotations":[58771,65372],"is_not":false,"summary":null,"term":"GO:0006772"}],"cellular_component":[{"annotations":[63058],"is_not":false,"summary":null,"term":"GO:0005680"},{"annotations":[62457,65102],"is_not":false,"summary":null,"term":"GO:0005938"},{"annotations":[65101],"is_not":false,"summary":null,"term":"GO:0032153"},{"annotations":[58541],"is_not":false,"summary":null,"term":"GO:0000785"},{"annotations":[59149],"is_not":false,"summary":null,"term":"GO:0005737"}],"molecular_function":[{"annotations":[65103],"is_not":false,"summary":null,"term":"GO:0005096"},{"annotations":[59097],"is_not":false,"summary":null,"term":"GO:0097159"}]},"gene_count":13,"genes_by_uniquename":{"SJAG_00510":null,"SJAG_00551":null,"SJAG_00773":null,"SJAG_00907":null,"SJAG_01445":null,"SJAG_01742":null,"SJAG_01943":null,"SJAG_02047":null,"SJAG_03675":null,"SJAG_04180":null,"SJAG_05161":null,"SJAG_06608":null,"SJAG_06641":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0000785":null,"GO:0005096":null,"GO:0005680":null,"GO:0005737":null,"GO:0005938":null,"GO:0006281":null,"GO:0006338":null,"GO:0006772":null,"GO:0010468":null,"GO:0016197":null,"GO:0032153":null,"GO:0051649":null,"GO:0097159":null},"title":"Electronic Gene Ontology annotations created by ARBA machine learning models","uniquename":"GO_REF:0000117"}


id: GO_REF:0000024
data:
  {"abstract":"Method for transferring manual annotations to an entry based on a curator's judgment of its similarity to a putative ortholog that has annotations that are supported with experimental evidence. Annotations are created when a curator judges that the sequence of a protein shows high similarity to another protein that has annotation(s) supported by experimental evidence (and therefore display one of the evidence codes EXP, IDA, IGI, IMP, IPI or IEP). Annotations resulting from the transfer of GO terms display the 'ISS' evidence code and include an accession for the protein from which the annotation was projected in the 'with' field (column 8). This field can contain either a UniProtKB accession or an IPI (International Protein Index) identifier. Only annotations with an experimental evidence code and which do not have the 'NOT' qualifier are transferred. Putative orthologs are chosen using information combined from a variety of complementary sources. Potential orthologs are initially identified using sequence similarity search programs such as BLAST. Orthology relationships are then verified manually using a combination of resources including sequence analysis tools, phylogenetic and comparative genomics databases such as Ensembl Compara, INPARANOID and OrthoMCL, as well as other specialised databases such as species-specific collections (e.g. HGNC's HCOP). In all cases curators check each alignment and use their experience to assess whether similarity is considered to be strong enough to infer that the two proteins have a common function so that they can confidently project an annotation. While there is no fixed cut-off point in percentage sequence similarity, generally proteins which have greater than 30% identity that covers greater than 80% of the length of both proteins are examined further. For mammalian proteins this cut-off tends to be higher, with an average of 80% identity over 90% of the length of both proteins. Strict orthologs are desirable but not essential. In general, when there is evidence of multiple paralogs for a single species, annotations using less specific GO terms are transferred to the paralogs, however, annotations using more specific GO terms may be transferred to the most similar paralog in each species, this decision is taken on a case by case basis and may be influenced by statements by researchers in the field. Further detailed information on this procedure, including how ISS annotations are made to protein isoforms, can be found at: http://www.ebi.ac.uk/GOA/ISS_method.html.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"AgBase, BHF-UCL, Parkinson's UK-UCL, dictyBase, HGNC, Roslin Institute, FlyBase and UniProtKB curators.","canto_curator_role":"JaponicusDB","cv_annotations":{"biological_process":[{"annotations":[79207],"is_not":false,"summary":null,"term":"GO:0000122"}],"cellular_component":[{"annotations":[79204],"is_not":false,"summary":null,"term":"GO:0005869"}],"molecular_function":[{"annotations":[79205],"is_not":false,"summary":null,"term":"GO:0001227"},{"annotations":[79206],"is_not":false,"summary":null,"term":"GO:0000978"}]},"gene_count":2,"genes_by_uniquename":{"SJAG_00124":null,"SJAG_01739":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0000122":null,"GO:0000978":null,"GO:0001227":null,"GO:0005869":null},"title":"Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity.","uniquename":"GO_REF:0000024"}


id: PMID:7214237
data:
  {"abstract":"Hybridization studies based on the prototrophic selection technique, involving the use of auxotrophic mutants of strains of five accepted species of the genus Schizosaccharomyces, are reported. Intrastrain recombinants were recovered in five out of six tested parental pairs. Interstrain recombinants were recovered from crosses involving strains of S. japonicus and strains of S. pombe. No recombinants were recovered in 62 interspecific crosses involving all possible combinations of the six representatives of the genus.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Johannsen E","authors_abbrev":"Johannsen E","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Can J Microbiol 1981 Feb;27(2):184-91","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1981","pubmed_entrez_date":"1981-02-01","pubmed_publication_date":"Feb 1981","terms_by_termid":{},"title":"Hybridization studies within the genus Schizosaccharomyces Lindner.","uniquename":"PMID:7214237"}


id: PMID:26263485
data:
  {"abstract":"Cytokinesis must be regulated in time and space in order to preserve genome integrity during cell proliferation and to allow daughter cells to adopt distinct fates and geometries during differentiation. The fission yeast Schizosaccharomyces pombe has been a popular model organism for understanding spatiotemporal regulation of cytokinesis in a symmetrically dividing cell. Recent work on another member of the same genus, Schisozaccharomyces japonicus, suggests that S. pombe may have evolved an unusual division site placement mechanism based on a recently duplicated anillin paralog. Here we discuss an extraordinary evolutionary plasticity of cytokinesis within the fission yeast clade and argue that the comparative cell biology approach may provide functional insights beyond those afforded by scrutinizing individual model species.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Gu Y, Oliferenko S","authors_abbrev":"Gu Y et al.","canto_added_date":"2023-05-04 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Curr Opin Microbiol 2015 Dec;28:18-25","cv_annotations":{},"doi":"10.1016/j.mib.2015.07.011","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2015","pubmed_entrez_date":"2015-08-12","pubmed_publication_date":"Dec 2015","terms_by_termid":{},"title":"Comparative biology of cell division in the fission yeast clade.","uniquename":"PMID:26263485"}


id: GO_REF:0000118
data:
  {"abstract":"TreeGrafter is a software tool for annotating protein sequences using pre-annotated PANTHER phylogenetic trees. TreeGrafter takes an input query protein sequence, finds the best matching homologous family, and then grafts it to the best location in the tree. It then annotates the query sequence by propagating annotations from the appropriate ancestral node(s) in the reference tree, which were manually annotated using the PAN-GO method (see GOREF_0000033). This method is integrated into InterProScan, which produces annotations to millions of genes across tens of thousands of organisms.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Haiming Tang, Dustin Ebert, Matthias Blum, Robert Finn, Paul Thomas ","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"TreeGrafter-generated GO annotations","uniquename":"GO_REF:0000118"}


id: GO_REF:0000092
data:
  {"abstract":"We have created a standard template for classes describing the biosynthesis of a chemical entity from or via an other chemical entity as biological processes. The underlying equivalence axiom templates are \"GO:0009058 and 'has output' some T and 'has input' some F\" (biosynthesis from) and \"GO:0009058 and 'has output' some T and 'has intermediate' some I\" (biosynthesis via), where T,F, and I are chemical entities (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation for the biosynthesis from or via a chemical as biological process in the Gene Ontology","uniquename":"GO_REF:0000092"}


id: PMID:27697163
data:
  {"abstract":"The present work demonstrates that yeasts belonging to the Schizosaccharomyces genus release a high quantity of polysaccharides of cell wall origin starting from the onset of the alcoholic fermentation. By the end of the alcoholic fermentation, all of the Schizosaccharomyces yeast strains released a quantity of polysaccharides approximately 3-7 times higher than that released by a commercial Saccharomyces cerevisiae yeast strain under the same fermentative conditions of synthetic juice. A higher content of polysaccharide was found in media fermented by Schizosaccharomyces japonicus with respect to that of Schizosaccharomyces pombe. Some of the strains evaluated were also able to produce high levels of pyruvic acid, which has been shown to be an important compound for color stability of wine. The presence of strains with different malic acid consumption patterns along with high polysaccharide release would enable production of naturally modified wines with enhanced mouth feel and reduced acidity. The chemical analysis of the released polysaccharides demonstrated divergence between the two yeast species S. pombe and S. japonicus. A different mannose/galactose ratio and a different percentage of proteins was observed on the polysaccharides released by S. pombe as compared to S. japonicus. Analysis of the proteins released in the media revealed the presence of a glycoprotein with a molecular size around 32-33 kDa only for the species S. japonicus. Mass spectrometry analysis of carbohydrate moieties showed similar proportions among the N-glycan chains released in the media by both yeast species but differences between the two species were also observed. These observations suggest a possible role of rapid MALDI-TOF screening of N-glycans compositional fingerprint as a taxonomic tool for this genus. Polysaccharides release in the media, in particular galactomannoproteins in significant amounts, could make these yeasts particularly interesting also for the industrial production of exogenous polysaccharide preparations.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Domizio P, Liu Y, Bisson LF, Barile D","authors_abbrev":"Domizio P et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Food Microbiol 2017 Feb;61:136-149","cv_annotations":{},"doi":"10.1016/j.fm.2016.08.010","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2017","pubmed_entrez_date":"2016-10-05","pubmed_publication_date":"Feb 2017","terms_by_termid":{},"title":"Cell wall polysaccharides released during the alcoholic fermentation by Schizosaccharomyces pombe and S. japonicus: quantification and characterization.","uniquename":"PMID:27697163"}


id: PMID:9884240
data:
  {"abstract":"Fission yeast cells grow by extension at the ends (poles) and divide by transverse fission. It has previously been reported that Schizosaccharomyces japonicus var. japonicus can switch to unipolar, filamentous growth. Here it is shown that the yeast-to-mycelium transition is a gradual process involving a changeover to unipolar growth associated with asymmetric divisions, the development of large polarly located vacuoles, the modifications of the actin and microtubular cytoskeleton and the repression of cell separation after division. High concentrations of glucose in the medium or supplementation of the medium with caffeine or cAMP support the bipolar yeast phase, inhibit the transition to the mycelial phase and induce the conversion of hyphae to yeasts. These effects suggest that cAMP may be involved in the regulation of dimorphism. Temperatures below 18 degrees C or over 35 degrees C are restrictive for the mycelial phase and provoke a return to yeast phase.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-10-07","authors":"Sipiczki M, Takeo K, Grallert A","authors_abbrev":"Sipiczki M et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-10-07 12:31:51","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-10-07 12:31:51","canto_session_key":"5ac54d09f220d215","canto_session_submitted_date":"2021-09-30 09:01:47","canto_triage_status":"Curatable","citation":"Microbiology (Reading) 1998 Dec;144 ( Pt 12):3475-3485","cv_annotations":{},"doi":"10.1099/00221287-144-12-3475","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1998","pubmed_entrez_date":"1999-01-12","pubmed_publication_date":"Dec 1998","terms_by_termid":{},"title":"Growth polarity transitions in a dimorphic fission yeast.","uniquename":"PMID:9884240"}


id: PMID:37849458
data:
  {"abstract":"We previously demonstrated that we could hijack the fungal pheromone signaling pathway to provide a living yeast biosensor where peptide biomarkers were recognized by G-protein-coupled receptors and engineered to transcribe a readout. Here, we demonstrated that the protease could be reintroduced to the biosensor to provide a simple mechanism for distinguishing single-amino-acid changes in peptide ligands that, otherwise, would likely be difficult to detect using binding-based assays. We characterized the dose-response curves for five fungal pheromone G-protein-coupled receptors, peptides, and proteases -Saccharomyces cerevisiae ,  Candida albicans ,  Schizosaccharomyces pombe ,  Schizosaccharomyces octosporus , and  Schizosaccharomyces japonicus . Alanine scanning was carried out for the most selective of these- S. cerevisiae  and  C. albicans -with and without the protease. Two peptide variants were discovered, which showed diminished cleavage by the protease (CaPep2A and CaPep2A13A). Those peptides were then distinguished by utilizing the biosensor strains with and without the protease, which selectively cleaved and altered the apparent concentration of peptide required for half-maximal activation for 2 peptides-CaPep and CaPep13A, respectively-by more than one order of magnitude. These results support the hypothesis that the living yeast biosensor with a sequence-specific protease can translate single-amino-acid changes into more than one order of magnitude apparent shift in the concentration of peptide required for half-maximal activation. With further engineering by computational modeling and directed evolution, the biosensor could likely distinguish a wide variety of peptide sequences beyond the alanine scanning carried out here. In the future, we envision incorporating proteases into our living yeast biosensor for use as a point of care diagnostic, a scalable communication language, and other applications.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Crnković T, Bokor BJ, Lockwood ME, Cornish VW","authors_abbrev":"Crnković T et al.","canto_added_date":"2023-10-19 00:40:03","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Biodes Res 2023;5:0003","cv_annotations":{},"doi":"10.34133/bdr.0003","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2023","pubmed_entrez_date":"2023-10-18","pubmed_publication_date":"2023","terms_by_termid":{},"title":"Peptide Variant Detection by a Living Yeast Biosensor via an Epitope-Selective Protease.","uniquename":"PMID:37849458"}


