# refs

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: 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":[66956],"is_not":false,"summary":null,"term":"GO:0009088"}],"molecular_function":[{"annotations":[68362],"is_not":false,"summary":null,"term":"GO:0004812"},{"annotations":[57460],"is_not":false,"summary":null,"term":"GO:0005524"},{"annotations":[66315],"is_not":false,"summary":null,"term":"GO:0008061"},{"annotations":[57911,66493],"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_03692":null,"SJAG_03856":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0004812":null,"GO:0005524":null,"GO:0008061":null,"GO:0008483":null,"GO:0009088":null},"title":"Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping","uniquename":"GO_REF:0000043"}


id: PMID:12402243
data:
  {"abstract":"The structure and localization of the microtubule organization centres (MTOCs) of the fission yeast Schizosaccharomyces japonicus var. japonicus were examined by fluorescence microscopy and electron microscopy. Spindle pole bodies (SPBs), which are the fungal equivalent of centrosomes, of Sz. japonicus were visualized by immunofluorescent staining using a monoclonal anti-gamma-tubulin antibody. The behaviour of the SPBs during the cell cycle mostly coincided with previous reports on the most widely used fission yeast Schizosaccharomyces pombe. We cloned the gamma-tubulin gene from Sz. japonicus by PCR using redundant sets of primers corresponding to conserved regions of known gamma-tubulins. The predicted amino acid sequence of Sz. japonicus gamma-tubulin was most similar to the Sz. pombe gamma-tubulin. Under the electron microscope, the SPBs of Sz. japonicus were detected as electron-dense multilayered structures located just outside the nuclear envelope. The SPBs of Sz. japonicus were composed of three electron-dense layers and were surrounded by fuzzy material. Each layer showed structural changes according to the progression of the cell cycle. In mitotic cells, the SPBs were located on the fenestrae of the nuclear envelopes through which the mitotic spindle microtubules ran into the nucleoplasm. Our results show that Sz. japonicus is a very potent and attractive organism for the investigation of the microtubule nucleation system and morphogenesis in yeasts. The Accession No. for the nucleotide sequence of the Sz. japonicus gtb1(+) gene is AF159163.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Horio T, Kimura N, Basaki A, Tanaka Y, Noguchi T, Akashi T, Tanaka K","authors_abbrev":"Horio T et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Yeast 2002 Nov;19(15):1335-50","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":"2002-10-29","pubmed_publication_date":"Nov 2002","terms_by_termid":{},"title":"Molecular and structural characterization of the spindle pole bodies in the fission yeast Schizosaccharomyces japonicus var japonicus.","uniquename":"PMID:12402243"}


id: PMID:24184107
data:
  {"abstract":"During cellular proliferation, the mother nucleus divides into two daughters, each carrying a full complement of chromosomes and capable of driving the next cell cycle. Mitotic chromosome segregation must be coordinated with remodeling of other nuclear components, including the nuclear envelope (NE) and the non-membrane-bound nucleolus. Here, we show that in the fission yeast Schizosaccharomyces japonicus, which breaks and reforms the NE during mitosis, the evolutionary conserved LEM-domain protein Man1 promotes equal partitioning of the nuclear membrane, nucleolar remodeling, and efficient inheritance of the nuclear pore complexes (NPCs) by the daughter nuclei. Analyses of man1 mutants and results obtained using an artificial chromatin-nuclear pore tether suggest that Man1 may exert its function by linking the NPCs to segregating chromatin. By integrating the partitioning of the nuclear membrane and nucleolar material with chromosome segregation, cells build two nearly identical copies of the original nucleus.","alleles_by_uniquename":{"SJAG_01834:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01834","name":"pom152delta","uniquename":"SJAG_01834:allele-1"},"SJAG_03449:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03449","name":"man1delta","uniquename":"SJAG_03449:allele-1"},"SJAG_03449:allele-2":{"allele_type":"partial_amino_acid_deletion","description":"man1DHEH","gene_uniquename":"SJAG_03449","name":"Man1DHEH","uniquename":"SJAG_03449:allele-2"},"SJAG_03449:allele-3":{"allele_type":"amino_acid_insertion_and_deletion","description":"man1-1-488","gene_uniquename":"SJAG_03449","name":"man1-1-488","uniquename":"SJAG_03449:allele-3"}},"annotation_curators":[{"annotation_count":17,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"},{"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":"2021-07-27","authors":"Yam C, Gu Y, Oliferenko S","authors_abbrev":"Yam C et al.","canto_added_date":"2021-05-10 02:38:18","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-01 07:25:17","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-27 11:54:17","canto_session_key":"0f2dda384385121f","canto_session_submitted_date":"2021-07-27 11:54:10","canto_triage_status":"Curatable","citation":"Curr Biol 2013 Nov 18;23(22):2303-2310","cv_annotations":{"biological_process":[{"annotations":[115310],"is_not":false,"summary":null,"term":"GO:0101024"}],"cellular_component":[{"annotations":[115295],"is_not":false,"summary":null,"term":"GO:0000781"},{"annotations":[115294],"is_not":false,"summary":null,"term":"GO:0140573"},{"annotations":[115297],"is_not":false,"summary":null,"term":"GO:0005643"},{"annotations":[115296],"is_not":false,"summary":null,"term":"GO:0030875"}],"molecular_function":[{"annotations":[115311],"is_not":false,"summary":null,"term":"GO:0062239"}],"single_locus_phenotype":[{"annotations":[115298,115303,115305],"is_not":false,"summary":null,"term":"FYPO:0003779"},{"annotations":[115307,115308,115309],"is_not":false,"summary":null,"term":"FYPO:0000671"},{"annotations":[115300,115301,115302,115304],"is_not":false,"summary":null,"term":"FYPO:0004890"},{"annotations":[115299],"is_not":false,"summary":null,"term":"FYPO:0001234"},{"annotations":[115306],"is_not":false,"summary":null,"term":"FYPO:0004683"}]},"doi":"10.1016/j.cub.2013.09.057","gene_count":5,"genes_by_uniquename":{"SJAG_00302":null,"SJAG_01777":null,"SJAG_01834":null,"SJAG_03449":null,"SJAG_03603":null},"genotypes_by_uniquename":{"Man1DHEH-man1DHEH-partial_amino_acid_deletion-expression-not_assayed_or_wild_type":{"display_name":"Man1DHEH(man1DHEH)","display_uniquename":"Man1DHEH-man1DHEH-partial_amino_acid_deletion-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03449:allele-2","expression":"Not assayed or wild type"}]}]},"man1-1-488-man1-1-488-amino_acid_insertion_and_deletion-expression-not_assayed_or_wild_type":{"display_name":"man1-1-488(aa)","display_uniquename":"man1-1-488-man1-1-488-amino_acid_insertion_and_deletion-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03449:allele-3","expression":"Not assayed or wild type"}]}]},"man1delta":{"display_name":"man1delta","display_uniquename":"man1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03449:allele-1","expression":"Null"}]}]},"pom152delta":{"display_name":"pom152delta","display_uniquename":"pom152delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01834:allele-1","expression":"Null"}]}]}},"ltp_gene_count":5,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2013","pubmed_entrez_date":"2013-11-05","pubmed_publication_date":"18 Nov 2013","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000162":null,"FYPO:0000671":null,"FYPO:0001234":null,"FYPO:0003779":null,"FYPO:0004683":null,"FYPO:0004890":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"FYPO_EXT:0000003":null,"GO:0000781":null,"GO:0005643":null,"GO:0030875":null,"GO:0062239":null,"GO:0101024":null,"GO:0140573":null},"title":"Partitioning and remodeling of the Schizosaccharomyces japonicus mitotic nucleus require chromosome tethers.","uniquename":"PMID:24184107"}


