# refs

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


id: 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":[115532,115538],"is_not":false,"summary":null,"term":"GO:0097753"}],"cellular_component":[{"annotations":[115533,115534],"is_not":false,"summary":null,"term":"GO:0032541"},{"annotations":[115535,115536],"is_not":false,"summary":null,"term":"GO:0005643"}],"single_locus_phenotype":[{"annotations":[115537],"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: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:0000047
data:
  {"abstract":"This describes a method for supplying a NOT-qualified, IKR-evidenced GO annotation to a gene product, when general sequence homology considerations would suggest a function or location, or a role in a biological process, but where a curator has determined that the absence of key sequence residues, known to be required for an expected activity or location, indicating the gene product is unlikely to be able to carry out the implied activity, involvement in a process or cellular component location. This reference should only be used used when an IKR-evidenced annotation is made based on curator judgement from manually reviewing the sequence of the gene product and where no publication can be found to support the curators conclusion. It is preferable to cite a peer-reviewed publication (such as a PubMed identifier) for IKR-evidenced annotations whenever possible. Curators will have carefully reviewed the sequence of the annotated protein, and established that the key residues known to be required for an expected activity or location are not present. Inclusion of an identifier in the 'with/from' field, that highlights to the user the lacking residues(e.g. an alignment, domain or rule identifier) is absolutely required when annotating to IKR with this GO_REF. Documentation on the GOC website provides more details on the <a href = \"http://www.geneontology.org/GO.evidence.shtml#ikr\">correct use of the IKR evidence code</a>.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotation based on absence of key sequence residues.","uniquename":"GO_REF:0000047"}


id: PMID:25318672
data:
  {"abstract":"Excess fatty acids and sterols are stored as triacylglycerols and sterol esters in specialized cellular organelles, called lipid droplets. Understanding what determines the cellular amount of neutral lipids and their packaging into lipid droplets is of fundamental and applied interest. Using two species of fission yeast, we show that cycling cells deficient in the function of the ER-resident CDP-DG synthase Cds1 exhibit markedly increased triacylglycerol content and assemble large lipid droplets closely associated with the ER membranes. We demonstrate that these unusual structures recruit the triacylglycerol synthesis machinery and grow by expansion rather than by fusion. Our results suggest that interfering with the CDP-DG route of phosphatidic acid utilization rewires cellular metabolism to adopt a triacylglycerol-rich lifestyle reliant on the Kennedy pathway. ","alleles_by_uniquename":{"SJAG_00426:allele-1":{"allele_type":"amino_acid_mutation","description":"P363S","gene_uniquename":"SJAG_00426","name":"bbl1-P363S","uniquename":"SJAG_00426:allele-1"}},"annotation_curators":[{"annotation_count":8,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-05-17","authors":"He Y, Yam C, Pomraning K, Chin JS, Yew JY, Freitag M, Oliferenko S","authors_abbrev":"He Y et al.","canto_added_date":"2021-05-10 02:38:06","canto_annotation_status":"APPROVED","canto_approved_date":"2021-05-17 12:42:41","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-05-17 12:42:41","canto_session_key":"f89ee2d26032c510","canto_session_submitted_date":"2021-05-17 12:42:28","canto_triage_status":"Curatable","citation":"Mol Biol Cell 2014 Dec 15;25(25):4083-95","cv_annotations":{"biological_process":[{"annotations":[115628],"is_not":false,"summary":null,"term":"GO:0016024"}],"cellular_component":[{"annotations":[115629],"is_not":false,"summary":null,"term":"GO:0005783"}],"molecular_function":[{"annotations":[115627],"is_not":false,"summary":null,"term":"GO:0004605"}],"single_locus_phenotype":[{"annotations":[115631],"is_not":false,"summary":null,"term":"FYPO:0000356"},{"annotations":[115630],"is_not":false,"summary":null,"term":"FYPO:0006433"},{"annotations":[115633],"is_not":false,"summary":null,"term":"FYPO:0004695"},{"annotations":[115632],"is_not":false,"summary":null,"term":"FYPO:0002227"},{"annotations":[115634],"is_not":false,"summary":null,"term":"FYPO:0001357"}]},"doi":"10.1091/mbc.E14-03-0832","gene_count":1,"genes_by_uniquename":{"SJAG_00426":null},"genotypes_by_uniquename":{"bbl1-P363S-P363S-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"bbl1-P363S(aa)","display_uniquename":"bbl1-P363S-P363S-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00426:allele-1","expression":"Not assayed or wild type"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2014","pubmed_entrez_date":"2014-10-17","pubmed_publication_date":"15 Dec 2014","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000006":null,"FYECO:0000162":null,"FYPO:0000356":null,"FYPO:0001357":null,"FYPO:0002227":null,"FYPO:0004695":null,"FYPO:0006433":null,"FYPO_EXT:0000001":null,"GO:0004605":null,"GO:0005783":null,"GO:0008654":null,"GO:0016024":null},"title":"Increase in cellular triacylglycerol content and emergence of large ER-associated lipid droplets in the absence of CDP-DG synthase function.","uniquename":"PMID:25318672"}