id: GO_REF:0000115
data:
  {"abstract":"Rfam (http://rfam.org, PMID:29112718) is a database of non-coding RNA families which are manually","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"RNAcentral (1). (1) European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, United Kingdom","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Automatic Gene Ontology annotation of non-coding RNA sequences through association of Rfam records with GO terms","uniquename":"GO_REF:0000115"}


id: GO_REF:0000044
data:
  {"abstract":"Transitive assignment of GO terms based on the UniProtKB/Swiss-Prot Subcellular Location vocabulary. UniProtKB Subcellular Location is a controlled vocabulary used to supply subcellular location information to UniProtKB entries in the SUBCELLULAR LOCATION lines. Terms from this vocabulary are annotated manually to UniProtKB/Swiss-Prot entries but are automatically assigned to UniProtKB/TrEMBL entries from the underlying nucleic acid databases and/or by the UniProt automatic annotation program.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"UniProt-GOA","canto_curator_role":"JaponicusDB","cv_annotations":{"cellular_component":[{"annotations":[65281],"is_not":false,"summary":null,"term":"GO:0001725"}]},"gene_count":1,"genes_by_uniquename":{"SJAG_01739":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0001725":null},"title":"Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt. ","uniquename":"GO_REF:0000044"}


id: PMID:35380656
data:
  {"abstract":"The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realize the full potential of studying a newly emerging model species and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Rutherford KM, Harris MA, Oliferenko S, Wood V","authors_abbrev":"Rutherford KM et al.","canto_added_date":"2023-05-04 00:40:03","canto_curator_role":"JaponicusDB","canto_triage_status":"Database","citation":"Genetics 2022 Apr 04;220(4)","cv_annotations":{},"doi":"10.1093/genetics/iyab223","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2022","pubmed_entrez_date":"2022-04-05","pubmed_publication_date":"04 Apr 2022","terms_by_termid":{},"title":"JaponicusDB: rapid deployment of a model organism database for an emerging model species.","uniquename":"PMID:35380656"}


id: PMID:12236685
data:
  {"abstract":"Dimethyl dicarbonate (DMDC) was added to grape must and to synthetic media and results showed that, at 20 degrees C, 150 mg.L(-)(1) DMDC completely inhibited the fermentation of a grape must that was previously inoculated with 10(6) cells.mL(-)(1) Saccharomyces bayanus and Saccharomyces uvarum. Brettanomyces intermedius, Candida guilliermondii, Hansenula jadinii, Hansenula petersonii, Kloeckera apiculata, Pichia membranaefaciens, and Saccharomyces cerevisiae were inhibited by 250 mg.L(-)(1). Candida valida was inhibited in the presence of 350 mg.L(-)(1), whereas Hanseniaspora osmophila, Saccharomycodes ludwigii, Schizosaccharomyces pombe, and Zygosaccharomyces bailii required 400 mg.L(-)(1). Delay of fermentation (but not inhibition) was noted in the presence of 400 mg.L(-)(1) for the following cultures: Brettanomyces anomalus, Hanseniaspora uvarum, Metschnikowia pulcherrima, Schizosaccharomyces japonicus, Torulaspora delbrueckii, and Zygosaccharomyces florentinus. Acetobacter aceti and Lactobacillus sp. were completely inhibited using 1000 and 500 mg.L(-)(1) DMDC, respectively. The fermentation of a grape must inoculated with 10(6) cells.mL(-)(1) of different wine yeasts was delayed for 4 days after the prior addition of 200 mg.L(-)(1) of DMDC; 200 mg.L(-)(1) DMDC did not show any residual inhibitory effect after 12 h, nor did 300 mg.L(-)(1) 24 h after the addition. In cellar experiments, indigenously contaminated grape musts (with and without skins) showed a delay in fermentation of 48 h after the addition of only 50 mg.L(-)(1) DMDC. The possibility of using DMDC (as pure grade as commercially available) in grape must as a disinfectant for the decontamination of musts indigenously contaminated with wild yeast should be considered seriously, despite its apparent low solubility in water.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Delfini C, Gaia P, Schellino R, Strano M, Pagliara A, Ambrò S","authors_abbrev":"Delfini C et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Biotech","citation":"J Agric Food Chem 2002 Sep 25;50(20):5605-11","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2002","pubmed_entrez_date":"2002-09-19","pubmed_publication_date":"25 Sep 2002","terms_by_termid":{},"title":"Fermentability of grape must after inhibition with dimethyl dicarbonate (DMDC).","uniquename":"PMID:12236685"}


id: GO_REF:0000114
data:
  {"abstract":"Method for transferring manual annotations to an entry based on a curator's judgment of its similarity to a putative homolog that has annotations that are supported with experimental evidence. Annotations are created when a curator judges that the sequence, composition and function of a complex shows high similarity to another complex that has annotation(s) supported by experimental evidence (and therefore display one of the evidence codes ECO:0000353 [IPI] or ECO:0005543). Annotations resulting from the transfer of GO terms display the ECO:0005610, ECO:0005544 or ECO:0005546 evidence codes and include an accession for the complex from which the annotation was projected in the 'with/from' field (column 8). This field MUST contain a Complex Portal accession identifier. Putative homologs are chosen using information combined from a variety of complementary sources. Potential homologs are initially identified using sequence similarity search programs such as BLAST. Homologous relationships are then verified manually using a combination of resources including sequence analysis tools, phylogenetic and comparative genomics databases such as Ensembl Compara, INPARANOID and OrthoMCL, as well as other specialised databases such as species-specific collections (e.g. HGNC's HCOP). In all cases curators check the alignments for each complex component and use their experience to assess whether similarity is considered to be strong enough to infer that the two proteins have a common function so that they can confidently project an annotation. While there is no fixed cut-off point in percentage sequence similarity, generally proteins which have greater than 70% identity that covers greater than 90% of the length of both proteins are examined further. Whilst we expect subunit composition to be conserved between closely related species, this is not an absolute rule and orthologous complexes may differ if a subunit cannot be traced in one species or is experimentally shown not to be present. When there is evidence of multiple paralogs for a single species, multiple variants of the complex can be inferred.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Birgit Meldal and Sandra Orchard (1). (1) European Bioinformatics Institute (EBI), Hinxton, Cambridgeshire, United Kingdom","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Manual transfer of experimentally-verified manual GO annotation data to homologous complexes by curator judgment of sequence, composition and function similarity","uniquename":"GO_REF:0000114"}


id: PMID:7166567
data:
  {"abstract":"The fine structure of ascospore formation in the fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus var. japonicus was studied by serial thin-sectioning and electron microscopy. The morphogenetic events were almost the same in both species. Ascospore development was initiated by the formation of the forespore membrane on the cytoplasmic side of the differentiated nucleus-associated organelle (NAO) in the interval between meiosis I and II in S. pombe, or during the post-meiotic nuclear division in S. japonicus, and the process proceeded almost synchronously through the two or four nuclei in the ascus. The forespore membrane developed by fusion of the cytoplasmic vesicles and this was clearly demonstrated in S. japonicus where the behaviour of vesicles involved in the forespore membrane development could be traced as they were marked by the presence of electron-dense granules. The staining technique, by phosphotungustic acid--chromic acid (PTA-CA) after treatment with periodic acid, was used to attempt to elucidate the origin and the nature of the forespore membrane. The method specific to plasmalemma-type membranes stained both ascus and ascospore plasmalemmas; the forespore membrane was not stained at first but developed the same affinity for stain as the plasma membrane in the course of ascospore development. The results suggest that the forespore membrane did not come directly from the ascus plasma membrane, but from another membrane system such as the endoplasmic reticulum. Spore wall material was deposited in the space between the inner and outer leaflets of the forespore membrane.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Tanaka K, Hirata A","authors_abbrev":"Tanaka K et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"J Cell Sci 1982 Aug;56:263-79","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1982","pubmed_entrez_date":"1982-08-01","pubmed_publication_date":"Aug 1982","terms_by_termid":{},"title":"Ascospore development in the fission yeasts Schizosaccharomyces pombe and S. japonicus.","uniquename":"PMID:7166567"}


id: GO_REF:0000041
data:
  {"abstract":"Transitive assignment of GO terms based on the UniPathway pathway vocabulary. UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways. Descriptions of the pathway(s) that a particular protein is involved in are included in UniProtKB records.<br>UniPathway data are cross-linked to existing pathway resources such as KEGG and MetaCyc. Further information on the UniPathway resource is available at http://www.unipathway.org/obiwarehouse/unipathway.<br>When a UniPathway pathway describes a concept that is within the scope of the Gene Ontology, it is investigated to determine whether it is appropriate to map the term to an equivalent term in GO. The mapping between UniPathway terms and GO terms is carried out manually. Definitions and hierarchies of the terms in the two resources are compared and the mapping generated will reflect the most correct correspondence. The translation table between GO terms and UniPathway pathways is maintained by the UniPathway team and is available at http://www.grenoble.prabi.fr/dev/obiwarehouse/download/unipathway/public/unipathway2go.tsv.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"UniProt-GOA","canto_curator_role":"JaponicusDB","cv_annotations":{"biological_process":[{"annotations":[65191],"is_not":false,"summary":null,"term":"GO:0006021"},{"annotations":[66680],"is_not":false,"summary":null,"term":"GO:0006782"},{"annotations":[57708],"is_not":false,"summary":null,"term":"GO:0006048"}]},"gene_count":3,"genes_by_uniquename":{"SJAG_00097":null,"SJAG_00519":null,"SJAG_03739":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0006021":null,"GO:0006048":null,"GO:0006782":null},"title":"Gene Ontology annotation based on UniPathway vocabulary mapping. ","uniquename":"GO_REF:0000041"}


id: PMID:9611807
data:
  {"abstract":"The fission yeast Schizosaccharomyces pombe shows bipolar growth and is a convenient model for studying cell polarity and polar growth. This paper shows that the related Schiz. japonicus var. japonicus can switch to unipolar growth and can exist in both yeast and mycelial phases. On solid media, the yeast phase is unstable and prone to switch to the mycelial form, which shows unipolar growth by tip elongation. The hyphae can colonize the body of the substrate (true mycelium) or just its surface (pseudo-mycelium). The yeast-to-mycelium transition and the growth of the mycelium are regulated by a nutritional gradient and are associated with extensive vacuolation. The mycelium can convert into arthroconidia or return to the yeast phase in response to environmental changes. These environmentally controlled morphological transitions make Schiz. japonicus var. japonicus an attractive model for the investigation of cell polarity and morphogenesis.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-10-07","authors":"Sipiczki M, Takeo K, Yamaguchi M, Yoshida S, Miklos I","authors_abbrev":"Sipiczki M et al.","canto_added_date":"2021-09-30 08:50:02","canto_annotation_status":"APPROVED","canto_approved_date":"2021-10-07 12:30:26","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-10-07 12:30:26","canto_session_key":"fced61f1377cd206","canto_session_submitted_date":"2021-09-30 08:52:46","canto_triage_status":"Curatable","citation":"Microbiology (Reading) 1998 May;144 ( Pt 5):1319-1330","cv_annotations":{},"doi":"10.1099/00221287-144-5-1319","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1998","pubmed_entrez_date":"1998-06-05","pubmed_publication_date":"May 1998","terms_by_termid":{},"title":"Environmentally controlled dimorphic cycle in a fission yeast.","uniquename":"PMID:9611807"}


id: GO_REF:0000051
data:
  {"abstract":"Keywords derived from manually curated primary annotation, e.g. gene product descriptions, are mapped to GO terms. Annotations made by this method have the evidence code Non-traceable Author Statement (NAS), and are filtered from the PomBase annotation files wherever another annotation exists that is equally or more specific, and supported by experimental or manually evaluated comparative evidence (such as ISS and its subtypes). Formerly GOC:pombekw2GO.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"PomBase curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"S. pombe keyword mapping","uniquename":"GO_REF:0000051"}