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: GO_REF:0000087
data:
  {"abstract":"We have created a standard template for classes describing the protein localization and establishment of protein localization to a cellular component as a biological process. The underlying equivalence axiom templates are \"GO:0008104 and 'has_target_end_location' some C\" (protein localization) and \"GO:0045184 and 'has_target_end_location' some C\" (establishment of protein localization), where C is 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 protein localization and establishment of protein localization as biological process in the Gene Ontology","uniquename":"GO_REF:0000087"}


id: PMID:33837814
data:
  {"abstract":"The capability of RNA isolation with good efficiency and high quality is essential for a downstream application such as RNA sequencing. It requires successful cell culturing and an effective RNA isolation method. Although effective methods are available, production of the homogenous mycelia and extraction of good-quality mycelial RNA from true invasive hyphae, which penetrated into the agar plates, are difficult. To overcome these problems, the aim of this study was to develop technical modifications which allow production of homogenous mycelial biomass without extra stimuli agents and improve quality of the RNA extracted from the fungal hyphae. Our alternative culture medium was suitable for production both yeast-phase cells and hyphae of the Schizosaccharomyces japonicus and other dimorphic species, such as the Candida albicans, Saccharomyces cerevisiae, and Jaminaea angkorensis. To improve quality of the mycelial RNA, we developed an isolation procedure of the hyphal tip, which eliminated the unnecessary vacuoles-containing parts of the hyphae. To increase RNA quantity, we used glass beads in the RNA extraction protocol to achieve stronger breaking of the mycelial walls. All these modifications can also be useful for researchers working with other dimorphic fungi and can contribute to the higher comparability of the transcriptional data coming from yeast-phase cells and hyphae or even from different species.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Papp LA, Ács-Szabó L, Póliska S, Miklós I","authors_abbrev":"Papp LA et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Curr Genet 2021 Oct;67(5):823-830","cv_annotations":{},"doi":"10.1007/s00294-021-01181-4","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":"2021-04-10","pubmed_publication_date":"Oct 2021","terms_by_termid":{},"title":"A modified culture medium and hyphae isolation method can increase quality of the RNA extracted from mycelia of a dimorphic fungal species.","uniquename":"PMID:33837814"}


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: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: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: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: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:0000097
data:
  {"abstract":"FlyBase occasionally makes GO annotations based on information that has been sent to us directly by researchers as a personal communication to FlyBase. In each case, the full details of the communication including any associated data and analyses are recorded in a FlyBase publication (FBrf) available from our website (http://flybase.org).","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 based on personal communication to FlyBase","uniquename":"GO_REF:0000097"}


id: PMID:35693892
data:
  {"abstract":"The S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 catalyzes biosynthesis of 4-demethylwyosine (imG-14), the precursor for wyosine, the hypermodified guanine-derived nucleotide present at position 37 of phenylalanine tRNAs of archaea and eukarya. Eukaryotic TYW1 enzymes contain N-terminal flavodoxin-like and C-terminal radical-SAM domains. We determined co-crystal structures of the flavodoxin-like domain of the putative Tyw1 from  Schizosaccharomyces japonicus  in complex with flavin mononucleotide (FMN), exploiting an unexpected anomalous scatterer present in the recombinant protein. Our results show how eukaryotic TYW1 enzymes bind the coenzyme FMN and will help further elucidation of the structural enzymology of 4-demethylwyosine synthesis.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Sjekloća L, Ferré-D'Amaré AR","authors_abbrev":"Sjekloća L et al.","canto_added_date":"2023-05-04 00:40:03","canto_curator_role":"JaponicusDB","canto_triage_status":"Structure","citation":"MicroPubl Biol 2022;2022","cv_annotations":{},"doi":"10.17912/micropub.biology.000570","gene_count":1,"genes_by_uniquename":{"SJAG_04265":null},"genotypes_by_uniquename":{},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"pdb_entries":[{"entry_authors":"Sjekloca L,Ferre D'Amare AR","entry_authors_abbrev":"Sjekloca L et al.","experimental_method":"X-ray","gene_chains":[{"chain":"A","gene_uniquename":"SJAG_04265","position":"76-251"}],"pdb_id":"6pup","reference_uniquename":"PMID:35693892","resolution":"1.89","title":"1.9 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN"},{"entry_authors":"Sjekloca L,Ferre-D'Amare AR","entry_authors_abbrev":"Sjekloca L et al.","experimental_method":"X-ray","gene_chains":[{"chain":"A","gene_uniquename":"SJAG_04265","position":"30-251"}],"pdb_id":"6puq","reference_uniquename":"PMID:35693892","resolution":"1.56","title":"1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN"}],"physical_interactions":[],"publication_year":"2022","pubmed_entrez_date":"2022-06-13","pubmed_publication_date":"2022","terms_by_termid":{},"title":"Biochemical and structural characterization of the flavodoxin-like domain of the  Schizosaccharomyces japonicus  putative tRNA  Phe  4-demethylwyosine synthase Tyw1 in complex with FMN.","uniquename":"PMID:35693892"}


id: GO_REF:0000071
data:
  {"abstract":"We have created a standard template for classes describing the response to and cellular response to a chemical entity (ChEBI) as a biological process. The underlying equivalence axiom templates are \"GO:0050896 and 'has input' some X\" (response to) and \"GO:0070887 and 'has input' some X\" (cellular response to), 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 response to and cellular response to a chemical as biological process in the Gene Ontology","uniquename":"GO_REF:0000071"}


id: PMID:23150598
data:
  {"abstract":"A key question in developmental biology addresses the mechanism of asymmetric cell division. Asymmetry is crucial for generating cellular diversity required for development in multicellular organisms. As one of the potential mechanisms, chromosomally borne epigenetic difference between sister cells that changes mating/cell type has been demonstrated only in the Schizosaccharomyces pombe fission yeast. For technical reasons, it is nearly impossible to determine the existence of such a mechanism operating during embryonic development of multicellular organisms. Our work addresses whether such an epigenetic mechanism causes asymmetric cell division in the recently sequenced fission yeast, S. japonicus (with 36% GC content), which is highly diverged from the well-studied S. pombe species (with 44% GC content). We find that the genomic location and DNA sequences of the mating-type loci of S. japonicus differ vastly from those of the S. pombe species. Remarkably however, similar to S. pombe, the S. japonicus cells switch cell/mating type after undergoing two consecutive cycles of asymmetric cell divisions: only one among four \"granddaughter\" cells switches. The DNA-strand-specific epigenetic imprint at the mating-type locus1 initiates the recombination event, which is required for cellular differentiation. Therefore the S. pombe and S. japonicus mating systems provide the first two examples in which the intrinsic chirality of double helical structure of DNA forms the primary determinant of asymmetric cell division. Our results show that this unique strand-specific imprinting/segregation epigenetic mechanism for asymmetric cell division is evolutionary conserved. Motivated by these findings, we speculate that DNA-strand-specific epigenetic mechanisms might have evolved to dictate asymmetric cell division in diploid, higher eukaryotes as well.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Yu C, Bonaduce MJ, Klar AJ","authors_abbrev":"Yu C et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Genetics 2013 Jan;193(1):85-94","cv_annotations":{},"doi":"10.1534/genetics.112.146233","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2013","pubmed_entrez_date":"2012-11-15","pubmed_publication_date":"Jan 2013","terms_by_termid":{},"title":"Defining the epigenetic mechanism of asymmetric cell division of Schizosaccharomyces japonicus yeast.","uniquename":"PMID:23150598"}