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


id: GO_REF:0000117
data:
  {"abstract":"Association-Rule-Based Annotator (ARBA) predicts Gene Ontology (GO) terms among other types of functional annotation such as Protein Description (DE), Keywords (KW), Enzyme Commission numbers (EC), subcellular LOcation (LO), etc. For all annotation types, reviewed UniProtKB/Swiss-Prot records having manual annotations as reference data are used to perform the machine learning phase and generate prediction models. For GO terms, ARBA has an additional feature to augment reference data using the relations between GO terms in the GO graph. The data augmentation is based on adding more general annotations into records containing manual GO terms, which will result in richer reference data. The predicted GO terms are then propagated to all unreviewed UniProtKB/TrEMBL proteins that meet the conditions of ARBA models. GO annotations using this technique receive the evidence code Inferred from Electronic Annotation (IEA; ECO:0000501).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"UniProt","canto_curator_role":"JaponicusDB","cv_annotations":{"biological_process":[{"annotations":[59099,64384,67497],"is_not":false,"summary":null,"term":"GO:0006338"},{"annotations":[59331],"is_not":false,"summary":null,"term":"GO:0006281"},{"annotations":[67586],"is_not":false,"summary":null,"term":"GO:0016197"},{"annotations":[63313],"is_not":false,"summary":null,"term":"GO:0051649"},{"annotations":[59098,64383,67496],"is_not":false,"summary":null,"term":"GO:0010468"},{"annotations":[58775,65357],"is_not":false,"summary":null,"term":"GO:0006772"}],"cellular_component":[{"annotations":[63053],"is_not":false,"summary":null,"term":"GO:0005680"},{"annotations":[62454,65089],"is_not":false,"summary":null,"term":"GO:0005938"},{"annotations":[65088],"is_not":false,"summary":null,"term":"GO:0032153"},{"annotations":[58547],"is_not":false,"summary":null,"term":"GO:0000785"},{"annotations":[59152],"is_not":false,"summary":null,"term":"GO:0005737"}],"molecular_function":[{"annotations":[65090],"is_not":false,"summary":null,"term":"GO:0005096"},{"annotations":[59100],"is_not":false,"summary":null,"term":"GO:0097159"}]},"gene_count":13,"genes_by_uniquename":{"SJAG_00510":null,"SJAG_00551":null,"SJAG_00773":null,"SJAG_00907":null,"SJAG_01445":null,"SJAG_01742":null,"SJAG_01943":null,"SJAG_02047":null,"SJAG_03675":null,"SJAG_04180":null,"SJAG_05161":null,"SJAG_06608":null,"SJAG_06641":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0000785":null,"GO:0005096":null,"GO:0005680":null,"GO:0005737":null,"GO:0005938":null,"GO:0006281":null,"GO:0006338":null,"GO:0006772":null,"GO:0010468":null,"GO:0016197":null,"GO:0032153":null,"GO:0051649":null,"GO:0097159":null},"title":"Electronic Gene Ontology annotations created by ARBA machine learning models","uniquename":"GO_REF:0000117"}


id: PMID:12795405
data:
  {"abstract":"Spectrin, a component of the membrane skeleton in erythrocytes and other animal cells, has also been identified in plant and fungal cells. However, its postulated role, i.e., the maintenance of shape and elasticity of the plasma membrane, is probably not exerted in walled cells. To study spectrin in these cells, we chose yeasts because of a high morphological variability of their life cycle. The localization of spectrin in the cells and protoplasts of Saccharomyces cerevisiae and Schizosaccharomyces japonicus var. versatilis was detected by immunoblotting, indirect immunofluorescence, and immunogold electron microscopy techniques with the use of anti-chicken and anti-human erythrocyte spectrin antibodies. A protein band of 220-240 kDa and some bands of lower relative mass were detected in cell and protoplast extracts of both yeast strains. Spectrin-like proteins were revealed by fluorescence microscopy at cell surfaces and in vacuolar membranes. Immunogold-labelling showed spectrin-like proteins in the plasma membrane, endoplasmic reticulum, vacuoles, nuclei, vesicles, mitochondria, and cell walls. The topology of spectrin was not affected by actin depolymerization with Latrunculin B nor was it changed in either act1-1 or cdc42 mutants, under restrictive conditions. Under osmotic stress, both spectrin and actin were delocalized and appeared in the form of large clusters in the cytoplasm. It is concluded that a protein cross-reacting with spectrin antibodies is present in fission and budding yeasts. Generally, it is located in the proximity of the plasma membrane and other intracellular membranes, probably as a part of the membrane skeleton. No evidence of its relationship to either actin or growth zones of the cell can be provided.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Slaninová I, Holubárová A, Svoboda A","authors_abbrev":"Slaninová I et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Can J Microbiol 2003 Mar;49(3):189-96","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2003","pubmed_entrez_date":"2003-06-11","pubmed_publication_date":"Mar 2003","terms_by_termid":{},"title":"Immunodetection of spectrin-like proteins in yeasts.","uniquename":"PMID:12795405"}