id: GO_REF:0000067
data:
  {"abstract":"We have created a standard template for classes describing the binding to a chemical entity (ChEBI) as a molecular function. The underlying equivalence axiom template is \"GO:0005488 and 'has input' some X\", where X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of binding to a chemical entity as molecular function in the Gene Ontology","uniquename":"GO_REF:0000067"}


id: PMID:21733045
data:
  {"abstract":"During open mitosis in higher eukaryotic cells, the nuclear envelope completely breaks down and then mitotic chromosomes are exposed in the cytoplasm. By contrast, mitosis in lower eukaryotes, including fungi, proceeds with the nucleus enclosed in an intact nuclear envelope. The mechanism of mitosis has been studied extensively in yeast, a closed mitosis organism. Here, we describe a form of mitosis in which the nuclear envelope is torn by elongation of the nucleus in the fission yeast Schizosaccharomyces japonicus. The mitotic nucleus of Sz. japonicus adopted a fusiform shape in anaphase, and its following extension caused separation. Finally, a tear in the nuclear envelope occurred in late anaphase. At the same time, a polarized-biased localization of nuclear pores was seen in the fusiform-shaped nuclear envelope, suggesting a compromise in the mechanical integrity of the lipid membrane. It has been known that nuclear membrane remains intact in some metazoan mitosis. We found that a similar tear of the nuclear envelope was also observed in late mitosis of the Caenorhabditis elegans embryo. These findings provide insight into the diversity of mitosis and the biological significance of breakdown of the nuclear envelope.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":2,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-21","authors":"Aoki K, Hayashi H, Furuya K, Sato M, Takagi T, Osumi M, Kimura A, Niki H","authors_abbrev":"Aoki K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-21 17:28:56","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-21 17:28:56","canto_session_key":"6063f08db89b54c7","canto_session_submitted_date":"2022-11-21 17:28:46","canto_triage_status":"Curatable","citation":"Genes Cells 2011 Sep;16(9):911-26","cv_annotations":{"cellular_component":[{"annotations":[115155],"is_not":false,"summary":null,"term":"GO:0070762"},{"annotations":[115156],"is_not":false,"summary":null,"term":"GO:0005816"}]},"doi":"10.1111/j.1365-2443.2011.01540.x","gene_count":1,"genes_by_uniquename":{"SJAG_03200":null},"genotypes_by_uniquename":{},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2011","pubmed_entrez_date":"2011-07-08","pubmed_publication_date":"Sep 2011","terms_by_termid":{"GO:0005816":null,"GO:0070762":null},"title":"Breakage of the nuclear envelope by an extending mitotic nucleus occurs during anaphase in Schizosaccharomyces japonicus.","uniquename":"PMID:21733045"}


id: GO_REF:0000084
data:
  {"abstract":"We have created a standard template for classes describing the structural organization of a plant structure as a biological process. The underlying equivalence axiom template is \"'anatomical structure arrangement' and 'results in structural organization of' some P\", where P is a plant anatomical entity (PO:0025131).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of plant structural organization as biological process in the Gene Ontology","uniquename":"GO_REF:0000084"}


id: PMID:37684233
data:
  {"abstract":"Cellular metabolism relies on just a few redox cofactors. Selective compartmentalization may prevent competition between metabolic reactions requiring the same cofactor. Is such compartmentalization necessary for optimal cell function? Is there an optimal compartment size? Here we probe these fundamental questions using peroxisomal compartmentalization of the last steps of lysine and histidine biosynthesis in the fission yeast Schizosaccharomyces japonicus. We show that compartmentalization of these NAD +  dependent reactions together with a dedicated NADH/NAD +  recycling enzyme supports optimal growth when an increased demand for anabolic reactions taxes cellular redox balance. In turn, compartmentalization constrains the size of individual organelles, with larger peroxisomes accumulating all the required enzymes but unable to support both biosynthetic reactions at the same time. Our reengineering and physiological experiments indicate that compartmentalized biosynthetic reactions are sensitive to the size of the compartment, likely due to scaling-dependent changes within the system, such as enzyme packing density.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Gu Y, Alam S, Oliferenko S","authors_abbrev":"Gu Y et al.","canto_added_date":"2023-09-10 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Nat Commun 2023 Sep 08;14(1):5544","cv_annotations":{},"doi":"10.1038/s41467-023-41347-x","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2023","pubmed_entrez_date":"2023-09-08","pubmed_publication_date":"08 Sep 2023","terms_by_termid":{},"title":"Peroxisomal compartmentalization of amino acid biosynthesis reactions imposes an upper limit on compartment size.","uniquename":"PMID:37684233"}


id: GO_REF:0000065
data:
  {"abstract":"We have created a standard template for classes describing transport of a chemical entity (ChEBI) as a biological process. The underlying equivalence axiom template is \"GO:0006810 and 'transports or maintains localization of' some X\", where X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of transport of a chemical entity as a biological process in the Gene Ontology","uniquename":"GO_REF:0000065"}


id: PMID:19473263
data:
  {"abstract":"Schizosaccharomyces cells divide by medial septation, followed by enzymatic degradation of parts of the septum (septum cleavage) to allow the sister cells to separate from each other. In a previous study we found that the cell separation mutant sep9-307 was defective in a gene that encodes a protein highly similar in sequence to the Saccharomyces cerevisiae protein Spt8, a subunit of the SAGA complex. Here, we show that the sep9-307 mutation causes a frameshift in translation. The deletion of sep9(+) is not lethal but abolishes normal septum cleavage by reducing the activity of ace2(+), a gene coding for a transcription factor of numerous genes producing proteins for septum cleavage. Indirect evidence indicates that Sep9 might also act directly in the transcription of certain target genes (e.g. eng1(+)) of this regulator. sep9-307 is synthetically lethal with mutations in the cell separation genes sep11/med18(+) and sep15/med8(+), which encode subunits of the general transcription factor mediator. Heterologous expression of SPT8 and the putative Schizosaccharomyces japonicus sep9(+) orthologue cannot substitute for sep9(+). Both Spt8 and the fission yeast proteins have highly acidic (74-76 amino-acid long) N-terminal regions with no sequence conservation.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Batta G, Szilagyi Z, Laczik M, Sipiczki M","authors_abbrev":"Batta G et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"FEMS Yeast Res 2009 Aug;9(5):757-67","cv_annotations":{},"doi":"10.1111/j.1567-1364.2009.00522.x","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2009","pubmed_entrez_date":"2009-05-29","pubmed_publication_date":"Aug 2009","terms_by_termid":{},"title":"The involvement of the Schizosaccharomyces pombe sep9/spt8 gene in the regulation of septum cleavage.","uniquename":"PMID:19473263"}


id: PMID:38451028
data:
  {"abstract":"Schizosaccharomyces japonicus belongs to the single-genus class Schizosaccharomycetes, otherwise known as \"fission yeasts.\" As part of a composite model system with its widely studied S. pombe sister species, S. japonicus has provided critical insights into the workings and the evolution of cell biological mechanisms. Furthermore, its divergent biology makes S. japonicus a valuable model organism in its own right. However, the currently available genome assembly contains gaps and has been unable to resolve centromeres and other repeat-rich chromosomal regions. Here we present a telomere-to-telomere long-read genome assembly of the S. japonicus genome. This includes the three megabase-length chromosomes, with centromeres hundreds of kilobases long, rich in 5S ribosomal RNA genes, transfer RNA genes, long terminal repeats, and short repeats. We identify a gene-sparse region on chromosome 2 that resembles a 331 kb centromeric duplication. We revise the genome size of S. japonicus to at least 16.6 Mb and possibly up to 18.12 Mb, at least 30% larger than previous estimates. Our whole genome assembly will support the growing S. japonicus research community and facilitate research in new directions, including centromere and DNA repeat evolution, and yeast comparative genomics.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Etherington GJ, Wu PS, Oliferenko S, Uhlmann F, Nieduszynski CA","authors_abbrev":"Etherington GJ et al.","canto_added_date":"2024-03-09 02:40:03","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Yeast 2024 Mar;41(3):73-86","cv_annotations":{},"doi":"10.1002/yea.3912","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2024","pubmed_entrez_date":"2024-03-07","pubmed_publication_date":"Mar 2024","terms_by_termid":{},"title":"Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features.","uniquename":"PMID:38451028"}


id: GO_REF:0000108
data:
  {"abstract":"GO terms are automatically assigned based on inter-ontology links to generate inferred annotations. Annotations from Molecular Function to Biological Process can be propagated, as well as between Biological Process and Cellular Component. Annotations that are created using this inference method receive either the evidence code ECO:0000366 (evidence based on logical inference from automatic annotation used in automatic assertion) or ECO:0000364 (evidence based on logical inference from manual annotation used in automatic assertion), depending on whether the source annotation has a manual or automatic evidence code. Both of these codes map up to the GO Inferred from Electronic Annotation (IEA) evidence code.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GOA 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id: PMID:2226803
data:
  {"abstract":"In the fission yeast Schizosaccharomyces pombe, the enzyme RNAse P copurifies with two RNAs, K1- and K2-RNA, which are identical except for their termini [1] and which are encoded by a single gene [2]. We have undertaken the cloning of the K-RNA genes in related organisms in order to gain comparative structural information. Because the K-RNA sequence is poorly conserved across species, we have cloned the K-RNA genes in the Schizosaccharomyces species S. malidevorans, S. japonicus, S. versatilis, and S. octosporus. Of the 4 species, only S. octosporus contains a K-RNA gene different from that in S. pombe; the gene diverges by 20%. Based on the two sequences, nuclease protection data and computer analysis, we have proposed a secondary structure model for the K-RNA. Northern analysis shows the K-RNA genes in all four Schizosaccharomyces species to be expressed as two RNAs, as in S. pombe.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Zimmerly S, Gamulin V, Burkard U, Söll D","authors_abbrev":"Zimmerly S et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"FEBS Lett 1990 Oct 01;271(1-2):189-93","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1990","pubmed_entrez_date":"1990-10-01","pubmed_publication_date":"01 Oct 1990","terms_by_termid":{},"title":"The RNA component of RNase P in Schizosaccharomyces species.","uniquename":"PMID:2226803"}


id: PMID:34656184
data:
  {"abstract":"In most fungi, quinone-dependent Class-II dihydroorotate dehydrogenases (DHODs) are essential for pyrimidine biosynthesis. Coupling of these Class-II DHODHs to mitochondrial respiration makes their in vivo activity dependent on oxygen availability. Saccharomyces cerevisiae and closely related yeast species harbor a cytosolic Class-I DHOD (Ura1) that uses fumarate as electron acceptor and thereby enables anaerobic pyrimidine synthesis. Here, we investigate DHODs from three fungi (the Neocallimastigomycete Anaeromyces robustus and the yeasts Schizosaccharomyces japonicus and Dekkera bruxellensis) that can grow anaerobically but, based on genome analysis, only harbor a Class-II DHOD.\nHeterologous expression of putative Class-II DHOD-encoding genes from fungi capable of anaerobic, pyrimidine-prototrophic growth (Arura9, SjURA9, DbURA9) in an S. cerevisiae ura1Δ strain supported aerobic as well as anaerobic pyrimidine prototrophy. A strain expressing DbURA9 showed delayed anaerobic growth without pyrimidine supplementation. Adapted faster growing DbURA9-expressing strains showed mutations in FUM1, which encodes fumarase. GFP-tagged SjUra9 and DbUra9 were localized to S. cerevisiae mitochondria, while ArUra9, whose sequence lacked a mitochondrial targeting sequence, was localized to the yeast cytosol. Experiments with cell extracts showed that ArUra9 used free FAD and FMN as electron acceptors. Expression of SjURA9 in S. cerevisiae reproducibly led to loss of respiratory competence and mitochondrial DNA. A cysteine residue (C265 in SjUra9) in the active sites of all three anaerobically active Ura9 orthologs was shown to be essential for anaerobic activity of SjUra9 but not of ArUra9.\nActivity of fungal Class-II DHODs was long thought to be dependent on an active respiratory chain, which in most fungi requires the presence of oxygen. By heterologous expression experiments in S. cerevisiae, this study shows that phylogenetically distant fungi independently evolved Class-II dihydroorotate dehydrogenases that enable anaerobic pyrimidine biosynthesis. Further structure-function studies are required to understand the mechanistic basis for the anaerobic activity of Class-II DHODs and an observed loss of respiratory competence in S. cerevisiae strains expressing an anaerobically active DHOD from Sch. japonicus.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Bouwknegt J, Koster CC, Vos AM, Ortiz-Merino RA, Wassink M, Luttik MAH, van den Broek M, Hagedoorn PL, Pronk JT","authors_abbrev":"Bouwknegt J et al.","canto_added_date":"2023-05-04 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Fungal Biol Biotechnol 2021 Oct 16;8(1):10","cv_annotations":{},"doi":"10.1186/s40694-021-00117-4","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-10-17","pubmed_publication_date":"16 Oct 2021","terms_by_termid":{},"title":"Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis.","uniquename":"PMID:34656184"}