id: PMID:37233261
data:
  {"abstract":"Gene targeting is a commonly used method to reveal the function of genes. Although it is an attractive tool for molecular studies, it can frequently be a challenge because its efficiency can be low and it requires the screening of a large number of transformants. Generally, these problems originate from the elevated level of ectopic integration caused by non-homologous DNA end joining (NHEJ). To eliminate this problem, NHEJ-related genes are frequently deleted or disrupted. Although these manipulations can improve gene targeting, the phenotype of the mutant strains raised the question of whether mutations have side effects. The aim of this study was to disrupt the  lig4  gene in the dimorphic fission yeast,  S. japonicus , and investigate the phenotypic changes of the mutant strain. The mutant cells have shown various phenotypic changes, such as increased sporulation on complete medium, decreased hyphal growth, faster chronological aging, and higher sensitivity to heat shock, UV light, and caffeine. In addition, higher flocculation capacity has been observed, especially at lower sugar concentrations. These changes were supported by transcriptional profiling. Many genes belonging to metabolic and transport processes, cell division, or signaling had altered mRNA levels compared to the control strain. Although the disruption improved the gene targeting, we assume that the  lig4  inactivation can cause unexpected physiological side effects, and we have to be very careful with the manipulations of the NHEJ-related genes. To reveal the exact mechanisms behind these changes, further investigations are required.","alleles_by_uniquename":{"SJAG_02527:allele-1":{"allele_type":"disruption","description":"RNA sequencing revealed that only the 5' end of the disrupted allele showed low RNA expression and coverage","gene_uniquename":"SJAG_02527","name":"lig4::KanMX6","uniquename":"SJAG_02527:allele-1"}},"annotation_curators":[{"annotation_count":7,"community_curator":true,"file_name":null,"file_type":null,"name":"Ida Miklos","orcid":"0000-0002-7074-4019"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2023-08-08","authors":"Acs-Szabo L, Papp LA, Takacs S, Miklos I","authors_abbrev":"Acs-Szabo L et al.","canto_added_date":"2023-05-27 00:40:04","canto_annotation_status":"APPROVED","canto_approved_date":"2023-08-08 20:07:33","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Ida Miklos","canto_curator_role":"community","canto_first_approved_date":"2023-08-08 20:07:33","canto_session_key":"c74bdd0a67b132f8","canto_session_submitted_date":"2023-08-08 20:07:15","canto_triage_status":"Curatable","citation":"J Fungi (Basel) 2023 May 10;9(5)","cv_annotations":{"single_locus_phenotype":[{"annotations":[115597],"is_not":false,"summary":null,"term":"FYPO:0007776"},{"annotations":[115599],"is_not":false,"summary":null,"term":"FYPO:0009111"},{"annotations":[115596],"is_not":false,"summary":null,"term":"FYPO:0000588"},{"annotations":[115602],"is_not":false,"summary":null,"term":"FYPO:0005705"},{"annotations":[115600],"is_not":false,"summary":null,"term":"FYPO:0005231"},{"annotations":[115598],"is_not":false,"summary":null,"term":"FYPO:0000097"},{"annotations":[115601],"is_not":false,"summary":null,"term":"FYPO:0001408"}]},"doi":"10.3390/jof9050550","gene_count":1,"genes_by_uniquename":{"SJAG_02527":null},"genotypes_by_uniquename":{"lig4::KanMX6-RNA_sequencing_revealed_that_only_the_5'_end_of_the_disrupted_allele_showed_low_RNA_expression_and_coverage-disruption-expression-knockdown":{"display_name":"lig4::KanMX6(RNA sequencing revealed that only the 5' end of the disrupted allele showed low RNA expression and coverage)[Knockdown]","display_uniquename":"lig4::KanMX6-RNA_sequencing_revealed_that_only_the_5'_end_of_the_disrupted_allele_showed_low_RNA_expression_and_coverage-disruption-expression-knockdown","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02527:allele-1","expression":"Knockdown"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2023","pubmed_entrez_date":"2023-05-26","pubmed_publication_date":"10 May 2023","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000081":null,"FYECO:0000117":null,"FYECO:0000126":null,"FYECO:0000137":null,"FYECO:0000315":null,"FYPO:0000097":null,"FYPO:0000588":null,"FYPO:0001408":null,"FYPO:0005231":null,"FYPO:0005705":null,"FYPO:0007776":null,"FYPO:0009111":null},"title":"Disruption of the  Schizosaccharomyces japonicus lig4  Disturbs Several Cellular Processes and Leads to a Pleiotropic Phenotype.","uniquename":"PMID:37233261"}


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: 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: 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":[115714],"is_not":false,"summary":null,"term":"GO:0101024"},{"annotations":[115719],"is_not":false,"summary":null,"term":"GO:0006998"}],"cellular_component":[{"annotations":[115718],"is_not":false,"summary":null,"term":"GO:0120321"}],"multi_locus_phenotype":[{"annotations":[115721],"is_not":false,"summary":null,"term":"FYPO:0000619"},{"annotations":[115720],"is_not":false,"summary":null,"term":"FYPO:0001489"}],"single_locus_phenotype":[{"annotations":[115722],"is_not":false,"summary":null,"term":"FYPO:0000619"},{"annotations":[115716],"is_not":false,"summary":null,"term":"FYPO:0003738"},{"annotations":[115723],"is_not":false,"summary":null,"term":"FYPO:0000815"},{"annotations":[115715],"is_not":false,"summary":null,"term":"FYPO:0000082"},{"annotations":[115717],"is_not":false,"summary":null,"term":"FYPO:0003976"},{"annotations":[115713],"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","references_by_uniquename":{"PMID:28954740":null},"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: GO_REF:0000058
data:
  {"abstract":"We have created a standard template for the definition of classes for the regulation of a biological process. This includes the definitions for positive and negative regulation. The equivalence axiom templates are \"GO:0065007 and 'regulates' some X\" (regulation), \"GO:0065007 and 'negatively_regulates' some X\" (negative regulation), and \"GO:0065007 and 'positively_regulates' some X\" (positive regulation), where X 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 regulation in the Gene Ontology (biological process) ","uniquename":"GO_REF:0000058"}


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":[115646,115647],"is_not":false,"summary":null,"term":"GO:0071483"}],"molecular_function":[{"annotations":[115645],"is_not":false,"summary":null,"term":"GO:0009882"}],"single_locus_phenotype":[{"annotations":[115648,115649],"is_not":false,"summary":null,"term":"FYPO:0008031"},{"annotations":[115650,115651],"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: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":[115208,115209],"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:21802294
data:
  {"abstract":"Eukaryotes segregate chromosomes in \"open\" or \"closed\" mitosis, depending on whether their nuclear envelopes (NEs) break down or remain intact. Here we show that the control of the nuclear surface area may determine the choice between these two modes. The dividing nucleus does not expand its surface in the fission yeast Schizosaccharomyces japonicus, confining the mitotic spindle and causing it to buckle. The NE ruptures in anaphase, releasing the compressive stress and allowing chromosome segregation. Blocking the NE expansion in the related species Schizosaccharomyces pombe that undergoes closed mitosis induces spindle buckling and collapse in the absence of an intrinsic NE rupture mechanism. We propose that scaling considerations could have shaped the evolution of eukaryotic mitosis by necessitating either nuclear surface expansion or the NE breakdown.","alleles_by_uniquename":{"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"}},"annotation_curators":[{"annotation_count":16,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"},{"annotation_count":1,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-05","authors":"Yam C, He Y, Zhang D, Chiam KH, Oliferenko S","authors_abbrev":"Yam C et al.","canto_added_date":"2021-05-10 02:38:30","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-01 07:44:20","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-05 11:58:24","canto_session_key":"ec486c9b0898d3c4","canto_session_submitted_date":"2021-07-05 12:18:55","canto_triage_status":"Curatable","citation":"Curr Biol 2011 Aug 09;21(15):1314-9","cv_annotations":{"biological_process":[{"annotations":[115591],"is_not":false,"summary":null,"term":"GO:0101024"}],"cellular_component":[{"annotations":[115580],"is_not":false,"summary":null,"term":"GO:0000785"},{"annotations":[115584,115585],"is_not":false,"summary":null,"term":"GO:0005783"},{"annotations":[115586],"is_not":false,"summary":null,"term":"GO:0098826"},{"annotations":[115579],"is_not":false,"summary":null,"term":"GO:0000776"},{"annotations":[115576],"is_not":false,"summary":null,"term":"GO:0005874"},{"annotations":[115581,115582,115583,115587],"is_not":false,"summary":null,"term":"GO:0005643"},{"annotations":[115577,115578],"is_not":false,"summary":null,"term":"GO:0005730"}],"single_locus_phenotype":[{"annotations":[115589],"is_not":false,"summary":null,"term":"FYPO:0003779"},{"annotations":[115588],"is_not":false,"summary":null,"term":"FYPO:0004318"},{"annotations":[115590],"is_not":false,"summary":null,"term":"FYPO:0007772"}]},"doi":"10.1016/j.cub.2011.06.052","gene_count":13,"genes_by_uniquename":{"SJAG_00175":null,"SJAG_00471":null,"SJAG_00684":null,"SJAG_00943":null,"SJAG_01006":null,"SJAG_01330":null,"SJAG_01374":null,"SJAG_01460":null,"SJAG_01745":null,"SJAG_02509":null,"SJAG_02830":null,"SJAG_03299":null,"SJAG_03603":null},"genotypes_by_uniquename":{"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"}]}]}},"ltp_gene_count":13,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2011","pubmed_entrez_date":"2011-08-02","pubmed_publication_date":"09 Aug 2011","terms_by_termid":{"FYECO:0000162":null,"FYPO:0003779":null,"FYPO:0004318":null,"FYPO:0007772":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"GO:0000776":null,"GO:0000785":null,"GO:0005643":null,"GO:0005730":null,"GO:0005783":null,"GO:0005874":null,"GO:0098826":null,"GO:0101024":null},"title":"Divergent strategies for controlling the nuclear membrane satisfy geometric constraints during nuclear division.","uniquename":"PMID:21802294"}