id: PMID:11921097
data:
  {"abstract":"The dimorphic fission yeast Schizosaccharomyces japonicus has proved to be an excellent experimental model for the investigation of the eukaryotic cell. Here we show that it has a haplontic life cycle, in which the diploid phase is confined to the zygote. To make it amenable to genetic and molecular analysis, we generated genetic markers and cloned a genomic sequence which acts as ars when integrated into a plasmid. Diploids suitable for testing complementation and recombination between markers can be formed by protoplast fusion. The complementation tests and the recombination frequencies determined in octads of spores identified 28 non-allelic groups (genes) of mutations of the auxotrophic and mycelium-negative mutants. Two groups of linked markers were also identified. The cloned fragment, which expresses ars activity, encodes a putative amino acid sequence highly similar to a conserved domain of proteins Cut1 (Schizosaccharomyces pombe), BimB (Aspergillus nidulans) and Esp1 (Saccharomyces cerevisiae).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Bozsik A, Szilagyi Z, Benko Z, Sipiczki M","authors_abbrev":"Bozsik A et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Yeast 2002 Apr;19(6):485-98","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":"2002-03-29","pubmed_publication_date":"Apr 2002","terms_by_termid":{},"title":"Marker construction and cloning of a cut1-like sequence with ARS activity in the fission yeast Schizosaccharomyces japonicus.","uniquename":"PMID:11921097"}


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


id: PMID:23145069
data:
  {"abstract":"The ERH gene encodes a highly conserved small nuclear protein with a unique amino acid sequence and three-dimensional structure but unknown function. The gene is present in animals, plants, and protists but to date has only been found in few fungi. Here we report that ERH homologs are also present in all four species from the genus Schizosaccharomyces, S. pombe, S. octosporus, S. cryophilus, and S. japonicus, which, however, are an exception in this respect among Ascomycota and Basidiomycota. The ERH protein sequence is moderately conserved within the genus (58% identity between S. pombe and S.japonicus), but the intron-rich genes have almost identical intron-exon organizations in all four species. In S. pombe, erh1(+) is expressed at a roughly constant level during vegetative growth and adaptation to unfavorable conditions such as nutrient limitation and hyperosmotic stress caused by sorbitol. Erh1p localizes preferentially to the nucleus with the exception of the nucleolus, but is also present in the cytoplasm. Cells lacking erh1(+) have an aberrant cell morphology and a comma-like shape when cultured to the stationary phase, and exhibit a delayed recovery from this phase followed by slower growth. Loss of erh1(+) in an auxotrophic background results in enhanced arrest in the G1 phase following nutritional stress, and also leads to hypersensitivity to agents inducing hyperosmotic stress (sorbitol), inhibiting DNA replication (hydroxyurea), and destabilizing the plasma membrane (SDS); this hypersensitivity can be abolished by expression of S. pombe erh1(+) and, to a lesser extent, S. japonicus erh1(+) or human ERH. Erh1p fails to interact with the human Ciz1 and PDIP46/SKAR proteins, known molecular partners of human ERH. Our data suggest that in Schizosaccharomyces sp. erh1(+) is non-essential for normal growth and Erh1p could play a role in response to adverse environmental conditions and in cell cycle regulation.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Krzyzanowski MK, Kozlowska E, Kozlowski P","authors_abbrev":"Krzyzanowski MK et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"PLoS One 2012;7(11):e49059","cv_annotations":{},"doi":"10.1371/journal.pone.0049059","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":"2012-11-13","pubmed_publication_date":"2012","terms_by_termid":{},"title":"Identification and functional analysis of the erh1(+) gene encoding enhancer of rudimentary homolog from the fission yeast Schizosaccharomyces pombe.","uniquename":"PMID:23145069"}