id: PMID:23337086
data:
  {"abstract":"During meiosis, chromosomes adopt a bouquet arrangement, which is widely conserved among eukaryotes. This arrangement is assumed to play an important role in the normal progression of meiosis, by mediating the proper pairing of homologous chromosomes. In Schizosaccharomyces pombe, the complex of Bqt1 and Bqt2 plays a key role in telomere clustering and the subsequent bouquet arrangement of chromosomes during early meiotic prophase. Bqt1 and Bqt2 are part of a multi-protein complex that mediates the attachment of the telomere to the nuclear membrane. However, the structural details of the complex are needed to clarify the mechanism of telomere clustering. To enable biophysical studies of Bqt1 and Bqt2, we established a purification procedure for the Schizosaccharomyces japonicus Bqt1-Bqt2 complex, which is closely related to the S. pombe Bqt1-Bqt2 complex. A co-expression vector, in which one of the expressed subunits is fused to a removable SUMO tag, yielded high amounts of the proteins in the soluble fraction. The solubility of the Bqt1-Bqt2 complex after the removal of the SUMO tag was maintained by including CHAPS, a nondenaturing, zwitterionic detergent, in the purification buffers. These procedures enabled us to rapidly purify the stable Bqt1-Bqt2 complex. The co-purified Bqt1 and Bqt2 proteins formed a stable heterodimer, consistent with results from in vivo studies showing the requirement of both proteins for the bouquet arrangement. The expression and purification procedures established here will facilitate further biophysical studies of the Bqt1-Bqt2 complex.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":2,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-05-12","authors":"Ichikawa Y, Kagawa W, Saito K, Chikashige Y, Haraguchi T, Hiraoka Y, Kurumizaka H","authors_abbrev":"Ichikawa Y et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-05-12 14:11:00","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Val Wood","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-05-12 14:11:00","canto_session_key":"34571f3accd180c4","canto_session_submitted_date":"2021-05-11 18:50:05","canto_triage_status":"Curatable","citation":"Protein Expr Purif 2013 Apr;88(2):207-13","cv_annotations":{"molecular_function":[{"annotations":[115157,115158],"is_not":false,"summary":null,"term":"GO:0005515"}]},"doi":"10.1016/j.pep.2013.01.006","gene_count":2,"genes_by_uniquename":{"SJAG_03287":null,"SJAG_05260":null},"genotypes_by_uniquename":{},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[{"evidence":"Co-purification","gene_uniquename":"SJAG_03287","interactor_uniquename":"SJAG_05260","reference_uniquename":"PMID:23337086","throughput":"low"}],"publication_year":"2013","pubmed_entrez_date":"2013-01-23","pubmed_publication_date":"Apr 2013","terms_by_termid":{"GO:0005515":null},"title":"Purification and characterization of the fission yeast telomere clustering factors, Bqt1 and Bqt2.","uniquename":"PMID:23337086"}


id: PMID:1093
data:
  {"abstract":"(11 Cell extracts and extracellular culture fluids of species of the yeast genus Schizosaccharomyces exhibited exo-beta-(1 leads to 3)- and exo-beta-(1 leads to 6)-glucanase (EC 3.2.1.-) activities. (2) Using a combination of Sephadex G-100 and DEAE-cellulose chromatography, the exo-beta-(1 leads to 3)-glucanases from the cell extracts and culture fluid of Schizosaccharomyces japonicus var. versatilis were purified extensively. The enzymes from either location exhibited similar purification and other properties. (3) The purified enzymes hydrolysed the beta-(1 leads to 6)-glucosidic linkage in addition to the beta-(1 leads to 3) linkage. Heat denaturation, inhibition and electrophoretic studies indicated that both hydrolytic activities were properties of a single protein. Laminarin and pustulan hydrolysis followed Michaelis-Menten kinetics. The Km and V for laminarin hydrolysis were 6.25 mg/ml and 350 mumol of glucose released/min/mg protein, and for pustulan they were 166 mg/ml and 52 mumol of glucose released/min/mg protein. (4) The exo-beta-glucanase was assigned a molecular weight of 43 000. (5) the purified enzyme failed to hydrolyse isolated cell walls from either baker's yeast or Schizosaccharomyces pombe or to induce protoplast formation from intact cells of S. japonicus var. versatilis or Saccharomyces cerevisiae.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Fleet GH, Phaff HJ","authors_abbrev":"Fleet GH et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Biochim Biophys Acta 1975 Dec 18;410(2):318-32","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1975","pubmed_entrez_date":"1975-12-18","pubmed_publication_date":"18 Dec 1975","terms_by_termid":{},"title":"Glucanases in Schizosaccharomyces. Isolation and properties of an exo-beta-glucanase from the cell extracts and culture fluid of Schizosaccharomyces japonicus var. versatilis.","uniquename":"PMID:1093"}


id: GO_REF:0000070
data:
  {"abstract":"We have created a standard template for classes describing the transmembrane transporter activity a chemical entity (ChEBI) as molecular function. This includes variants for secondary active transmembrane transporter activity (GO:0015291), uptake transmembrane transporter activity (GO:0015563), and ATPase activity, coupled to transmembrane movement of substances (GO:0042626). The underlying equivalence axiom template is \"G and 'transports or maintains localization of' some X\",  where the genus G is either GO:0022857 (transmembrane transporter activity), GO:0015291, GO:0015563, or GO:0042626 depending on the variant. The variable X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of transmembrane transporter activity as molecular function in the Gene Ontology","uniquename":"GO_REF:0000070"}


id: PMID:33232355
data:
  {"abstract":"Coenzyme Q (CoQ, ubiquinone) is an essential component of the electron transport system in aerobic organisms. Human type CoQ10, which has 10 units of isoprene in its quinone structure, is especially valuable as a food supplement. Therefore, studying the biosynthesis of CoQ10 is important not only for increasing metabolic knowledge, but also for improving biotechnological production. Herein, we show that Schizosaccharomyces pombe utilizes p-aminobenzoate (PABA) in addition to p-hydroxybenzoate (PHB) as a precursor for CoQ10 synthesis. We explored compounds that affect the synthesis of CoQ10 and found benzoic acid (Bz) at >5 μg/mL inhibited CoQ biosynthesis without accumulation of apparent CoQ intermediates. This inhibition was counteracted by incubation with a 10-fold lower amount of PABA or PHB. Overexpression of PHB-polyprenyl transferase encoded by ppt1 (coq2) also overcame the inhibition of CoQ biosynthesis by Bz. Inhibition by Bz was efficient in S. pombe and Schizosaccharomyces japonicus, but less so in Saccharomyces cerevisiae, Aureobasidium pullulans, and Escherichia coli. Bz also inhibited a S. pombe ppt1 (coq2) deletion strain expressing human COQ2, and this strain also utilized PABA as a precursor of CoQ10. Thus, Bz is likely to inhibit prenylation reactions involving PHB or PABA catalyzed by Coq2.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Nishida I, Yanai R, Matsuo Y, Kaino T, Kawamukai M","authors_abbrev":"Nishida I et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"PLoS One 2020;15(11):e0242616","cv_annotations":{},"doi":"10.1371/journal.pone.0242616","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2020","pubmed_entrez_date":"2020-11-24","pubmed_publication_date":"2020","terms_by_termid":{},"title":"Benzoic acid inhibits Coenzyme Q biosynthesis in Schizosaccharomyces pombe.","uniquename":"PMID:33232355"}


id: PMID:28655757
data:
  {"abstract":"Cytokinesis in many eukaryotes involves a tension-generating actomyosin-based contractile ring. Many components of actomyosin rings turn over during contraction, although the significance of this turnover has remained enigmatic. Here, using  Schizosaccharomyces japonicus , we investigate the role of turnover of actin and myosin II in its contraction. Actomyosin ring components self-organize into ∼1-µm-spaced clusters instead of undergoing full-ring contraction in the absence of continuous actin polymerization. This effect is reversed when actin filaments are stabilized. We tested the idea that the function of turnover is to ensure actin filament homeostasis in a synthetic system, in which we abolished turnover by fixing rings in cell ghosts with formaldehyde. We found that these rings contracted fully upon exogenous addition of a vertebrate myosin. We conclude that actin turnover is required to maintain actin filament homeostasis during ring contraction and that the requirement for turnover can be bypassed if homeostasis is achieved artificially.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":5,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-09","authors":"Chew TG, Huang J, Palani S, Sommese R, Kamnev A, Hatano T, Gu Y, Oliferenko S, Sivaramakrishnan S, Balasubramanian MK","authors_abbrev":"Chew TG et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-09 13:45:34","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 13:45:34","canto_session_key":"5ead7a365a97d8ab","canto_session_submitted_date":"2021-07-09 13:45:28","canto_triage_status":"Curatable","citation":"J Cell Biol 2017 09 04;216(9):2657-2667","cv_annotations":{"cellular_component":[{"annotations":[115177,115178,115179,115180,115181],"is_not":false,"summary":null,"term":"GO:0005826"}]},"doi":"10.1083/jcb.201701104","gene_count":5,"genes_by_uniquename":{"SJAG_01665":null,"SJAG_02431":null,"SJAG_03596":null,"SJAG_03703":null,"SJAG_04498":null},"genotypes_by_uniquename":{},"ltp_gene_count":5,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2017","pubmed_entrez_date":"2017-06-29","pubmed_publication_date":"04 09 2017","terms_by_termid":{"GO:0005826":null},"title":"Actin turnover maintains actin filament homeostasis during cytokinetic ring contraction.","uniquename":"PMID:28655757"}


id: PMID:37903220
data:
  {"abstract":"Walled cells, such as plants, fungi, and bacteria cells, possess a high internal hydrostatic pressure, termed turgor pressure, that drives volume growth and contributes to cell shape determination. Rigorous measurement of turgor pressure, however, remains challenging, and reliable quantitative measurements, even in budding yeast are still lacking. Here, we present a simple and robust experimental approach to access turgor pressure in yeasts based upon the determination of isotonic concentration using protoplasts as osmometers. We propose three methods to identify the isotonic condition - three-dimensional cell volume, cytoplasmic fluorophore intensity, and mobility of a cytGEMs nano-rheology probe - that all yield consistent values. Our results provide turgor pressure estimates of 1.0 ± 0.1 MPa for  Schizosaccharomyces pombe , 0.49 ± 0.01 MPa for  Schizosaccharomyces japonicus , 0.5 ± 0.1 MPa for  Saccharomyces cerevisiae   W303a  and 0.31 ± 0.03 MPa for  Saccharomyces cerevisiae BY4741 . Large differences in turgor pressure and nano-rheology measurements between the  Saccharomyces cerevisiae  strains demonstrate how fundamental biophysical parameters can vary even among wild-type strains of the same species. These side-by-side measurements of turgor pressure in multiple yeast species provide critical values for quantitative studies on cellular mechanics and comparative evolution.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Lemière J, Chang F","authors_abbrev":"Lemière J et al.","canto_added_date":"2023-10-31 02:40:03","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Mol Biol Cell 2023 Dec 01;34(13):ar133","cv_annotations":{},"doi":"10.1091/mbc.E23-06-0215","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2023","pubmed_entrez_date":"2023-10-30","pubmed_publication_date":"01 Dec 2023","terms_by_termid":{},"title":"Quantifying turgor pressure in budding and fission yeasts based upon osmotic properties.","uniquename":"PMID:37903220"}