id: PMID:7612397
data:
  {"abstract":"The ultrastructure of isolated cell walls of Schizosaccharomyces pombe was studied by electron microscopy after treatment with the following purified enzymes: endo-beta-(1-->3)-glucanase, endo-beta-(-->6)-glucanase, and endo-alpha-(1-->3)-glucanase produced by Bacillus circulans; exo-beta-(1-->3)-glucanase and endo-beta-(1-->3)-glucanase produced by Schizosaccharomyces japonicus var. versatilis. The exo-beta-(1-->3)-glucanase had no detectable effect on the walls, but amorphous wall material was removed by action of the endo-beta-(1-->3)- and endo-beta-(1-->6)-glucanases of B. circulans to reveal a wall component consisting of densely interwoven microfibrils. The fibrils were hydrolyzed by treatment with the Schiz. japonicus endo-beta-(1-->3)-glucanase followed by B. circulans endo-alpha-(1-->3)-glucanase--suggesting that they were composed of -beta-(1-->3)-linked glucan and alpha-(1-->3)-linked glucan. The presence of a fibrillar component in untreated walls was evident after negative staining.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Kopecká M, Fleet GH, Phaff HJ","authors_abbrev":"Kopecká M 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 Struct Biol 1995 Mar;114(2):140-52","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":"1995-03-01","pubmed_publication_date":"Mar 1995","terms_by_termid":{},"title":"Ultrastructure of the cell wall of Schizosaccharomyces pombe following treatment with various glucanases.","uniquename":"PMID:7612397"}


id: PMID:29173643
data:
  {"abstract":"In the beverage fermentation industry, especially at the craft or micro level, there is a movement to incorporate as many local ingredients as possible to both capture terroir and stimulate local economies. In the case of craft beer, this has traditionally only encompassed locally sourced barley, hops, and other agricultural adjuncts. The identification and use of novel yeasts in brewing lags behind. We sought to bridge this gap by bio-prospecting for wild yeasts, with a focus on the American Midwest. We isolated 284 different strains from 54 species of yeast and have begun to determine their fermentation characteristics. During this work, we found several isolates of five species that produce lactic acid and ethanol during wort fermentation: Hanseniaspora vineae, Lachancea fermentati, Lachancea thermotolerans, Schizosaccharomyces japonicus, and Wickerhamomyces anomalus. Tested representatives of these species yielded excellent attenuation, lactic acid production, and sensory characteristics, positioning them as viable alternatives to lactic acid bacteria (LAB) for the production of sour beers. Indeed, we suggest a new LAB-free paradigm for sour beer production that we term \"primary souring\" because the lactic acid production and resultant pH decrease occurs during primary fermentation, as opposed to kettle souring or souring via mixed culture fermentation.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Osburn K, Amaral J, Metcalf SR, Nickens DM, Rogers CM, Sausen C, Caputo R, Miller J, Li H, Tennessen JM, Bochman ML","authors_abbrev":"Osburn K et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Biotech","citation":"Food Microbiol 2018 Apr;70:76-84","cv_annotations":{},"doi":"10.1016/j.fm.2017.09.007","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2018","pubmed_entrez_date":"2017-11-28","pubmed_publication_date":"Apr 2018","terms_by_termid":{},"title":"Primary souring: A novel bacteria-free method for sour beer production.","uniquename":"PMID:29173643"}


id: PMID:25942548
data:
  {"abstract":"New work shows the anillin-related protein Mid1 does not position the cytokinetic ring in the fission yeast Schizosaccharomyces japonicus, unlike its role in S. pombe. Further analysis suggests the conserved function of Mid1-like anillin proteins may be in scaffolding, not positioning, the cytokinetic ring. ","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Moseley JB","authors_abbrev":"Moseley JB","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Curr Biol 2015 May 04;25(9):R364-6","cv_annotations":{},"doi":"10.1016/j.cub.2015.03.017","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":"2015-05-06","pubmed_publication_date":"04 May 2015","terms_by_termid":{},"title":"Cytokinesis: does Mid1 have an identity crisis?","uniquename":"PMID:25942548"}


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:36058798
data:
  {"abstract":"Schizosaccharomyces japonicus is a dimorphic yeast, transiting between unicellular and hyphal growth. The glycoproteins of fission yeast contain, in addition to mannose (Man), a large number of galactose (Gal) residues. Previously, we reported that the cell-surface O-glycans of S. japonicus comprise mainly tri-saccharides (Gal-Man-Man) as a main component, in contrast to the tetra-saccharides observed in other Schizosaccharomyces species. Here we have investigated the function of cell-surface Gal residues in S. japonicus. Because disruption of gms1 + , encoding the UDP-Gal transporter required for galactomannan synthesis, abolishes cell-surface galactosylation in Schizosaccharomyces pombe, we constructed a deletion mutant of the homologous gene in S. japonicus gms1Δ [gms1 (S.j)] and determined the N- and O-linked oligosaccharide structures present on the cell surface. Disruption of gms1 (S.j) resulted in a complete lack of Gal on the cell surface, indicating that Gms1 plays an essential role in supplying UDP-Gal from the cytoplasm to the Golgi lumen. Analytical microscopy of gms1Δ demonstrated that the lack of cell-surface Gal did not affect cell growth or morphology during vegetative growth. However, hyphal development was blocked in gms1Δ, even in the presence of the topoisomerase I inhibitor camptothecin, which is known to induce hyphal differentiation in wild-type S. japonicus. Collectively, these findings show that Gal-containing oligosaccharides are required for cell wall integrity during filamentous growth in S. japonicus.","alleles_by_uniquename":{"SJAG_04697:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04697","name":"gms1delta","uniquename":"SJAG_04697: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":"2022-12-01","authors":"Fukunaga T, Ohashi T, Tanaka Y, Yoshimatsu T, Higuchi Y, Maekawa H, Takegawa K","authors_abbrev":"Fukunaga T et al.","canto_added_date":"2022-11-25 12:12:27","canto_annotation_status":"APPROVED","canto_approved_date":"2022-12-01 10:35:53","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2022-12-01 10:35:53","canto_session_key":"465355706dc223a3","canto_session_submitted_date":"2022-11-25 12:49:07","canto_triage_status":"Curatable","citation":"J Biosci Bioeng 2022 Nov;134(5):384-392","cv_annotations":{"single_locus_phenotype":[{"annotations":[115378],"is_not":false,"summary":null,"term":"FYPO:0008029"},{"annotations":[115374],"is_not":false,"summary":null,"term":"FYPO:0000082"},{"annotations":[115377],"is_not":false,"summary":null,"term":"FYPO:0007776"},{"annotations":[115376],"is_not":false,"summary":null,"term":"FYPO:0007780"},{"annotations":[115373],"is_not":false,"summary":null,"term":"FYPO:0003727"},{"annotations":[115375],"is_not":false,"summary":null,"term":"FYPO:0000106"}]},"doi":"10.1016/j.jbiosc.2022.07.014","gene_count":1,"genes_by_uniquename":{"SJAG_04697":null},"genotypes_by_uniquename":{"gms1delta":{"display_name":"gms1delta","display_uniquename":"gms1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04697:allele-1","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2022","pubmed_entrez_date":"2022-09-04","pubmed_publication_date":"Nov 2022","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000005":null,"FYECO:0000126":null,"FYECO:0000137":null,"FYECO:0000314":null,"FYPO:0000082":null,"FYPO:0000106":null,"FYPO:0003727":null,"FYPO:0007776":null,"FYPO:0007780":null,"FYPO:0008029":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null},"title":"Galactosylation of cell-surface glycoprotein required for hyphal growth and cell wall integrity in Schizosaccharomyces japonicus.","uniquename":"PMID:36058798"}