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


id: GO_REF:0000003
data:
  {"abstract":"Transitive assignment using Enzyme Commission identifiers. This method is used for any database entry, such as a protein record in UniProtKB or TrEMBL, that has had an Enzyme Commission number assigned. The corresponding GO term is determined using the EC cross-references in the GO molecular function ontology. Also see Hill et al., Genomics (2001) 74:121-128. The mapping file is available at http://www.geneontology.org/external2go/ec2go.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GOA curators, MGI curators","canto_curator_role":"JaponicusDB","cv_annotations":{"molecular_function":[{"annotations":[68411],"is_not":false,"summary":null,"term":"GO:0003925"},{"annotations":[59030],"is_not":false,"summary":null,"term":"GO:0043864"},{"annotations":[65175],"is_not":false,"summary":null,"term":"GO:0052832"},{"annotations":[65176],"is_not":false,"summary":null,"term":"GO:0052833"},{"annotations":[67974],"is_not":false,"summary":null,"term":"GO:1990817"}]},"gene_count":4,"genes_by_uniquename":{"SJAG_02383":null,"SJAG_02721":null,"SJAG_03739":null,"SJAG_04509":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0003925":null,"GO:0043864":null,"GO:0052832":null,"GO:0052833":null,"GO:1990817":null},"title":"Gene Ontology annotation based on Enzyme Commission mapping","uniquename":"GO_REF:0000003"}