id: PMID:21905090
data:
  {"abstract":"The construction of diploid cells eases genetic analysis in haploid genetic systems because diploid cells allow for the characterization of essential genes. Here, we report the construction of diploid cells using ade6 point mutants that suppress each other via interallelic complementation in the fission yeast Schizosaccharomyces japonicus var japonicus (Sz. japonicus). We constructed an ade6-domK mutant in addition to the previously described ade6-domE. Phenotypes of both mutants exhibited adenine auxotrophy and red colonies. The mutations complemented the phenotypes in a mutually dependent manner. Diploid zygotes, in which the two mutations were introduced simultaneously into the same cells, were isolated by selecting for adenine independence. Such diploid cells are apparently larger in size than haploid cells, yet have a similar nuclear/cytoplasmic ratio, and thus the nuclear size control that has been reported in Sz. pombe is also present in Sz. japonicus.","alleles_by_uniquename":{"SJAG_01081:allele-1":{"allele_type":"nonsense_mutation","description":"S427>stop","gene_uniquename":"SJAG_01081","name":"ade6-domE","uniquename":"SJAG_01081:allele-1"},"SJAG_01081:allele-2":{"allele_type":"amino_acid_mutation","description":"Q262A","gene_uniquename":"SJAG_01081","name":"ade6-domK","uniquename":"SJAG_01081:allele-2"},"SJAG_01081:allele-3":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01081","name":"ade6delta","uniquename":"SJAG_01081:allele-3"}},"annotation_curators":[{"annotation_count":3,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-23","authors":"Furuya K, Niki H","authors_abbrev":"Furuya K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-23 13:21:47","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-23 13:21:47","canto_session_key":"7c1c894d4ee8d8d3","canto_session_submitted_date":"2022-11-23 13:21:40","canto_triage_status":"Curatable","citation":"Yeast 2011 Oct;28(10):747-54","cv_annotations":{"single_locus_phenotype":[{"annotations":[115312,115313,115314],"is_not":false,"summary":null,"term":"FYPO:0000747"}]},"doi":"10.1002/yea.1898","gene_count":1,"genes_by_uniquename":{"SJAG_01081":null},"genotypes_by_uniquename":{"ade6-domE-S427>stop-nonsense_mutation-expression-not_assayed_or_wild_type":{"display_name":"ade6-domE(S427>stop)","display_uniquename":"ade6-domE-S427>stop-nonsense_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-1","expression":"Not assayed or wild type"}]}]},"ade6-domK-Q262A-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ade6-domK(Q262A aa)","display_uniquename":"ade6-domK-Q262A-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-2","expression":"Not assayed or wild type"}]}]},"ade6delta":{"display_name":"ade6delta","display_uniquename":"ade6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-3","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2011","pubmed_entrez_date":"2011-09-10","pubmed_publication_date":"Oct 2011","terms_by_termid":{"FYPO:0000747":null},"title":"Construction of diploid zygotes by interallelic complementation of ade6 in Schizosaccharomyces japonicus.","uniquename":"PMID:21905090"}


id: PMID:24375690
data:
  {"abstract":"The clade of Schizosaccharomyces includes 4 species: S. pombe, S. octosporus, S. cryophilus, and S. japonicus. Although all 4 species exhibit unicellular growth with a binary fission mode of cell division, S. japonicus alone is dimorphic yeast, which can transit from unicellular yeast to long filamentous hyphae. Recently it was found that the hyphal cells response to light and then synchronously activate cytokinesis of hyphae. In addition to hyphal growth, S. japonicas has many properties that aren't shared with other fission yeast. Mitosis of S. japonicas is referred to as semi-open mitosis because dynamics of nuclear membrane is an intermediate mode between open mitosis and closed mitosis. Novel genetic tools and the whole genomic sequencing of S. japonicas now provide us with an opportunity for revealing unique characters of the dimorphic yeast.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Niki H","authors_abbrev":"Niki H","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Yeast 2014 Mar;31(3):83-90","cv_annotations":{},"doi":"10.1002/yea.2996","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2014","pubmed_entrez_date":"2013-12-31","pubmed_publication_date":"Mar 2014","terms_by_termid":{},"title":"Schizosaccharomyces japonicus: the fission yeast is a fusion of yeast and hyphae.","uniquename":"PMID:24375690"}


id: GO_REF:0000052
data:
  {"abstract":"GO Cellular Component terms are manually assigned by curators studying high resolution confocal microscopy images of immunohistochemically stained tissue. The methodology uses antibody-based proteomics which combines high-throughput generation of affinity-purified antibodies with protein profiling in a variety of cells and tissues. Further information on the annotation methods can be found at http://www.proteinatlas.org/about/assays+annotation <br>Annotations are only exported to the GO Consortium if the localizations are supported by literature, according to the following validation grading:<br>Supportive - Subcellular localization supported by literature.<br>1) One/multiple localizations supported by literature.<br>2) Multiple localizations partly supported (at least one) by literature.<br>3) One/multiple localizations in cytoplasm (i.e. Golgi, mitochondria, ER etc) with literature supporting cytoplasmic localization. <br>Prior to February 2013, all Human Protein Atlas annotations were referenced by PMID:18029348 (Barbe et al. 2008 Mol. Cell Proteomics. 7:499-508), a paper describing the protein localization pilot study and methodology used by the Human Protein Atlas. However, it has been decided that these annotations are more correctly described by a GO reference.<br>Resource URL: http://www.proteinatlas.org <br>Protein subcellular localization images can be viewed on the Human Protein Atlas website, e.g. http://www.proteinatlas.org/ENSG00000175899/summary#ifcelline","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Human Protein Atlas","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotation based on curation of immunofluorescence data","uniquename":"GO_REF:0000052"}


id: GO_REF:0000050
data:
  {"abstract":"Transitive assignment of GO terms to a gene based on a curator's judgment of its match to a sequence model,such as a Pfam or InterPro entry, that has manually curated GO annotations, mappings to GO terms, or a description from which GO terms can be inferred. A statistical model of a sequence or group of sequences is used to make a prediction about the function of a protein or RNA. Annotations are created when a curator evaluates the results, using criteria that include excluding false positives and ensuring that the annotation is accurate for all matches. Statistical scores (such as e values and cutoff scores) and the functional specificity of the model may also be (but are not always) considered. Annotations resulting from the transfer of GO terms use the 'ISM' evidence code and include an accession for the model from which the annotation was projected in the 'with' field (column 8).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"PomBase curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Manual transfer of GO annotation data to genes by curator judgment of sequence model","uniquename":"GO_REF:0000050"}


id: GO_REF:0000036
data:
  {"abstract":"The Gene Ontology Consortium uses the IC (Inferred by Curator) evidence code when an annotation cannot be supported by any direct evidence, but can be inferred by GO annotations that have been annotated to the same gene/gene product identifier in conjunction with the curator's knowledge of biology (supporting GO annotations must not be IC-evidenced). In many cases an IC-evidenced annotation simply applies the same reference that was used in the supporting GO annotation.  The use of IC evidence code in an annotation with reference GO_REF:0000036 signifies a curator inferred the GO term based on evidence from multiple sources of evidence/GO annotations. The 'with/from' field in these annotations will therefore supply more than one GO identifier, obtained from the set of supporting GO annotations assigned to the same gene/gene product identifier which cite publicly-available references.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO Annotation working group","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Manual annotations that require more than one source of functional data to support the assignment of the associated GO term","uniquename":"GO_REF:0000036"}


id: PMID:22300943
data:
  {"abstract":"The fission yeasts (Schizosaccharomyces) representing a highly divergent phylogenetic branch of Fungi evolved from filamentous ancestors by gradual transition from mycelial growth to yeast morphology. For the transition, a mechanism had been developed that separates the sister cells after the completion of cytokinesis. Numerous components of the separation mechanism have been characterised in Schizosaccharomycespombe, including the zinc-finger transcription factor Ace2p and the fork-head transcription factor Sep1p. Here we show that both regulators have regions conserved within the genus. The most conserved parts contain the DNA-binding domains whose amino-acid sequences perfectly reflect the phylogenetic positions of the species. The less conserved parts of the proteins contain sequence blocks specific for the whole genus or only for the species propagating predominantly or exclusively as yeasts. Inactivation of either gene in the dimorphic species Schizosaccharomycesjaponicus abolished cell separation in the yeast phase conferring hypha-like morphology but did not change the growth pattern to unipolar and did not cause extensive polar vacuolation characteristic of the true mycelium. Neither mutation affected the mycelial phase, but both mutations hampered the hyphal fragmentation at the mycelium-to-yeast transition. Ace2p(Sj) acts downstream of Sep1p(Sj) and regulates the orthologues of the Ace2p-dependent S.pombe genes agn1(+) (1,3-alpha-glucanase) and eng1(+) (1,3-beta-glucanase) but does not regulate the orthologue of cfh4(+) (chitin synthase regulatory factor). These results and the complementation of the cell separation defects of the ace2(-) and sep1(-) mutations of S.pombe by heterologously expressed ace2(Sj) and sep1(Sj) indicate that the cell separation mechanism is conserved in the Schizosaccharomyces genus.","alleles_by_uniquename":{"SJAG_02252:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02252","name":"ace2delta","uniquename":"SJAG_02252:allele-1"},"SJAG_03143:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03143","name":"sep1delta","uniquename":"SJAG_03143:allele-1"}},"annotation_curators":[{"annotation_count":7,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-12-09","authors":"Balazs A, Batta G, Miklos I, Acs-Szabo L, Vazquez de Aldana CR, Sipiczki M","authors_abbrev":"Balazs A et al.","canto_added_date":"2022-12-09 17:19:01","canto_annotation_status":"APPROVED","canto_approved_date":"2022-12-09 17:39:12","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2022-12-09 17:39:12","canto_session_key":"f106e12e6366fbad","canto_session_submitted_date":"2022-12-09 17:38:34","canto_triage_status":"Curatable","citation":"Fungal Genet Biol 2012 Mar;49(3):235-49","cv_annotations":{"single_locus_phenotype":[{"annotations":[115145,115146],"is_not":false,"summary":null,"term":"FYPO:0006557"}]},"doi":"10.1016/j.fgb.2012.01.003","gene_count":2,"genes_by_uniquename":{"SJAG_02252":null,"SJAG_03143":null},"genotypes_by_uniquename":{"ace2delta":{"display_name":"ace2delta","display_uniquename":"ace2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02252:allele-1","expression":"Null"}]}]},"sep1delta":{"display_name":"sep1delta","display_uniquename":"sep1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03143:allele-1","expression":"Null"}]}]}},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-02-04","pubmed_publication_date":"Mar 2012","terms_by_termid":{"FYECO:0000137":null,"FYPO:0006557":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null},"title":"Conserved regulators of the cell separation process in Schizosaccharomyces.","uniquename":"PMID:22300943"}


id: GO_REF:0000083
data:
  {"abstract":"We have created a standard template for classes describing the morphogenesis of a plant structure as a biological process. The underlying equivalence axiom template is \"'anatomical structure morphogenesis' and 'results in morphogenesis of' some P\", where P is a plant anatomical entity (PO:0025131).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of plant morphogenesis as biological process in the Gene Ontology","uniquename":"GO_REF:0000083"}


id: PMID:5315726
data:
  {"abstract":"","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Bulder CJ","authors_abbrev":"Bulder CJ","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Antonie Van Leeuwenhoek 1971;37(3):353-8","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1971","pubmed_entrez_date":"1971-01-01","pubmed_publication_date":"1971","terms_by_termid":{},"title":"Anaerobic growth, ergosterol content and sensitivity to a polyene antibiotic, of the yeast Schizosaccharomyces japonicus.","uniquename":"PMID:5315726"}