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: PMID:20368354
data:
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id: GO_REF:0000108
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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":[115366,115372],"is_not":false,"summary":null,"term":"GO:0097753"}],"cellular_component":[{"annotations":[115367,115368],"is_not":false,"summary":null,"term":"GO:0032541"},{"annotations":[115369,115370],"is_not":false,"summary":null,"term":"GO:0005643"}],"single_locus_phenotype":[{"annotations":[115371],"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: PMID:22586155
data:
  {"abstract":"tRNA genes are interspersed throughout eukaryotic DNA, contributing to genome architecture and evolution in addition to translation of the transcriptome. Codon use correlates with tRNA gene copy number in noncomplex organisms including yeasts. Synonymous codons impact translation with various outcomes, dependent on relative tRNA abundances. Availability of whole-genome sequences allowed us to examine tRNA gene copy number variation (tgCNV) and codon use in four Schizosaccharomyces species and Saccharomyces cerevisiae. tRNA gene numbers vary from 171 to 322 in the four Schizosaccharomyces despite very high similarity in other features of their genomes. In addition, we performed whole-genome sequencing of several related laboratory strains of Schizosaccharomyces pombe and found tgCNV at a cluster of tRNA genes. We examined for the first time effects of wobble rules on correlation of tRNA gene number and codon use and showed improvement for S. cerevisiae and three of the Schizosaccharomyces species. In contrast, correlation in Schizosaccharomyces japonicus is poor due to markedly divergent tRNA gene content, and much worsened by the wobble rules. In japonicus, some tRNA iso-acceptor genes are absent and others are greatly reduced relative to the other yeasts, while genes for synonymous wobble iso-acceptors are amplified, indicating wobble use not apparent in any other eukaryote. We identified a subset of japonicus-specific wobbles that improves correlation of codon use and tRNA gene content in japonicus. We conclude that tgCNV is high among Schizo species and occurs in related laboratory strains of S. pombe (and expectedly other species), and tRNAome-codon analyses can provide insight into species-specific wobble decoding.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Iben JR, Maraia RJ","authors_abbrev":"Iben JR et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"RNA 2012 Jul;18(7):1358-72","cv_annotations":{},"doi":"10.1261/rna.032151.111","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":"2012-05-16","pubmed_publication_date":"Jul 2012","terms_by_termid":{},"title":"tRNAomics: tRNA gene copy number variation and codon use provide bioinformatic evidence of a new anticodon:codon wobble pair in a eukaryote.","uniquename":"PMID:22586155"}


id: GO_REF:0000095
data:
  {"abstract":"This article is not referenced in PubMed. Please see contributing data resource for details.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Mouse Genome Informatics scientific curators and 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":"Literature reference not indexed by PubMed","uniquename":"GO_REF:0000095"}


id: PMID:9720056
data:
  {"abstract":"The cells of Schizosaccharomyces japonicus var. versatilis responded to the presence of cytochalasin D (CD), an inhibitor of actin polymerization, by the disappearance of contractile actin rings (ARs) that had already formed and by inhibition of new ring formation. Actin cables disappeared. Actin patches remained preserved and became co-localized with regions of actual cell wall formation (at cell poles and at the site of septum development). Removal of the AR arrested formation of the primary septum and led to the production of aberrant septum protrusions in that region. Nuclear division was accomplished in the presence of CD but new ARs were not produced. The wall (septum) material was deposited in the form of a wide band at the inner surface of the lateral cell wall in the cell centre. This layer showed a thin fibrillar structure. The removal of CD resulted in rapid formation of new ARs in the equatorial region of the cells. This implies that the signal for AR localization was not abolished either by CD effects or by removal of an AR already formed. Some of the newly developed ARs showed atypical localization and orientation. In addition, redundant, subcortically situated actin bundles were produced. The removal of CD was quickly followed by the development of primary septa co-localized with ARs. Wall protrusions occurred co-localized with the redundant actin bundles. If these were completed in a circle, redundant septa developed. The AR is a mechanism which, in time and space, triggers cytokinesis by building a septum sequentially dependent on the AR. Aberrant septa were not capable of separating daughter cells. However, non-separated daughter cells subsequently gave rise to normal cells.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Gabriel M, Horký D, Svoboda A, Kopecká M","authors_abbrev":"Gabriel M et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Microbiology (Reading) 1998 Aug;144 ( Pt 8):2331-2344","cv_annotations":{},"doi":"10.1099/00221287-144-8-2331","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":"1998-08-28","pubmed_publication_date":"Aug 1998","terms_by_termid":{},"title":"Cytochalasin D interferes with contractile actin ring and septum formation in Schizosaccharomyces japonicus var. versatilis.","uniquename":"PMID:9720056"}


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: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: 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: 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: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: 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: GO_REF:0000110
data:
  {"abstract":"Gene Ontology annotation of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion based on analysis by MitoDrome (http://mitodrome.ba.itb.cnr.it/) by comparison of human mitochondrial proteins available in SWISSPROT vs. the Drosophila genome, ESTs and cDNA sequences available in the FlyBase database (PMID:12520013).","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 Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion.","uniquename":"GO_REF:0000110"}


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:37279666
data:
  {"abstract":"A new study finds that Schizosaccharomyces japonicus, a eukaryote that lost the ability to respire, modified its central carbon metabolism to maintain efficient ATP production, cofactor regeneration, and amino-acid production. This remarkable metabolic flexibility opens new avenues towards applications.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Cool L, Hanon S, Verstrepen KJ","authors_abbrev":"Cool L et al.","canto_added_date":"2023-06-08 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Curr Biol 2023 Jun 05;33(11):R444-R447","cv_annotations":{},"doi":"10.1016/j.cub.2023.05.002","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":"2023-06-06","pubmed_publication_date":"05 Jun 2023","terms_by_termid":{},"title":"Metabolism: How a eukaryote adapted to life without respiration.","uniquename":"PMID:37279666"}


id: PMID:28733395
data:
  {"abstract":" Schizosaccharomyces japonicus  is a dimorphic yeast. Depending on the nutrient conditions, the transition between growth as yeast cells and growth as hyphal cells can be reversibly induced. In addition to nutrient stress, induced DNA lesions, such as those produced by camptothecin, also induce hyphal growth regardless of the nutrient status. This protocol describes both methods of induction.","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":"Method or reagent","citation":"Cold Spring Harb Protoc 2017 Dec 01;2017(12):pdb.prot091868","cv_annotations":{},"doi":"10.1101/pdb.prot091868","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":"Induction of Hyphal Growth in  Schizosaccharomyces japonicus .","uniquename":"PMID:28733395"}