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


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


id: PMID:32109380
data:
  {"abstract":"Eukaryotic genomes are organized within the nucleus through interactions with inner nuclear membrane (INM) proteins. How chromatin tethering to the INM is controlled in interphase and how this process contributes to subsequent mitotic nuclear envelope (NE) remodeling remains unclear. We have probed these fundamental questions using the fission yeast Schizosaccharomyces japonicus, which breaks and reforms the NE during mitosis. We show that attachments between heterochromatin and the transmembrane Lem2-Nur1 complex at the INM are remodeled in interphase by the ESCRT-III/Vps4 machinery. Failure of ESCRT-III/Vps4 to release Lem2-Nur1 from heterochromatin leads to persistent association of chromosomes with the INM throughout mitosis. At mitotic exit, such trapping of Lem2-Nur1 on heterochromatin prevents it from re-establishing nucleocytoplasmic compartmentalization. Our work identifies the Lem2-Nur1 complex as a substrate for the nuclear ESCRT machinery and explains how the dynamic tethering of chromosomes to the INM is linked to the establishment of nuclear compartmentalization.","alleles_by_uniquename":{"SJAG_01050:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01050","name":"nur1delta","uniquename":"SJAG_01050:allele-1"},"SJAG_01242:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01242","name":"vps32delta","uniquename":"SJAG_01242:allele-1"},"SJAG_01330:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01330","name":"mad2delta","uniquename":"SJAG_01330:allele-1"},"SJAG_01745:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01745","name":"lem2delta","uniquename":"SJAG_01745:allele-1"},"SJAG_03250:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03250","name":"sst4delta","uniquename":"SJAG_03250:allele-1"},"SJAG_03783:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03783","name":"vps24delta","uniquename":"SJAG_03783:allele-1"},"SJAG_03892:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03892","name":"vps4delta","uniquename":"SJAG_03892:allele-1"},"SJAG_03892:allele-2":{"allele_type":"amino_acid_mutation","description":"E233Q","gene_uniquename":"SJAG_03892","name":"Vps4-EQ","uniquename":"SJAG_03892:allele-2"},"SJAG_03892:allele-3":{"allele_type":"amino_acid_mutation","description":"I307T L327S","gene_uniquename":"SJAG_03892","name":"vps4-ts","uniquename":"SJAG_03892:allele-3"},"SJAG_04349:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04349","name":"vps28delta","uniquename":"SJAG_04349:allele-1"},"SJAG_04489:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04489","name":"did4delta","uniquename":"SJAG_04489:allele-1"},"SJAG_04912:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04912","name":"vps25delta","uniquename":"SJAG_04912:allele-1"},"SJAG_05207:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_05207","name":"cmp7delta","uniquename":"SJAG_05207:allele-1"}},"annotation_curators":[{"annotation_count":53,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-06-17","authors":"Pieper GH, Sprenger S, Teis D, Oliferenko S","authors_abbrev":"Pieper GH et al.","canto_added_date":"2021-05-10 02:37:07","canto_annotation_status":"APPROVED","canto_approved_date":"2021-06-17 17:46:25","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-06-17 17:46:25","canto_session_key":"89c611dbc0229af1","canto_session_submitted_date":"2021-06-17 17:46:16","canto_triage_status":"Curatable","citation":"Dev Cell 2020 04 06;53(1):27-41.e6","cv_annotations":{"cellular_component":[{"annotations":[115307],"is_not":false,"summary":null,"term":"GO:0000781"},{"annotations":[115305],"is_not":false,"summary":null,"term":"GO:0005783"},{"annotations":[115327],"is_not":false,"summary":null,"term":"GO:0000792"},{"annotations":[115332],"is_not":false,"summary":null,"term":"GO:1990343"},{"annotations":[115289],"is_not":false,"summary":null,"term":"GO:0000776"},{"annotations":[115309],"is_not":false,"summary":null,"term":"GO:0005771"},{"annotations":[115311],"is_not":false,"summary":null,"term":"GO:0032585"},{"annotations":[115310,115312],"is_not":false,"summary":null,"term":"GO:0031965"},{"annotations":[115333],"is_not":false,"summary":null,"term":"GO:0005643"},{"annotations":[115290,115295,115313],"is_not":false,"summary":null,"term":"GO:0005816"}],"molecular_function":[{"annotations":[115288],"is_not":false,"summary":null,"term":"GO:0043515"}],"multi_locus_phenotype":[{"annotations":[115318],"is_not":false,"summary":null,"term":"FYPO:0007771"},{"annotations":[115329],"is_not":false,"summary":null,"term":"FYPO:0001132"}],"single_locus_phenotype":[{"annotations":[115314,115315,115316],"is_not":false,"summary":null,"term":"FYPO:0001440"},{"annotations":[115325,115326],"is_not":false,"summary":null,"term":"FYPO:0001370"},{"annotations":[115328],"is_not":false,"summary":null,"term":"FYPO:0004718"},{"annotations":[115293,115294,115300,115301,115303,115304,115317,115319,115320,115321,115322,115323,115324],"is_not":false,"summary":null,"term":"FYPO:0007771"},{"annotations":[115306],"is_not":false,"summary":null,"term":"FYPO:0004318"},{"annotations":[115297],"is_not":false,"summary":null,"term":"FYPO:0007073"},{"annotations":[115291,115292,115298,115299],"is_not":false,"summary":null,"term":"FYPO:0007772"},{"annotations":[115302],"is_not":false,"summary":null,"term":"FYPO:0007770"},{"annotations":[115308],"is_not":false,"summary":null,"term":"FYPO:0003780"},{"annotations":[115296],"is_not":false,"summary":null,"term":"FYPO:0003657"},{"annotations":[115330,115331],"is_not":false,"summary":null,"term":"FYPO:0001234"}]},"doi":"10.1016/j.devcel.2020.01.028","gene_count":15,"genes_by_uniquename":{"SJAG_00684":null,"SJAG_01050":null,"SJAG_01242":null,"SJAG_01330":null,"SJAG_01601":null,"SJAG_01745":null,"SJAG_01777":null,"SJAG_03250":null,"SJAG_03299":null,"SJAG_03783":null,"SJAG_03892":null,"SJAG_04349":null,"SJAG_04489":null,"SJAG_04912":null,"SJAG_05207":null},"genotypes_by_uniquename":{"Vps4-EQ-E233Q-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"Vps4-EQ(E233Q aa)","display_uniquename":"Vps4-EQ-E233Q-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03892:allele-2","expression":"Not assayed or wild type"}]}]},"cmp7delta":{"display_name":"cmp7delta","display_uniquename":"cmp7delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_05207:allele-1","expression":"Null"}]}]},"cmp7delta__vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cmp7delta vps4-ts(I307T L327S aa)","display_uniquename":"cmp7delta__vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_05207:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03892:allele-3","expression":"Not assayed or wild type"}]}]},"did4delta":{"display_name":"did4delta","display_uniquename":"did4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04489:allele-1","expression":"Null"}]}]},"lem2delta":{"display_name":"lem2delta","display_uniquename":"lem2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01745:allele-1","expression":"Null"}]}]},"mad2delta":{"display_name":"mad2delta","display_uniquename":"mad2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01330:allele-1","expression":"Null"}]}]},"nur1delta":{"display_name":"nur1delta","display_uniquename":"nur1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01050:allele-1","expression":"Null"}]}]},"nur1delta__vps4delta":{"display_name":"nur1delta vps4delta","display_uniquename":"nur1delta__vps4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01050:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03892:allele-1","expression":"Null"}]}]},"sst4delta":{"display_name":"sst4delta","display_uniquename":"sst4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03250:allele-1","expression":"Null"}]}]},"vps24delta":{"display_name":"vps24delta","display_uniquename":"vps24delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03783:allele-1","expression":"Null"}]}]},"vps25delta":{"display_name":"vps25delta","display_uniquename":"vps25delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04912:allele-1","expression":"Null"}]}]},"vps28delta":{"display_name":"vps28delta","display_uniquename":"vps28delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04349:allele-1","expression":"Null"}]}]},"vps32delta":{"display_name":"vps32delta","display_uniquename":"vps32delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01242:allele-1","expression":"Null"}]}]},"vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"vps4-ts(I307T L327S aa)","display_uniquename":"vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03892:allele-3","expression":"Not assayed or wild type"}]}]},"vps4delta":{"display_name":"vps4delta","display_uniquename":"vps4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03892:allele-1","expression":"Null"}]}]}},"ltp_gene_count":15,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_01242","interactor_uniquename":"SJAG_03892","reference_uniquename":"PMID:32109380","throughput":"low"},{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_04489","interactor_uniquename":"SJAG_03892","reference_uniquename":"PMID:32109380","throughput":"low"},{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_05207","interactor_uniquename":"SJAG_01242","reference_uniquename":"PMID:32109380","throughput":"low"},{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_05207","interactor_uniquename":"SJAG_01745","reference_uniquename":"PMID:32109380","throughput":"low"},{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_05207","interactor_uniquename":"SJAG_03892","reference_uniquename":"PMID:32109380","throughput":"low"}],"publication_year":"2020","pubmed_entrez_date":"2020-02-29","pubmed_publication_date":"06 04 2020","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000137":null,"FYPO:0001132":null,"FYPO:0001234":null,"FYPO:0001370":null,"FYPO:0001440":null,"FYPO:0003657":null,"FYPO:0003780":null,"FYPO:0004318":null,"FYPO:0004718":null,"FYPO:0007073":null,"FYPO:0007770":null,"FYPO:0007771":null,"FYPO:0007772":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"GO:0000093":null,"GO:0000776":null,"GO:0000781":null,"GO:0000792":null,"GO:0000815":null,"GO:0005643":null,"GO:0005771":null,"GO:0005783":null,"GO:0005816":null,"GO:0031965":null,"GO:0032585":null,"GO:0043515":null,"GO:1990343":null},"title":"ESCRT-III/Vps4 Controls Heterochromatin-Nuclear Envelope Attachments.","uniquename":"PMID:32109380"}