id: PMID:28954740
data:
  {"abstract":"After mitosis, nuclear reorganization occurs together with decondensation of mitotic chromosomes and reformation of the nuclear envelope, thereby restoring the Ran-GTP gradient between the nucleus and cytoplasm. The Ran-GTP gradient is dependent on Pim1/RCC1. Interestingly, a defect in Pim1/RCC1 in  Schizosaccharomyces pombe  causes postmitotic condensation of chromatin, namely hypercondensation, suggesting a relationship between the Ran-GTP gradient and chromosome decondensation. However, how Ran-GTP interacts with chromosome decondensation is unresolved. To examine this interaction, we used  Schizosaccharomyces japonicus , which is known to undergo partial breakdown of the nuclear membrane during mitosis. We found that Pim1/RCC1 was localized on nuclear pores, but this localization failed in a temperature-sensitive mutant of Pim1/RCC1. The mutant cells exhibited hypercondensed chromatin after mitosis due to prolonged association of condensin on the chromosomes. Conceivably, a condensin-dephosphorylation defect might cause hypercondensed chromatin, since chromosomal localization of condensin is dependent on phosphorylation by cyclin-dependent kinase (CDK). Indeed, CDK-phospho-mimic mutation of condensin alone caused untimely condensin localization, resulting in hypercondensed chromatin. Together, these results suggest that dephosphorylation of CDK sites of condensin might require the Ran-GTP gradient produced by nuclear pore-localized Pim1/RCC1.","alleles_by_uniquename":{"SJAG_00871:allele-1":{"allele_type":"amino_acid_mutation","description":"cut3-T19E","gene_uniquename":"SJAG_00871","name":"cut3-T19E","uniquename":"SJAG_00871:allele-1"},"SJAG_04284:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04284","name":"nup61delta","uniquename":"SJAG_04284:allele-1"},"SJAG_04464:allele-1":{"allele_type":"amino_acid_mutation","description":"R152C","gene_uniquename":"SJAG_04464","name":"pim1-R152C","synonyms":[{"name":"Inferred CDK-phospho-mimic mutation","reference":"PMID:28954740","type":"exact"}],"uniquename":"SJAG_04464:allele-1"}},"annotation_curators":[{"annotation_count":12,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-23","authors":"Aoki K, Niki H","authors_abbrev":"Aoki K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-23 15:00:26","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-23 15:00:26","canto_session_key":"7c26b8235c98c3eb","canto_session_submitted_date":"2022-11-23 15:00:18","canto_triage_status":"Curatable","citation":"Biol Open 2017 Nov 15;6(11):1614-1628","cv_annotations":{"biological_process":[{"annotations":[115418],"is_not":false,"summary":null,"term":"GO:0101024"},{"annotations":[115423],"is_not":false,"summary":null,"term":"GO:0006998"}],"cellular_component":[{"annotations":[115422],"is_not":false,"summary":null,"term":"GO:0120321"}],"multi_locus_phenotype":[{"annotations":[115425],"is_not":false,"summary":null,"term":"FYPO:0000619"},{"annotations":[115424],"is_not":false,"summary":null,"term":"FYPO:0001489"}],"single_locus_phenotype":[{"annotations":[115426],"is_not":false,"summary":null,"term":"FYPO:0000619"},{"annotations":[115420],"is_not":false,"summary":null,"term":"FYPO:0003738"},{"annotations":[115427],"is_not":false,"summary":null,"term":"FYPO:0000815"},{"annotations":[115419],"is_not":false,"summary":null,"term":"FYPO:0000082"},{"annotations":[115421],"is_not":false,"summary":null,"term":"FYPO:0003976"},{"annotations":[115417],"is_not":false,"summary":null,"term":"FYPO:0001387"}]},"doi":"10.1242/bio.027193","gene_count":4,"genes_by_uniquename":{"SJAG_00471":null,"SJAG_00871":null,"SJAG_04284":null,"SJAG_04464":null},"genotypes_by_uniquename":{"cut3-T19E-cut3-T19E-amino_acid_mutation-expression-not_assayed_or_wild_type__pim1-R152C-R152C-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cut3-T19E(aa) pim1-R152C(aa)","display_uniquename":"cut3-T19E-cut3-T19E-amino_acid_mutation-expression-not_assayed_or_wild_type__pim1-R152C-R152C-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00871:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04464:allele-1","expression":"Not assayed or wild type"}]}]},"nup61delta":{"display_name":"nup61delta","display_uniquename":"nup61delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04284:allele-1","expression":"Null"}]}]},"pim1-R152C-R152C-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"pim1-R152C(aa)","display_uniquename":"pim1-R152C-R152C-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04464:allele-1","expression":"Not assayed or wild type"}]}]}},"ltp_gene_count":4,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[{"evidence":"Affinity Capture-Western","gene_uniquename":"SJAG_04464","interactor_uniquename":"SJAG_00471","reference_uniquename":"PMID:28954740","throughput":"low"}],"publication_year":"2017","pubmed_entrez_date":"2017-09-29","pubmed_publication_date":"15 Nov 2017","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000005":null,"FYECO:0000137":null,"FYPO:0000082":null,"FYPO:0000619":null,"FYPO:0000815":null,"FYPO:0001387":null,"FYPO:0001489":null,"FYPO:0003738":null,"FYPO:0003976":null,"FYPO_EXT:0000001":null,"GO:0006998":null,"GO:0101024":null,"GO:0120321":null},"title":"Release of condensin from mitotic chromosomes requires the Ran-GTP gradient in the reorganized nucleus.","uniquename":"PMID:28954740"}


id: PMID:20737410
data:
  {"abstract":"Schizosaccharomyces japonicus is a fission yeast for which new genetic tools have recently been developed. Here, we report novel plasmid vectors with high transformation efficiency and an electroporation method for Sz. japonicus. We isolated 44 replicating segments from 12 166 transformants of Sz. japonicus genomic fragments and found a chromosomal fragment, RS1, as a new replicating sequence that conferred high transformation activity to Sz. japonicus cells. This sequence was cloned into a pUC19 vector with ura4(+) of Sz. pombe (pSJU11) or the kan gene on the kanMX6 module (pSJK11) as selection markers. These plasmids transformed Sz. japonicus cells in the early-log phase by electroporation at a frequency of 123 cfu/µg for pSJK11 and 301 cfu/µg for pSJU11, which were higher than previously reported autonomously replicating sequences. Although a portion of plasmids remained in host cells by integration into the chromosome via RS1 segment, the plasmids could be recovered from transformants. The plasmid copy number was estimated to be 1.88 copies per cell by Southern blot analysis using a Sz. pombe ura4(+) probe. The plasmid containing ade6(+) suppressed the auxotrophic growth of the ade6-domE mutant, indicating that the plasmid would be useful for suppressor screening and complementation assays in Sz. japonicus. Furthermore, pSJU11 transformed Sz. pombe cells with the same frequency as the pREP2 plasmid. This study is a report to demonstrate practical use of episomal plasmid vectors for genetic research in Sz. japonicus.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Aoki K, Nakajima R, Furuya K, Niki H","authors_abbrev":"Aoki K et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Yeast 2010 Dec;27(12):1049-60","cv_annotations":{},"doi":"10.1002/yea.1815","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2010","pubmed_entrez_date":"2010-08-26","pubmed_publication_date":"Dec 2010","terms_by_termid":{},"title":"Novel episomal vectors and a highly efficient transformation procedure for the fission yeast Schizosaccharomyces japonicus.","uniquename":"PMID:20737410"}


id: PMID:8590481
data:
  {"abstract":"Fission yeasts form a small but heterogeneous group of ascomycetes and it is still unclear whether they should be subdivided into three genera (Schizosaccharomyces, Octosporomyces, Hasegawaea) or remain a single genus (Schizosaccharomyces). In order to decide whether a new genus Hasegawaea should be established for the species Schizosaccharomyces japonicus and Schizosaccharomyces versatilis, we have characterized the entire rDNA cluster in Schizosaccharomyces japonicus var. versatilis and compared it with the homologous region from Schizosaccharomyces pombe and with complete rRNA gene sequences from other yeast genera. From a phage genomic library a recombinant lambda phage containing the entire rDNA repeat unit was isolated. In this paper we report the primary sequence of the 18s, 5.8s and 25s rRNA coding regions. The S. japonicus var. versatilis rRNA genes are 1823 (18s), 158 (5.8s) and 3422 (25s) nucleotides long. The two sequences of the larger rRNA genes exhibit 95.7% (18s) and 93% (25s) similarity with the homologous genes from S. pombe. The differences between the rRNA genes of S. japonicus and S. pombe, however, are much smaller than the intrageneric differences within the rDNA sequences of other yeast genera. Therefore, subdivision of fission yeasts into the genera Schizosaccharomyces and Hasegawaea does not to seem to be justified.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Naehring J, Kiefer S, Wolf K","authors_abbrev":"Naehring J et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Curr Genet 1995 Sep;28(4):353-9","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1995","pubmed_entrez_date":"1995-09-01","pubmed_publication_date":"Sep 1995","terms_by_termid":{},"title":"Nucleotide sequence of the Schizosaccharomyces japonicus var. versatilis ribosomal RNA gene cluster and its phylogenetic implications.","uniquename":"PMID:8590481"}


id: GO_REF:0000073
data:
  {"abstract":"We have created a standard template for classes describing the import of a chemical entity (ChEBI) as a biological process. The underlying equivalence axiom template is \"GO:0006810 and 'imports' some X\", where X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of import of a chemical as biological process in the Gene Ontology","uniquename":"GO_REF:0000073"}


id: GO_REF:0000015
data:
  {"abstract":"Direct annotations to any of the three root terms 'molecular function; GO:0003674', 'biological process; GO:0008150' or 'cellular component; GO:0005575' indicate that curators have found no data supporting an annotation to a more specific term, either in the literature and/or by sequence similarity for this gene or protein as of the date of the annotation.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO Curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Use of the ND evidence code for Gene Ontology (GO) terms.","uniquename":"GO_REF:0000015"}


id: PMID:29566183
data:
  {"abstract":"Dimorphic yeasts transform into filamentous cells or hyphae in response to environmental cues. The mechanisms for the hyphal transition of dimorphic yeasts have mainly been studied in Candida albicans, an opportunistic human fungal pathogen. The Ras1-MAPK pathway is a major signal transduction pathway for hyphal transition in C. albicans. Recently, the non-pathogenic dimorphic yeast Schizosaccharomyces japonicus has also been used for genetic analyses of hyphal induction. We confirmed that Ras1-MAPK and other MAPK pathways exist in Sz. japonicus. To examine how hyphal transition is induced by environmental stress-triggered signal transduction, we studied the hyphal transition of deletion mutants of MAPK pathways in Sz. japonicus. We found that the MAPK pathways are not involved in hyphal induction, although the mating response is dependent on these pathways. However, only Ras1 deletion caused a severe defect in hyphal development via both DNA damage and environmental stressors. In fact, genes on the Cdc42 branch of the Ras1 (Ras1-Cdc42) pathway, efc25Sj, scd1Sj and scd2Sj, are required for hyphal development. Cell morphology analysis indicated that the apical growth of hyphal cells was inhibited in Ras1-Cdc42-pathway deletion mutants. Thus, the control of cell polarity by the Ras1-Cdc42 pathway is crucial for hyphal development.","alleles_by_uniquename":{"SJAG_00514:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00514","name":"scd1delta","uniquename":"SJAG_00514:allele-1"},"SJAG_00993:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00993","name":"byr1delta","uniquename":"SJAG_00993:allele-1"},"SJAG_01181:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01181","name":"pek1delta","uniquename":"SJAG_01181:allele-1"},"SJAG_01718:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01718","name":"byr2delta","uniquename":"SJAG_01718:allele-1"},"SJAG_01794:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01794","name":"scd2delta","uniquename":"SJAG_01794:allele-1"},"SJAG_02342:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02342","name":"wis1delta","uniquename":"SJAG_02342:allele-1"},"SJAG_02379:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02379","name":"gap1delta","uniquename":"SJAG_02379:allele-1"},"SJAG_02486:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02486","name":"ste6delta","uniquename":"SJAG_02486:allele-1"},"SJAG_02592:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02592","name":"sty1delta","uniquename":"SJAG_02592:allele-1"},"SJAG_02819:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02819","name":"efc25delta","uniquename":"SJAG_02819:allele-1"},"SJAG_02923:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02923","name":"spk1delta","uniquename":"SJAG_02923:allele-1"},"SJAG_03384:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03384","name":"wis4delta","uniquename":"SJAG_03384:allele-1"},"SJAG_03453:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03453","name":"ras1delta","uniquename":"SJAG_03453:allele-1"},"SJAG_03753:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03753","name":"mkh1delta","uniquename":"SJAG_03753:allele-1"},"SJAG_04009:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04009","name":"ste11delta","uniquename":"SJAG_04009:allele-1"},"SJAG_04551:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04551","name":"pmk1delta","uniquename":"SJAG_04551:allele-1"},"SJAG_04777:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04777","name":"win1delta","uniquename":"SJAG_04777:allele-1"}},"annotation_curators":[{"annotation_count":38,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-18","authors":"Nozaki S, Furuya K, Niki H","authors_abbrev":"Nozaki S et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-18 13:44:52","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-18 13:44:52","canto_session_key":"18862c3d67da0cb0","canto_session_submitted_date":"2022-11-18 13:44:26","canto_triage_status":"Curatable","citation":"FEMS Yeast Res 2018 06 01;18(4)","cv_annotations":{"single_locus_phenotype":[{"annotations":[115516],"is_not":false,"summary":null,"term":"FYPO:0007773"},{"annotations":[115499,115500,115509,115531,115532],"is_not":false,"summary":null,"term":"FYPO:0007789"},{"annotations":[115528],"is_not":false,"summary":null,"term":"FYPO:0000584"},{"annotations":[115498,115502,115506],"is_not":false,"summary":null,"term":"FYPO:0001355"},{"annotations":[115530],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115497,115503,115504,115508,115511,115513,115514,115527,115529],"is_not":false,"summary":null,"term":"FYPO:0000280"},{"annotations":[115505,115510,115512,115515,115517,115518,115519,115520,115521,115522,115523,115524,115525,115526],"is_not":false,"summary":null,"term":"FYPO:0000124"},{"annotations":[115496,115501,115507,115533],"is_not":false,"summary":null,"term":"FYPO:0002380"}]},"doi":"10.1093/femsyr/foy031","gene_count":17,"genes_by_uniquename":{"SJAG_00514":null,"SJAG_00993":null,"SJAG_01181":null,"SJAG_01718":null,"SJAG_01794":null,"SJAG_02342":null,"SJAG_02379":null,"SJAG_02486":null,"SJAG_02592":null,"SJAG_02819":null,"SJAG_02923":null,"SJAG_03384":null,"SJAG_03453":null,"SJAG_03753":null,"SJAG_04009":null,"SJAG_04551":null,"SJAG_04777":null},"genotypes_by_uniquename":{"byr1delta":{"display_name":"byr1delta","display_uniquename":"byr1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00993:allele-1","expression":"Null"}]}]},"byr2delta":{"display_name":"byr2delta","display_uniquename":"byr2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01718:allele-1","expression":"Null"}]}]},"efc25delta":{"display_name":"efc25delta","display_uniquename":"efc25delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02819:allele-1","expression":"Null"}]}]},"gap1delta":{"display_name":"gap1delta","display_uniquename":"gap1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02379:allele-1","expression":"Null"}]}]},"mkh1delta":{"display_name":"mkh1delta","display_uniquename":"mkh1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03753:allele-1","expression":"Null"}]}]},"pek1delta":{"display_name":"pek1delta","display_uniquename":"pek1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01181:allele-1","expression":"Null"}]}]},"pmk1delta":{"display_name":"pmk1delta","display_uniquename":"pmk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04551:allele-1","expression":"Null"}]}]},"ras1delta":{"display_name":"ras1delta","display_uniquename":"ras1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03453:allele-1","expression":"Null"}]}]},"scd1delta":{"display_name":"scd1delta","display_uniquename":"scd1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00514:allele-1","expression":"Null"}]}]},"scd2delta":{"display_name":"scd2delta","display_uniquename":"scd2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01794:allele-1","expression":"Null"}]}]},"spk1delta":{"display_name":"spk1delta","display_uniquename":"spk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02923:allele-1","expression":"Null"}]}]},"ste11delta":{"display_name":"ste11delta","display_uniquename":"ste11delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04009:allele-1","expression":"Null"}]}]},"ste6delta":{"display_name":"ste6delta","display_uniquename":"ste6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02486:allele-1","expression":"Null"}]}]},"sty1delta":{"display_name":"sty1delta","display_uniquename":"sty1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02592:allele-1","expression":"Null"}]}]},"win1delta":{"display_name":"win1delta","display_uniquename":"win1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04777:allele-1","expression":"Null"}]}]},"wis1delta":{"display_name":"wis1delta","display_uniquename":"wis1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02342:allele-1","expression":"Null"}]}]},"wis4delta":{"display_name":"wis4delta","display_uniquename":"wis4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03384:allele-1","expression":"Null"}]}]}},"ltp_gene_count":17,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2018","pubmed_entrez_date":"2018-03-23","pubmed_publication_date":"01 06 2018","terms_by_termid":{"FYECO:0000137":null,"FYPO:0000124":null,"FYPO:0000280":null,"FYPO:0000584":null,"FYPO:0001355":null,"FYPO:0002380":null,"FYPO:0007773":null,"FYPO:0007789":null,"FYPO:0007790":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null},"title":"The Ras1-Cdc42 pathway is involved in hyphal development of Schizosaccharomyces japonicus.","uniquename":"PMID:29566183"}