# genotypes

id: ptp4delta
data:
  {"alleles_by_uniquename":{"SJAG_04883:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04883","name":"ptp4delta","uniquename":"SJAG_04883:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115595],"is_not":false,"summary":null,"term":"FYPO:0001007"}]},"display_name":"ptp4delta","display_uniquename":"ptp4delta","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"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04883:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:36695178":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYPO:0001007":null}}


id: etr1delta
data:
  {"alleles_by_uniquename":{},"annotation_count":0,"annotation_details":{},"comment":null,"cv_annotations":{},"display_name":"etr1delta","display_uniquename":"etr1delta","genes_by_uniquename":{},"genotypes_by_uniquename":{},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02007:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{},"taxonid":4897,"terms_by_termid":{}}


id: gef1delta
data:
  {"alleles_by_uniquename":{"SJAG_03581:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03581","name":"gef1delta","uniquename":"SJAG_03581:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115325],"is_not":false,"summary":null,"term":"FYPO:0001877"}]},"display_name":"gef1delta","display_uniquename":"gef1delta","genes_by_uniquename":{"SJAG_03581":null},"genotypes_by_uniquename":{"gef1delta":{"display_name":"gef1delta","display_uniquename":"gef1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03581:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03581:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:30664646":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYPO:0001877":null,"FYPO_EXT:0000002":null}}


id: fum1delta
data:
  {"alleles_by_uniquename":{"SJAG_04843:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04843","name":"fum1delta","uniquename":"SJAG_04843:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115278],"is_not":false,"summary":null,"term":"FYPO:0002058"}]},"display_name":"fum1delta","display_uniquename":"fum1delta","genes_by_uniquename":{"SJAG_04843":null},"genotypes_by_uniquename":{"fum1delta":{"display_name":"fum1delta","display_uniquename":"fum1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04843:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04843:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:37164017":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000126":null,"FYECO:0000137":null,"FYPO:0002058":null}}


id: cut3-T19E-cut3-T19E-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
  {"alleles_by_uniquename":{},"annotation_count":0,"annotation_details":{},"comment":null,"cv_annotations":{},"display_name":"cut3-T19E(aa)","display_uniquename":"cut3-T19E-cut3-T19E-amino_acid_mutation-expression-not_assayed_or_wild_type","genes_by_uniquename":{},"genotypes_by_uniquename":{},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00871:allele-1","expression":"Not assayed or wild type"}]}],"ploidiness":"haploid","references_by_uniquename":{},"taxonid":4897,"terms_by_termid":{}}


id: alx1delta
data:
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id: ste6delta
data:
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id: pom1delta
data:
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id: leo1delta
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id: vps32delta
data:
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id: man1-1-488-man1-1-488-amino_acid_insertion_and_deletion-expression-not_assayed_or_wild_type
data:
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id: rad26delta
data:
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id: mid1delta
data:
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id: cdc15-A-L264P,P442T-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: wis4delta
data:
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id: ned1S235A_S651-S235A__S651-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: pom152delta
data:
  {"alleles_by_uniquename":{"SJAG_01834:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01834","name":"pom152delta","uniquename":"SJAG_01834:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115301],"is_not":false,"summary":null,"term":"FYPO:0004890"}]},"display_name":"pom152delta","display_uniquename":"pom152delta","genes_by_uniquename":{"SJAG_01834":null},"genotypes_by_uniquename":{"pom152delta":{"display_name":"pom152delta","display_uniquename":"pom152delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01834:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01834:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:24184107":null},"taxonid":4897,"terms_by_termid":{"FYPO:0004890":null,"FYPO_EXT:0000002":null}}


id: vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: ras1delta
data:
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id: ned1delta
data:
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id: dcr1delta__mpe1-R77W-R77W-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: ned1-5E-S499E__S538E__T620E__T638E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: byr1delta
data:
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id: sty1delta
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id: cox6delta
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id: efc25delta
data:
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id: ade6-domK-Q262A-amino_acid_mutation-expression-not_assayed_or_wild_type
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id: apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type
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id: cds1delta
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id: cdc2-1w-G146D-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: pmk1delta
data:
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id: cem1delta
data:
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id: chp1delta
data:
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id: vps24delta
data:
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id: mat-Pc-R47K-R47K-amino_acid_mutation-expression-not_assayed_or_wild_type
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id: Man1DHEH-man1DHEH-partial_amino_acid_deletion-expression-not_assayed_or_wild_type
data:
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id: agn1delta
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id: nur1delta__vps4delta
data:
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id: wcs1delta
data:
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id: ade6delta
data:
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id: mrc1delta
data:
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id: ned1S235E_S651E-S235E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: chk1delta__crb2delta
data:
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id: cmp7delta__vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: win1delta
data:
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id: oar2-51-Y189D_cold_sensitive-amino_acid_mutation-expression-overexpression
data:
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id: chk1delta
data:
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id: rga4delta__rga6delta
data:
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id: crb2delta
data:
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id: dcr1delta
data:
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id: gap1delta
data:
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id: oar2delta
data:
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id: wcs2delta
data:
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id: stc1delta
data:
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id: sep1delta
data:
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id: pek1delta
data:
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id: vps4delta
data:
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id:
  Pmk1Sp(delta82-105)-Pmk1_from_S._pombe_with_deleted_residues_82-105-partial_amino_acid_deletion-expression-not_assayed_or_wild_type

data:
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id: rad3delta
data:
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id: clr4delta
data:
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id: pck1delta
data:
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id:
  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

data:
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id: lem2delta
data:
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id: sdh3delta
data:
  {"alleles_by_uniquename":{"SJAG_03920:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03920","name":"sdh3delta","uniquename":"SJAG_03920:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115277],"is_not":false,"summary":null,"term":"FYPO:0002058"}]},"display_name":"sdh3delta","display_uniquename":"sdh3delta","genes_by_uniquename":{"SJAG_03920":null},"genotypes_by_uniquename":{"sdh3delta":{"display_name":"sdh3delta","display_uniquename":"sdh3delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03920:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03920:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:37164017":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000126":null,"FYECO:0000137":null,"FYPO:0002058":null}}


id: rga4delta
data:
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id: apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__cem1delta
data:
  {"alleles_by_uniquename":{"SJAG_01946:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01946","name":"cem1delta","uniquename":"SJAG_01946:allele-1"},"SJAG_03575:allele-1":{"allele_type":"amino_acid_mutation","description":"E548K ts","gene_uniquename":"SJAG_03575","name":"apc2-361","uniquename":"SJAG_03575:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"multi_locus_phenotype":[{"annotations":[115225],"is_not":false,"summary":null,"term":"FYPO:0000674"}]},"display_name":"apc2-361(E548K ts) cem1delta","display_uniquename":"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__cem1delta","genes_by_uniquename":{"SJAG_01946":null,"SJAG_03575":null},"genotypes_by_uniquename":{"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__cem1delta":{"display_name":"apc2-361(E548K ts) cem1delta","display_uniquename":"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__cem1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03575:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_01946:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03575:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_01946:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:23786411":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000004":null,"FYECO:0000137":null,"FYPO:0000674":null}}


id: vps25delta
data:
  {"alleles_by_uniquename":{"SJAG_04912:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04912","name":"vps25delta","uniquename":"SJAG_04912:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115407],"is_not":false,"summary":null,"term":"FYPO:0001440"}]},"display_name":"vps25delta","display_uniquename":"vps25delta","genes_by_uniquename":{"SJAG_04912":null},"genotypes_by_uniquename":{"vps25delta":{"display_name":"vps25delta","display_uniquename":"vps25delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04912:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04912:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:32109380":null},"taxonid":4897,"terms_by_termid":{"FYPO:0001440":null,"FYPO_EXT:0000001":null,"GO:0000815":null}}


id: rdp1delta
data:
  {"alleles_by_uniquename":{"SJAG_03356:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03356","name":"rdp1delta","uniquename":"SJAG_03356:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115474],"is_not":false,"summary":null,"term":"FYPO:0002061"}]},"display_name":"rdp1delta","display_uniquename":"rdp1delta","genes_by_uniquename":{"SJAG_03356":null},"genotypes_by_uniquename":{"rdp1delta":{"display_name":"rdp1delta","display_uniquename":"rdp1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03356:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03356:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:35226668":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000162":null,"FYPO:0002061":null}}


id: rim20E308V-E308V-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: nup132delta
data:
  {"alleles_by_uniquename":{"SJAG_01374:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01374","name":"nup132delta","uniquename":"SJAG_01374:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115371],"is_not":false,"summary":null,"term":"FYPO:0003973"}]},"display_name":"nup132delta","display_uniquename":"nup132delta","genes_by_uniquename":{"SJAG_01374":null},"genotypes_by_uniquename":{"nup132delta":{"display_name":"nup132delta","display_uniquename":"nup132delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01374:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01374:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:33495454":null},"taxonid":4897,"terms_by_termid":{"FYPO:0003973":null}}