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


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


id: GO_REF:0000119
data:
  {"abstract":"The Alliance of Genome Resources (https://www.alliancegenome.org/) has procedures in place to establish orthology relationships","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"The Gene Ontology Consortium","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Automated transfer of experimentally-verified manual GO annotation data to mouse-human orthologs","uniquename":"GO_REF:0000119"}


id: GO_REF:0000054
data:
  {"abstract":"LIFEdb is a database that was created to manage the experimental data produced by the German Cancer Research Institute (DKFZ) and its collaborators, from work on cDNAs contained in the German cDNA Consortium collection. <br>A novel cloning technology was used to rapidly generate N- and C-terminal green fluorescent protein fusions of cDNAs to examine the intracellular localizations of expressed fusion proteins in living cells. GO Cellular Component terms are manually assigned by curators studying fluorescence microscope images of cells labelled with GFP-fused cDNAs. Protein coding regions of novel full length cDNAs are tagged with the coding sequence of the green fluorescent protein, the fusion proteins are then expressed and analyzed for their subcellular localization. <br>Prior to February 2013, all LIFEdb annotations were referenced by PMID: 11256614 (Simpson et al. 2000 EMBO Rep. 1:287-292), a paper describing the protein subcellular localization pilot study and methodology used by LIFEdb. However, it has been decided that these annotations are more correctly described by a GO reference. <br>Resource URL: http://www.dkfz.de/en/mga/Groups/LIFEdb-Database.html <br>Protein subcellular localization images can be viewed on the LIFEdb website, http://www.dkfz.de/gpcf/lifedb.php","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"LIFEdb","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotation based on curation of intracellular localizations of expressed fusion proteins in living cells.","uniquename":"GO_REF:0000054"}