id: PMID:28733403
data:
  {"abstract":"This protocol describes the use of electroporation to transform  Schizosaccharomyces japonicus  with plasmids or linear DNA. Plasmids are helpful for the complementation testing of mutations and for the expression of specific genes. Linear DNA fragments integrated into chromosomal DNA by homologous recombination are useful for gene deletion or to fuse a gene with a tag sequence (e.g., encoding a fluorescent protein). To introduce DNA into  S. japonicus , electroporation methods are recommended because  S. japonicus  is sensitive to lithium acetate (LiOAc).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Aoki K, Niki H","authors_abbrev":"Aoki K et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Cold Spring Harb Protoc 2017 Dec 01;2017(12):pdb.prot091850","cv_annotations":{},"doi":"10.1101/pdb.prot091850","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2017","pubmed_entrez_date":"2017-07-23","pubmed_publication_date":"01 Dec 2017","terms_by_termid":{},"title":"Transformation of  Schizosaccharomyces japonicus .","uniquename":"PMID:28733403"}


id: PMID:26104357
data:
  {"abstract":"Cells of the highly diverged Schizosaccharomyces (S.) pombe and S. japonicus fission yeasts exist in one of two sex/mating types, called P (for plus) or M (for minus), specified by which allele, M or P, resides at mat1. The fission yeasts have evolved an elegant mechanism for switching P or M information at mat1 by a programmed DNA recombination event with a copy of one of the two silent mating-type genes residing nearby in the genome. The switching process is highly cell-cycle and generation dependent such that only one of four grandchildren of a cell switches mating type. Extensive studies of fission yeast established the natural DNA strand chirality at the mat1 locus as the primary basis of asymmetric cell division. The asymmetry results from a unique site- and strand-specific epigenetic \"imprint\" at mat1 installed in one of the two chromatids during DNA replication. The imprint is inherited by one daughter cell, maintained for one cell cycle, and is then used for initiating recombination during mat1 replication in the following cell cycle. This mechanism of cell-type switching is considered to be unique to these two organisms, but determining the operation of such a mechanism in other organisms has not been possible for technical reasons. This review summarizes recent exciting developments in the understanding of mating-type switching in fission yeasts and extends these observations to suggest how such a DNA strand-based epigenetic mechanism of cellular differentiation could also operate in diploid organisms. ","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Klar AJS, Ishikawa K, Moore S","authors_abbrev":"Klar AJS et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Microbiol Spectr 2014 Oct;2(5)","cv_annotations":{},"doi":"10.1128/microbiolspec.MDNA3-0003-2014","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2014","pubmed_entrez_date":"2015-06-25","pubmed_publication_date":"Oct 2014","terms_by_termid":{},"title":"A Unique DNA Recombination Mechanism of the Mating/Cell-type Switching of Fission Yeasts: a Review.","uniquename":"PMID:26104357"}


id: GO_REF:0000080
data:
  {"abstract":"We have created a standard template for classes describing the development of a plant structure as a biological process. The underlying equivalence axiom template is \"'anatomical structure development' and 'results in development of' some P\", where P is a plant anatomical entity (PO:0025131).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of plant development as biological process in the Gene Ontology","uniquename":"GO_REF:0000080"}


id: PMID:33495454
data:
  {"abstract":"The endoplasmic reticulum (ER) network consists of tubules with high membrane curvature in cross-section, generated by the reticulons and REEPs. These proteins have two pairs of trans-membrane (TM) segments, followed by an amphipathic helix (APH), but how they induce curvature is poorly understood. Here, we show that REEPs form homodimers by interaction within the membrane. When overexpressed or reconstituted at high concentrations with phospholipids, REEPs cause extreme curvature through their TMs, generating lipoprotein particles instead of vesicles. The APH facilitates curvature generation, as its mutation prevents ER network formation of reconstituted proteoliposomes, and synthetic L- or D-amino acid peptides abolish ER network formation in Xenopus egg extracts. In Schizosaccharomyces japonicus, the APH is required for reticulon's exclusive ER-tubule localization and restricted mobility. Thus, the TMs and APH cooperate to generate high membrane curvature. We propose that the formation of splayed REEP/reticulon dimers is responsible for ER tubule formation.","alleles_by_uniquename":{"SJAG_01374:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01374","name":"nup132delta","uniquename":"SJAG_01374:allele-1"}},"annotation_curators":[{"annotation_count":8,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-09","authors":"Wang N, Clark LD, Gao Y, Kozlov MM, Shemesh T, Rapoport TA","authors_abbrev":"Wang N et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-09 16:24:24","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 16:24:24","canto_session_key":"23c6ae79d435aba5","canto_session_submitted_date":"2021-07-09 16:24:16","canto_triage_status":"Curatable","citation":"Nat Commun 2021 01 25;12(1):568","cv_annotations":{"biological_process":[{"annotations":[115570,115576],"is_not":false,"summary":null,"term":"GO:0097753"}],"cellular_component":[{"annotations":[115571,115572],"is_not":false,"summary":null,"term":"GO:0032541"},{"annotations":[115573,115574],"is_not":false,"summary":null,"term":"GO:0005643"}],"single_locus_phenotype":[{"annotations":[115575],"is_not":false,"summary":null,"term":"FYPO:0003973"}]},"doi":"10.1038/s41467-020-20625-y","gene_count":4,"genes_by_uniquename":{"SJAG_01374":null,"SJAG_01834":null,"SJAG_01848":null,"SJAG_03795":null},"genotypes_by_uniquename":{"nup132delta":{"display_name":"nup132delta","display_uniquename":"nup132delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01374:allele-1","expression":"Null"}]}]}},"ltp_gene_count":4,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_03795","interactor_uniquename":"SJAG_03795","reference_uniquename":"PMID:33495454","throughput":"low"}],"publication_year":"2021","pubmed_entrez_date":"2021-01-26","pubmed_publication_date":"25 01 2021","terms_by_termid":{"FYPO:0003973":null,"GO:0005643":null,"GO:0032541":null,"GO:0097753":null},"title":"Mechanism of membrane-curvature generation by ER-tubule shaping proteins.","uniquename":"PMID:33495454"}


id: GO_REF:0000081
data:
  {"abstract":"We have created a standard template for classes describing the formation of a plant structure as a biological process. The underlying equivalence axiom template is \"'anatomical structure formation involved in morphogenesis' and 'results in formation of' some P\", where P is a plant anatomical entity (PO:0025131).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of plant formation as biological process in the Gene Ontology","uniquename":"GO_REF:0000081"}


id: PMID:32915139
data:
  {"abstract":"Cytokinesis, which enables the physical separation of daughter cells once mitosis has been completed, is executed in fungal and animal cells by a contractile actin- and myosin-based ring (CAR). In the fission yeast  Schizosaccharomyces pombe,  the formin For3 nucleates actin cables and also co-operates for CAR assembly during cytokinesis. Mitogen-activated protein kinases (MAPKs) regulate essential adaptive responses in eukaryotic organisms to environmental changes. We show that the stress-activated protein kinase pathway (SAPK) and its effector, MAPK Sty1, downregulates CAR assembly in  S. pombe  when its integrity becomes compromised during cytoskeletal damage and stress by reducing For3 levels. Accurate control of For3 levels by the SAPK pathway may thus represent a novel regulatory mechanism of cytokinesis outcome in response to environmental cues. Conversely, SAPK signaling favors CAR assembly and integrity in its close relative  Schizosaccharomyces japonicus,  revealing a remarkable evolutionary divergence of this response within the fission yeast clade.","alleles_by_uniquename":{"SJAG_00266:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00266","name":"atf1delta","uniquename":"SJAG_00266:allele-1"},"SJAG_02592:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02592","name":"sty1delta","uniquename":"SJAG_02592:allele-1"}},"annotation_curators":[{"annotation_count":5,"community_curator":true,"file_name":null,"file_type":null,"name":"Elisa Gómez Gil","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-05-13","authors":"Gómez-Gil E, Martín-García R, Vicente-Soler J, Franco A, Vázquez-Marín B, Prieto-Ruiz F, Soto T, Pérez P, Madrid M, Cansado J","authors_abbrev":"Gómez-Gil E et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2023-06-24 05:18:12","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Elisa Gómez Gil","canto_curator_role":"community","canto_first_approved_date":"2021-05-13 16:19:42","canto_session_key":"382ba25ae62a1134","canto_session_submitted_date":"2021-05-13 14:28:51","canto_triage_status":"Curatable","citation":"Elife 2020 09 11;9","cv_annotations":{"PSI-MOD":[{"annotations":[115608],"is_not":false,"summary":null,"term":"MOD:00696"}],"biological_process":[{"annotations":[115609],"is_not":false,"summary":null,"term":"GO:1903499"}],"single_locus_phenotype":[{"annotations":[115607],"is_not":false,"summary":null,"term":"FYPO:0002998"},{"annotations":[115605,115606],"is_not":false,"summary":null,"term":"FYPO:0000107"}]},"doi":"10.7554/eLife.57951","gene_count":2,"genes_by_uniquename":{"SJAG_00266":null,"SJAG_02592":null},"genotypes_by_uniquename":{"atf1delta":{"display_name":"atf1delta","display_uniquename":"atf1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00266:allele-1","expression":"Null"}]}]},"sty1delta":{"display_name":"sty1delta","display_uniquename":"sty1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02592:allele-1","expression":"Null"}]}]}},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2020","pubmed_entrez_date":"2020-09-11","pubmed_publication_date":"11 09 2020","terms_by_termid":{"FYECO:0000137":null,"FYECO:0000248":null,"FYPO:0000107":null,"FYPO:0002998":null,"FYPO_EXT:0000001":null,"GO:0120306":null,"GO:1903499":null,"MOD:00696":null},"title":"Stress-activated MAPK signaling controls fission yeast actomyosin ring integrity by modulating formin For3 levels.","uniquename":"PMID:32915139"}