id: did4delta
data:
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id:
  apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2-51-Y189D_cold_sensitive-amino_acid_mutation-expression-not_assayed_or_wild_type

data:
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id: cut23-415-A186T_ts-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: ace2delta
data:
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id: arb2delta
data:
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id: ned1cat-D422E,D424E-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
  {"alleles_by_uniquename":{"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"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115697],"is_not":false,"summary":null,"term":"FYPO:0001556"}]},"display_name":"ned1cat(D422E,D424E aa)","display_uniquename":"ned1cat-D422E,D424E-amino_acid_mutation-expression-not_assayed_or_wild_type","genes_by_uniquename":{"SJAG_02763":null},"genotypes_by_uniquename":{"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"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-2","expression":"Not assayed or wild type"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:26774782":null},"taxonid":4897,"terms_by_termid":{"FYPO:0001556":null,"FYPO_EXT:0000001":null}}


id: acb1delta
data:
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id:
  lig4::KanMX6-RNA_sequencing_revealed_that_only_the_5'_end_of_the_disrupted_allele_showed_low_RNA_expression_and_coverage-disruption-expression-knockdown

data:
  {"alleles_by_uniquename":{"SJAG_02527:allele-1":{"allele_type":"disruption","description":"RNA sequencing revealed that only the 5' end of the disrupted allele showed low RNA expression and coverage","gene_uniquename":"SJAG_02527","name":"lig4::KanMX6","uniquename":"SJAG_02527:allele-1"}},"annotation_count":7,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115597],"is_not":false,"summary":null,"term":"FYPO:0007776"},{"annotations":[115599],"is_not":false,"summary":null,"term":"FYPO:0009111"},{"annotations":[115596],"is_not":false,"summary":null,"term":"FYPO:0000588"},{"annotations":[115602],"is_not":false,"summary":null,"term":"FYPO:0005705"},{"annotations":[115600],"is_not":false,"summary":null,"term":"FYPO:0005231"},{"annotations":[115598],"is_not":false,"summary":null,"term":"FYPO:0000097"},{"annotations":[115601],"is_not":false,"summary":null,"term":"FYPO:0001408"}]},"display_name":"lig4::KanMX6(RNA sequencing revealed that only the 5' end of the disrupted allele showed low RNA expression and coverage)[Knockdown]","display_uniquename":"lig4::KanMX6-RNA_sequencing_revealed_that_only_the_5'_end_of_the_disrupted_allele_showed_low_RNA_expression_and_coverage-disruption-expression-knockdown","genes_by_uniquename":{"SJAG_02527":null},"genotypes_by_uniquename":{"lig4::KanMX6-RNA_sequencing_revealed_that_only_the_5'_end_of_the_disrupted_allele_showed_low_RNA_expression_and_coverage-disruption-expression-knockdown":{"display_name":"lig4::KanMX6(RNA sequencing revealed that only the 5' end of the disrupted allele showed low RNA expression and coverage)[Knockdown]","display_uniquename":"lig4::KanMX6-RNA_sequencing_revealed_that_only_the_5'_end_of_the_disrupted_allele_showed_low_RNA_expression_and_coverage-disruption-expression-knockdown","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02527:allele-1","expression":"Knockdown"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02527:allele-1","expression":"Knockdown"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:37233261":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000081":null,"FYECO:0000117":null,"FYECO:0000126":null,"FYECO:0000137":null,"FYECO:0000315":null,"FYPO:0000097":null,"FYPO:0000588":null,"FYPO:0001408":null,"FYPO:0005231":null,"FYPO:0005705":null,"FYPO:0007776":null,"FYPO:0009111":null}}


id: ndi1delta
data:
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id: ago1delta
data:
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id: arb1delta
data:
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id: ago1delta__leo1delta
data:
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id: mkh1delta
data:
  {"alleles_by_uniquename":{"SJAG_03753:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03753","name":"mkh1delta","uniquename":"SJAG_03753:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115624],"is_not":false,"summary":null,"term":"FYPO:0000124"}]},"display_name":"mkh1delta","display_uniquename":"mkh1delta","genes_by_uniquename":{"SJAG_03753":null},"genotypes_by_uniquename":{"mkh1delta":{"display_name":"mkh1delta","display_uniquename":"mkh1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03753:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03753:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:29566183":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000137":null,"FYPO:0000124":null}}


id: pck1delta__pmk1delta
data:
  {"alleles_by_uniquename":{"SJAG_01787:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01787","name":"pck1delta","uniquename":"SJAG_01787:allele-1"},"SJAG_04551:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04551","name":"pmk1delta","uniquename":"SJAG_04551:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"multi_locus_phenotype":[{"annotations":[115524],"is_not":false,"summary":null,"term":"FYPO:0007780"}]},"display_name":"pck1delta pmk1delta","display_uniquename":"pck1delta__pmk1delta","genes_by_uniquename":{"SJAG_01787":null,"SJAG_04551":null},"genotypes_by_uniquename":{"pck1delta__pmk1delta":{"display_name":"pck1delta pmk1delta","display_uniquename":"pck1delta__pmk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01787:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04551:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01787:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04551:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:34198697":null},"taxonid":4897,"terms_by_termid":{"FYPO:0007780":null,"FYPO_EXT:0000001":null}}


id: clr4delta__leo1delta
data:
  {"alleles_by_uniquename":{"SJAG_03118:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03118","name":"leo1delta","uniquename":"SJAG_03118:allele-1"},"SJAG_04574:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04574","name":"clr4delta","uniquename":"SJAG_04574:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"multi_locus_phenotype":[{"annotations":[115487],"is_not":false,"summary":null,"term":"FYPO:0002061"}]},"display_name":"clr4delta leo1delta","display_uniquename":"clr4delta__leo1delta","genes_by_uniquename":{"SJAG_03118":null,"SJAG_04574":null},"genotypes_by_uniquename":{"clr4delta__leo1delta":{"display_name":"clr4delta leo1delta","display_uniquename":"clr4delta__leo1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04574:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03118:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04574:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03118:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:35226668":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000162":null,"FYPO:0002061":null}}


id: mdh1delta
data:
  {"alleles_by_uniquename":{"SJAG_01753:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01753","name":"mdh1delta","uniquename":"SJAG_01753:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115276],"is_not":false,"summary":null,"term":"FYPO:0002058"}]},"display_name":"mdh1delta","display_uniquename":"mdh1delta","genes_by_uniquename":{"SJAG_01753":null},"genotypes_by_uniquename":{"mdh1delta":{"display_name":"mdh1delta","display_uniquename":"mdh1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01753:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01753:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:37164017":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000126":null,"FYECO:0000137":null,"FYPO:0002058":null}}


id: ura4delta
data:
  {"alleles_by_uniquename":{"SJAG_03164:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03164","name":"ura4delta","uniquename":"SJAG_03164:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115736],"is_not":false,"summary":null,"term":"FYPO:0001012"}]},"display_name":"ura4delta","display_uniquename":"ura4delta","genes_by_uniquename":{"SJAG_03164":null},"genotypes_by_uniquename":{"ura4delta":{"display_name":"ura4delta","display_uniquename":"ura4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03164:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03164:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:19330769":null},"taxonid":4897,"terms_by_termid":{"FYPO:0001012":null}}


id: rga4delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
  {"alleles_by_uniquename":{"SJAG_04280:allele-2":{"allele_type":"amino_acid_mutation","description":"T582G","gene_uniquename":"SJAG_04280","name":"wee1-as8","uniquename":"SJAG_04280:allele-2"},"SJAG_04522:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04522","name":"rga4delta","uniquename":"SJAG_04522:allele-1"}},"annotation_count":2,"annotation_details":{},"comment":null,"cv_annotations":{"multi_locus_phenotype":[{"annotations":[115326],"is_not":false,"summary":null,"term":"FYPO:0007783"},{"annotations":[115328],"is_not":false,"summary":null,"term":"FYPO:0001369"}]},"display_name":"rga4delta wee1-as8(T582G aa)","display_uniquename":"rga4delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type","genes_by_uniquename":{"SJAG_04280":null,"SJAG_04522":null},"genotypes_by_uniquename":{"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"}]}]}},"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"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:30664646":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYECO:0000338":null,"FYPO:0001369":null,"FYPO:0007783":null,"FYPO_EXT:0000001":null}}