id: PMID:26343758
data:
  {"abstract":"CENP-A is a centromere-specific histone H3 variant that is required for kinetochore assembly and accurate chromosome segregation. For it to function properly, CENP-A must be specifically localized to centromeres. In fission yeast, Scm3sp and the Mis18 complex, composed of Mis16, Eic1, and Mis18, function as a CENP-A(Cnp1)-specific chaperone and a recruiting factor, respectively, and together ensure accurate delivery of CENP-A(Cnp1) to centromeres. Although how Scm3sp specifically recognizes CENP-A(Cnp1) has been revealed recently, the recruiting mechanism of CENP-A(Cnp1) via the Mis18 complex remains unknown. In this study, we have determined crystal structures of Schizosaccharomyces japonicus Mis16 alone and in complex with the helix 1 of histone H4 (H4α1). Crystal structures followed by mutant analysis and affinity pull-downs have revealed that Mis16 recognizes both H4α1 and Scm3sp independently within the CENP-A(Cnp1)/H4:Scm3sp complex. This observation suggests that Mis16 gains CENP-A(Cnp1) specificity by recognizing both Scm3sp and histone H4. Our studies provide insights into the molecular mechanisms underlying specific recruitment of CENP-A(Cnp1)/H4:Scm3sp into centromeres. ","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":4,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-05-13","authors":"An S, Kim H, Cho US","authors_abbrev":"An S et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-05-13 14:11:41","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Val Wood","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-05-13 14:11:41","canto_session_key":"fb189c5ef542852c","canto_session_submitted_date":"2021-05-12 16:00:22","canto_triage_status":"Curatable","citation":"J Mol Biol 2015 Oct 09;427(20):3230-3240","cv_annotations":{"molecular_function":[{"annotations":[115571,115572,115573,115574],"is_not":false,"summary":null,"term":"GO:0042393"}]},"doi":"10.1016/j.jmb.2015.08.022","gene_count":4,"genes_by_uniquename":{"SJAG_00303":null,"SJAG_02513":null,"SJAG_03542":null,"SJAG_03867":null},"genotypes_by_uniquename":{},"ltp_gene_count":3,"ortholog_annotations":[],"paralog_annotations":[],"pdb_entries":[{"entry_authors":"An S,Kim H,Cho U-S","entry_authors_abbrev":"An S et al.","experimental_method":"X-ray","gene_chains":[{"chain":"B","gene_uniquename":"SJAG_03542","position":"1-103"},{"chain":"A","gene_uniquename":"SJAG_03867","position":"1-427"}],"pdb_id":"4xyi","reference_uniquename":"PMID:26343758","resolution":"3.0","title":"Mis16 with H4 peptide"},{"entry_authors":"An S,Kim H,Cho U-S","entry_authors_abbrev":"An S et al.","experimental_method":"X-ray","gene_chains":[{"chain":"A","gene_uniquename":"SJAG_03867","position":"1-427"}],"pdb_id":"4xyh","reference_uniquename":"PMID:26343758","resolution":"2.3","title":"Wild-type full length Mis16 in Schizosaccharomyces japonicus"}],"physical_interactions":[],"publication_year":"2015","pubmed_entrez_date":"2015-09-08","pubmed_publication_date":"09 Oct 2015","terms_by_termid":{"GO:0042393":null},"title":"Mis16 Independently Recognizes Histone H4 and the CENP-ACnp1-Specific Chaperone Scm3sp.","uniquename":"PMID:26343758"}


id: PMID:20368354
data:
  {"abstract":"Dimorphic yeasts change between unicellular growth and filamentous growth. Many dimorphic yeasts species are pathogenic for humans and plants, being infectious as invasive hypha. We have studied the determinants of the dimorphic switch in the nonpathogenic fission yeast Schizosaccharomyces japonicus, which is evolutionarily close to the well-characterized fission yeast S. pombe. We report that camptothecin, an inhibitor of topoisomerase I, reversibly induced the unicellular to hyphal transition in S. japonicus at low concentrations of camptothecin that did not induce checkpoint arrest and the transition required the DNA checkpoint kinase Chk1. Furthermore, a mutation of chk1 induced hyphal transition without camptothecin. Thus, we identify a second function for Chk1 distinct from its role in checkpoint arrest. Activation of the switch from single cell bipolar growth to monopolar filamentous growth may assist cells to evade the source of DNA damage.","alleles_by_uniquename":{"SJAG_01410:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01410","name":"rad51delta","uniquename":"SJAG_01410:allele-1"},"SJAG_01605:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01605","name":"rad9delta","uniquename":"SJAG_01605:allele-1"},"SJAG_01680:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01680","name":"chk1delta","uniquename":"SJAG_01680:allele-1"},"SJAG_01680:allele-2":{"allele_type":"amino_acid_mutation","description":"P470L","gene_uniquename":"SJAG_01680","name":"chk1-P470L","synonyms":[{"name":"chk1- hyperactive (chk1-hyp)","reference":"PMID:23090706","type":"exact"},{"name":"chk1-hyperactive (chk1-hyp)","reference":"PMID:20368354","type":"exact"}],"uniquename":"SJAG_01680:allele-2"}},"annotation_curators":[{"annotation_count":6,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-21","authors":"Furuya K, Niki H","authors_abbrev":"Furuya K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-21 16:35:04","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-21 16:35:04","canto_session_key":"f81a194894ea8808","canto_session_submitted_date":"2022-11-21 16:34:55","canto_triage_status":"Curatable","citation":"Mol Cell Biol 2010 Jun;30(12):2909-17","cv_annotations":{"single_locus_phenotype":[{"annotations":[115643,115647],"is_not":false,"summary":null,"term":"FYPO:0007782"},{"annotations":[115642],"is_not":false,"summary":null,"term":"FYPO:0007774"},{"annotations":[115644,115645,115646],"is_not":false,"summary":null,"term":"FYPO:0000085"}]},"doi":"10.1128/MCB.00049-10","gene_count":3,"genes_by_uniquename":{"SJAG_01410":null,"SJAG_01605":null,"SJAG_01680":null},"genotypes_by_uniquename":{"chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"chk1-P470L(aa)","display_uniquename":"chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-2","expression":"Not assayed or wild type"}]}]},"chk1delta":{"display_name":"chk1delta","display_uniquename":"chk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-1","expression":"Null"}]}]},"rad51delta":{"display_name":"rad51delta","display_uniquename":"rad51delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01410:allele-1","expression":"Null"}]}]},"rad9delta":{"display_name":"rad9delta","display_uniquename":"rad9delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01605:allele-1","expression":"Null"}]}]}},"ltp_gene_count":3,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2010","pubmed_entrez_date":"2010-04-07","pubmed_publication_date":"Jun 2010","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYECO:0000314":null,"FYPO:0000085":null,"FYPO:0007774":null,"FYPO:0007782":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null},"title":"The DNA damage checkpoint regulates a transition between yeast and hyphal growth in Schizosaccharomyces japonicus.","uniquename":"PMID:20368354"}