id: GO_REF:0000085
data:
  {"abstract":"We have created a standard template for classes describing the apoptotic process for a cell type as a biological process. The underlying equivalence axiom template is \"'apoptotic process' and 'occurs in' some C\", where C is a native cell (CL:0000003).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of cell apoptotic process as biological process in the Gene Ontology","uniquename":"GO_REF:0000085"}


id: PMID:28733401
data:
  {"abstract":"Haploid yeast cells mate to form heterozygotes and subsequently undergo meiosis to form spores. This process can be used to produce gene combinations and variants that are useful for genetic analysis. For example, these spores can be used to generate double mutants or to measure genetic distances in a mutational analysis. Here, we describe mating and spore dissection procedures for  Schizosaccharomyces japonicus  cells. Although the overall procedures resemble those used in  Schizosaccharomyces pombe , some differences exist, including the use of EMM2 medium without nitrogen (EMM-N) for mating and the shorter incubation time of 16-20 h for  S. japonicus  cells. Furthermore, the  S. japonicus  zygotes produce eight spores and thus require an \"octad\" analysis.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Furuya K, Niki H","authors_abbrev":"Furuya K et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Cold Spring Harb Protoc 2017 Dec 01;2017(12):pdb.prot091843","cv_annotations":{},"doi":"10.1101/pdb.prot091843","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2017","pubmed_entrez_date":"2017-07-23","pubmed_publication_date":"01 Dec 2017","terms_by_termid":{},"title":"Mating, Spore Dissection, and Selection of Diploid Cells in  Schizosaccharomyces japonicus .","uniquename":"PMID:28733401"}


id: PMID:11504450
data:
  {"abstract":"We compared the effects of four quaternary benzo[c]phenanthridine alkaloids--chelerythrine, chelilutine, sanguinarine, and sanguilutine--and two quaternary protoberberine alkaloids-berberine and coptisine--on the human cell line HeLa (cervix carcinoma cells) and the yeasts Saccharomyces cerevisiae and Schizosaccharomyces japonicus var. versatilis. The ability of alkaloids to display primary fluorescence, allowed us to record their dynamics and localization in cells. Cytotoxic, anti-microtubular, and anti-actin effects in living cells were studied. In the yeasts, neither microtubules nor cell growth was seriously affected even at the alkaloid concentration of 100 microg/ml. The HeLa cells, however, responded to the toxic effect of alkaloids at concentrations ranging from 1 to 50 microg/ml. IC50 values for individual alkaloids were: sanguinarine IC50 = 0.8 microg/ml, sanguilutine IC50 = 8.3 microg/ml, chelerythrine IC50 = 6.2 microg/ml, chelilutine IC50 = 5.2 microg/ml, coptisine IC50 = 2.6 microg/ml and berberine IC50 > 10.0 microg/ml. In living cells, sanguinarine produced a decrease in microtubule numbers, particularly at the cell periphery, at a concentration of 0.1 microg/ml. The other alkaloids showed a similar effect but at higher concentrations (5-50 microg/ml). The strongest effects of sanguinarine were explained as a consequence of its easy penetration through the cell membrane owing to nonpolar pseudobase formation and to a high degree of molecular planarity.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Slaninová I, Táborská E, Bochoráková H, Slanina J","authors_abbrev":"Slaninová I et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Cell Biol Toxicol 2001;17(1):51-63","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2001","pubmed_entrez_date":"2001-08-16","pubmed_publication_date":"2001","terms_by_termid":{},"title":"Interaction of benzo[c]phenanthridine and protoberberine alkaloids with animal and yeast cells.","uniquename":"PMID:11504450"}


id: PMID:1934083
data:
  {"abstract":"By rhodamine-phalloidin fluorescence, distinct continuous F-actin rings were visualized in 18-20% of the protoplasts of Schizosaccharomyces pombe and S. japonicus var. versatilis, in addition to randomly distributed F-actin dots. Whereas the reversion of ring-lacking protoplasts coincided with the polarization of the dotted F-actin pattern, the ring-containing protoplasts became furrowed as the F-actin rings constricted. The furrowing was more conspicuous in S. japonicus var. versatilis than in S. pombe protoplasts and it was blocked when the reversion was inhibited by Novozyme 234 indicating that the cell wall formation is essential for the F-actin ring constriction.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Jochová J, Rupes I, Streiblová E","authors_abbrev":"Jochová J et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Cell Biol Int Rep 1991 Jul;15(7):607-10","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1991","pubmed_entrez_date":"1991-07-01","pubmed_publication_date":"Jul 1991","terms_by_termid":{},"title":"F-actin contractile rings in protoplasts of the yeast Schizosaccharomyces.","uniquename":"PMID:1934083"}


id: PMID:26774782
data:
  {"abstract":"Eukaryotes remodel the nucleus during mitosis using a variety of mechanisms that differ in the timing and the extent of nuclear envelope (NE) breakdown. Here, we probe the principles enabling this functional diversity by exploiting the natural divergence in NE management strategies between the related fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus [1-3]. We show that inactivation of Ned1, the phosphatidic acid phosphatase of the lipin family, by CDK phosphorylation is both necessary and sufficient to promote NE expansion required for \"closed\" mitosis in S. pombe. In contrast, Ned1 is not regulated during division in S. japonicus, thus limiting membrane availability and necessitating NE breakage. Interspecies gene swaps result in phenotypically normal divisions with the S. japonicus lipin acquiring an S. pombe-like mitotic phosphorylation pattern. Our results provide experimental evidence for the mitotic regulation of phosphatidic acid flux and suggest that the regulatory networks governing lipin activity diverged in evolution to give rise to strikingly dissimilar mitotic programs. ","alleles_by_uniquename":{"SJAG_01906:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01906","name":"nem1delta","uniquename":"SJAG_01906:allele-1"},"SJAG_02763:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02763","name":"ned1delta","uniquename":"SJAG_02763:allele-1"},"SJAG_02763:allele-2":{"allele_type":"amino_acid_mutation","description":"D422E,D424E","gene_uniquename":"SJAG_02763","name":"ned1cat","synonyms":[{"name":"Catalytic mutant","reference":"PMID:26774782","type":"exact"}],"uniquename":"SJAG_02763:allele-2"},"SJAG_02763:allele-3":{"allele_type":"amino_acid_mutation","description":"S235A; S651","gene_uniquename":"SJAG_02763","name":"ned1S235A/S651","synonyms":[{"name":"refractory to phosphorylation","reference":"PMID:26774782","type":"exact"}],"uniquename":"SJAG_02763:allele-3"},"SJAG_02763:allele-4":{"allele_type":"amino_acid_mutation","description":"S235E; S651E","gene_uniquename":"SJAG_02763","name":"ned1S235E/S651E","synonyms":[{"name":"phosphomimetic","reference":"PMID:26774782","type":"exact"}],"uniquename":"SJAG_02763:allele-4"},"SJAG_02763:allele-5":{"allele_type":"amino_acid_mutation","description":"S499E; S538E; T620E; T638E; S651E","gene_uniquename":"SJAG_02763","name":"ned1-5E","uniquename":"SJAG_02763:allele-5"},"SJAG_02763:allele-6":{"allele_type":"amino_acid_mutation","description":"S499A; S538A; T620A; T638A; S651A","gene_uniquename":"SJAG_02763","name":"ned1-5A","synonyms":[{"name":"refractory to potential proline-directed kinase phosphorylation","reference":"PMID:26774782","type":"exact"}],"uniquename":"SJAG_02763:allele-6"},"SJAG_03940:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03940","name":"nem2delta","uniquename":"SJAG_03940:allele-1"}},"annotation_curators":[{"annotation_count":21,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"},{"annotation_count":3,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-07","authors":"Makarova M, Gu Y, Chen JS, Beckley JR, Gould KL, Oliferenko S","authors_abbrev":"Makarova M et al.","canto_added_date":"2021-05-10 02:37:43","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-01 07:39:35","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-07 15:21:04","canto_session_key":"aa811803aa1555a2","canto_session_submitted_date":"2021-07-09 07:42:46","canto_triage_status":"Curatable","citation":"Curr Biol 2016 Jan 25;26(2):237-243","cv_annotations":{"PSI-MOD":[{"annotations":[115126,115127],"is_not":false,"summary":null,"term":"MOD:00046"}],"biological_process":[{"annotations":[115138],"is_not":false,"summary":null,"term":"GO:0090158"},{"annotations":[115140],"is_not":false,"summary":null,"term":"GO:0019915"},{"annotations":[115139],"is_not":false,"summary":null,"term":"GO:0071763"}],"cellular_component":[{"annotations":[115123],"is_not":false,"summary":null,"term":"GO:0005654"}],"single_locus_phenotype":[{"annotations":[115132,115135],"is_not":false,"summary":null,"term":"FYPO:0006054"},{"annotations":[115137],"is_not":false,"summary":null,"term":"FYPO:0005957"},{"annotations":[115119,115120,115122,115131,115134],"is_not":false,"summary":null,"term":"FYPO:0001784"},{"annotations":[115117,115118,115121,115125,115130,115133],"is_not":false,"summary":null,"term":"FYPO:0001556"},{"annotations":[115129,115136],"is_not":false,"summary":null,"term":"FYPO:0006945"},{"annotations":[115128],"is_not":false,"summary":null,"term":"FYPO:0003751"},{"annotations":[115124],"is_not":false,"summary":null,"term":"FYPO:0001234"}]},"doi":"10.1016/j.cub.2015.11.061","gene_count":4,"genes_by_uniquename":{"SJAG_00088":null,"SJAG_01906":null,"SJAG_02763":null,"SJAG_03940":null},"genotypes_by_uniquename":{"ned1-5A-S499A__S538A__T620A__T638A__S651A-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1-5A(S499A; S538A; T620A; T638A; S651A aa)","display_uniquename":"ned1-5A-S499A__S538A__T620A__T638A__S651A-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-6","expression":"Not assayed or wild type"}]}]},"ned1-5E-S499E__S538E__T620E__T638E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1-5E(S499E; S538E; T620E; T638E; S651E aa)","display_uniquename":"ned1-5E-S499E__S538E__T620E__T638E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-5","expression":"Not assayed or wild type"}]}]},"ned1S235A_S651-S235A__S651-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1S235A/S651(S235A; S651 aa)","display_uniquename":"ned1S235A_S651-S235A__S651-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-3","expression":"Not assayed or wild type"}]}]},"ned1S235E_S651E-S235E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1S235E/S651E(S235E; S651E aa)","display_uniquename":"ned1S235E_S651E-S235E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-4","expression":"Not assayed or wild type"}]}]},"ned1cat-D422E,D424E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1cat(D422E,D424E aa)","display_uniquename":"ned1cat-D422E,D424E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-2","expression":"Not assayed or wild type"}]}]},"ned1delta":{"display_name":"ned1delta","display_uniquename":"ned1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-1","expression":"Null"}]}]},"nem1delta":{"display_name":"nem1delta","display_uniquename":"nem1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01906:allele-1","expression":"Null"}]}]},"nem2delta":{"display_name":"nem2delta","display_uniquename":"nem2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03940:allele-1","expression":"Null"}]}]}},"ltp_gene_count":4,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2016","pubmed_entrez_date":"2016-01-18","pubmed_publication_date":"25 Jan 2016","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000162":null,"FYPO:0001234":null,"FYPO:0001556":null,"FYPO:0001784":null,"FYPO:0003751":null,"FYPO:0005957":null,"FYPO:0006054":null,"FYPO:0006945":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"GO:0005654":null,"GO:0019915":null,"GO:0071763":null,"GO:0090158":null,"MOD:00046":null},"title":"Temporal Regulation of Lipin Activity Diverged to Account for Differences in Mitotic Programs.","uniquename":"PMID:26774782"}