id: pyk1-A343T-A343T-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: mid2delta
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id: spk1delta
data:
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id: mid1delta__mid2delta
data:
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id: mad2delta
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id: cdc25-D9-I30T,T572P-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: byr2delta
data:
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id: rga4delta__wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: rad25delta
data:
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id: rad9delta
data:
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id: oar2-dm12-R72A,L75A,R106A,L109A-amino_acid_mutation-expression-overexpression
data:
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id: rip1delta
data:
  {"alleles_by_uniquename":{"SJAG_00601:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00601","name":"rip1delta","uniquename":"SJAG_00601:allele-1"}},"annotation_count":6,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115269],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115263],"is_not":false,"summary":null,"term":"FYPO:0000760"},{"annotations":[115265],"is_not":false,"summary":null,"term":"FYPO:0000579"},{"annotations":[115264],"is_not":false,"summary":null,"term":"FYPO:0000590"},{"annotations":[115261,115262],"is_not":false,"summary":null,"term":"FYPO:0001357"}]},"display_name":"rip1delta","display_uniquename":"rip1delta","genes_by_uniquename":{"SJAG_00601":null},"genotypes_by_uniquename":{"rip1delta":{"display_name":"rip1delta","display_uniquename":"rip1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00601:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00601:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:37164017":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000015":null,"FYECO:0000126":null,"FYECO:0000137":null,"FYPO:0000579":null,"FYPO:0000590":null,"FYPO:0000760":null,"FYPO:0001357":null,"FYPO:0007790":null}}


id: frameshift-aa61->stop-nonsense_mutation-expression-not_assayed_or_wild_type
data:
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id: scd1delta
data:
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id: gpd1delta
data:
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id: SJAG_00124delta__sty1delta
data:
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id: gms1delta
data:
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id: mid1-delta(711-723_a.a.)-711-723-partial_amino_acid_deletion-expression-not_assayed_or_wild_type
data:
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id: wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: vps28delta
data:
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id: pyp1delta
data:
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id: wis1delta
data:
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id: chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type__rad24delta
data:
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id: mid1delta__pom1delta
data:
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id: rga6delta
data:
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id: dcr1delta__frameshift-aa61->stop-nonsense_mutation-expression-not_assayed_or_wild_type
data:
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id: pka1delta
data:
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id: rad24delta
data:
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id: ste11delta
data:
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id: nem1delta
data:
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id: for3delta
data:
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id: dcr1delta__leo1delta
data:
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id: tip1delta
data:
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id: mpe1-R77W-R77W-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: nuc2-1051-E405K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: Pmk1Sp-Pmk1_from_S._pombe-other-expression-not_assayed_or_wild_type
data:
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id: SJAG_00124delta
data:
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id: rad51delta
data:
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id: man1delta
data:
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id: apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2delta
data:
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id: tel1delta
data:
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id:
  Pmk1Sj(ins82-105)-82-NITCIYDLDIIINPYNFNEVYIYEE-105-amino_acid_insertion-expression-not_assayed_or_wild_type

data:
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id: Vps4-EQ-E233Q-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: rga6delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
  {"alleles_by_uniquename":{"SJAG_00028:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00028","name":"rga6delta","uniquename":"SJAG_00028: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"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"multi_locus_phenotype":[{"annotations":[115331],"is_not":false,"summary":null,"term":"FYPO:0007783"}]},"display_name":"rga6delta wee1-as8(T582G aa)","display_uniquename":"rga6delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type","genes_by_uniquename":{"SJAG_00028":null,"SJAG_04280":null},"genotypes_by_uniquename":{"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"}]}]}},"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"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:30664646":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYECO:0000338":null,"FYPO:0007783":null,"FYPO_EXT:0000002":null}}


id: atf1delta
data:
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id: cdc15-A-L264P,P442T-amino_acid_mutation-expression-not_assayed_or_wild_type__mid1delta
data:
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id: nem2delta
data:
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id: pim1-R152C-R152C-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: ade6-domE-S427>stop-nonsense_mutation-expression-not_assayed_or_wild_type
data:
  {"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"}},"annotation_count":2,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115724,115735],"is_not":false,"summary":null,"term":"FYPO:0000747"}]},"display_name":"ade6-domE(S427>stop)","display_uniquename":"ade6-domE-S427>stop-nonsense_mutation-expression-not_assayed_or_wild_type","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"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-1","expression":"Not assayed or wild type"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:19330769":null,"PMID:21905090":null},"taxonid":4897,"terms_by_termid":{"FYPO:0000747":null}}


id: bbl1-P363S-P363S-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: sst4delta
data:
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id: cmp7delta
data:
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id:
  apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2-dm12-R72A,L75A,R106A,L109A-amino_acid_mutation-expression-overexpression

data:
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id: nur1delta
data:
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id: wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: wee1delta
data:
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id: pck2delta
data:
  {"alleles_by_uniquename":{"SJAG_00610:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00610","name":"pck2delta","uniquename":"SJAG_00610:allele-1"}},"annotation_count":5,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115522],"is_not":false,"summary":null,"term":"FYPO:0002678"},{"annotations":[115523],"is_not":false,"summary":null,"term":"FYPO:0007776"},{"annotations":[115521],"is_not":false,"summary":null,"term":"FYPO:0001838"},{"annotations":[115520],"is_not":false,"summary":null,"term":"FYPO:0007521"},{"annotations":[115519],"is_not":false,"summary":null,"term":"FYPO:0000079"}]},"display_name":"pck2delta","display_uniquename":"pck2delta","genes_by_uniquename":{"SJAG_00610":null,"SJAG_04551":null},"genotypes_by_uniquename":{"pck2delta":{"display_name":"pck2delta","display_uniquename":"pck2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00610:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00610:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:34198697":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000207":null,"FYECO:0000314":null,"FYPO:0000079":null,"FYPO:0001838":null,"FYPO:0002678":null,"FYPO:0007521":null,"FYPO:0007776":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null}}


id: scd2delta
data:
  {"alleles_by_uniquename":{"SJAG_01794:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01794","name":"scd2delta","uniquename":"SJAG_01794:allele-1"}},"annotation_count":4,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115606],"is_not":false,"summary":null,"term":"FYPO:0007789"},{"annotations":[115605],"is_not":false,"summary":null,"term":"FYPO:0001355"},{"annotations":[115604],"is_not":false,"summary":null,"term":"FYPO:0000280"},{"annotations":[115603],"is_not":false,"summary":null,"term":"FYPO:0002380"}]},"display_name":"scd2delta","display_uniquename":"scd2delta","genes_by_uniquename":{"SJAG_01794":null},"genotypes_by_uniquename":{"scd2delta":{"display_name":"scd2delta","display_uniquename":"scd2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01794:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01794:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:29566183":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000137":null,"FYPO:0000280":null,"FYPO:0001355":null,"FYPO:0002380":null,"FYPO:0007789":null}}


id: rad1delta
data:
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id: ned1-5A-S499A__S538A__T620A__T638A__S651A-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: nde1delta
data:
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id: nup61delta
data:
  {"alleles_by_uniquename":{"SJAG_04284:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04284","name":"nup61delta","uniquename":"SJAG_04284:allele-1"}},"annotation_count":2,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115722],"is_not":false,"summary":null,"term":"FYPO:0000619"},{"annotations":[115723],"is_not":false,"summary":null,"term":"FYPO:0000815"}]},"display_name":"nup61delta","display_uniquename":"nup61delta","genes_by_uniquename":{"SJAG_04284":null},"genotypes_by_uniquename":{"nup61delta":{"display_name":"nup61delta","display_uniquename":"nup61delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04284:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04284:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:28954740":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYPO:0000619":null,"FYPO:0000815":null,"FYPO_EXT:0000001":null}}


id: chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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