id: PMID:36695178
data:
  {"abstract":"Nuclear envelope (NE) expansion must be controlled to maintain nuclear shape and function. The nuclear membrane expands massively during closed mitosis, enabling chromosome segregation within an intact NE. Phosphatidic acid (PA) and diacylglycerol (DG) can both serve as biosynthetic precursors for membrane lipid synthesis. How they are regulated in time and space and what the implications are of changes in their flux for mitotic fidelity are largely unknown. Using genetically encoded PA and DG probes, we show that DG is depleted from the inner nuclear membrane during mitosis in the fission yeast Schizosaccharomyces pombe, but PA does not accumulate, indicating that it is rerouted to membrane synthesis. We demonstrate that DG-to-PA conversion catalyzed by the diacylglycerol kinase Dgk1 (also known as Ptp4) and direct glycerophospholipid synthesis from DG by diacylglycerol cholinephosphotransferase/ethanolaminephosphotransferase Ept1 reinforce NE expansion. We conclude that DG consumption through both the de novo pathway and the Kennedy pathway fuels a spike in glycerophospholipid biosynthesis, controlling NE expansion and, ultimately, mitotic fidelity.","alleles_by_uniquename":{"SJAG_04883:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04883","name":"ptp4delta","uniquename":"SJAG_04883:allele-1"}},"annotation_curators":[{"annotation_count":1,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2023-03-02","authors":"Foo S, Cazenave-Gassiot A, Wenk MR, Oliferenko S","authors_abbrev":"Foo S et al.","canto_added_date":"2023-03-02 10:54:59","canto_annotation_status":"APPROVED","canto_approved_date":"2023-03-02 10:59:33","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2023-03-02 10:59:33","canto_session_key":"d8cda300a89f71aa","canto_session_submitted_date":"2023-03-02 10:59:20","canto_triage_status":"Curatable","citation":"J Cell Sci 2023 Feb 01;136(3)","cv_annotations":{"single_locus_phenotype":[{"annotations":[115527],"is_not":false,"summary":null,"term":"FYPO:0001007"}]},"doi":"10.1242/jcs.260568","gene_count":1,"genes_by_uniquename":{"SJAG_04883":null},"genotypes_by_uniquename":{"ptp4delta":{"display_name":"ptp4delta","display_uniquename":"ptp4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04883:allele-1","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2023","pubmed_entrez_date":"2023-01-25","pubmed_publication_date":"01 Feb 2023","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYPO:0001007":null},"title":"Diacylglycerol at the inner nuclear membrane fuels nuclear envelope expansion in closed mitosis.","uniquename":"PMID:36695178"}


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


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


id: PMID:2226803
data:
  {"abstract":"In the fission yeast Schizosaccharomyces pombe, the enzyme RNAse P copurifies with two RNAs, K1- and K2-RNA, which are identical except for their termini [1] and which are encoded by a single gene [2]. We have undertaken the cloning of the K-RNA genes in related organisms in order to gain comparative structural information. Because the K-RNA sequence is poorly conserved across species, we have cloned the K-RNA genes in the Schizosaccharomyces species S. malidevorans, S. japonicus, S. versatilis, and S. octosporus. Of the 4 species, only S. octosporus contains a K-RNA gene different from that in S. pombe; the gene diverges by 20%. Based on the two sequences, nuclease protection data and computer analysis, we have proposed a secondary structure model for the K-RNA. Northern analysis shows the K-RNA genes in all four Schizosaccharomyces species to be expressed as two RNAs, as in S. pombe.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Zimmerly S, Gamulin V, Burkard U, Söll D","authors_abbrev":"Zimmerly S et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"FEBS Lett 1990 Oct 01;271(1-2):189-93","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1990","pubmed_entrez_date":"1990-10-01","pubmed_publication_date":"01 Oct 1990","terms_by_termid":{},"title":"The RNA component of RNase P in Schizosaccharomyces species.","uniquename":"PMID:2226803"}


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


id: 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: PMID:23090706
data:
  {"abstract":"DNA damage response includes DNA repair, nucleotide metabolism and even a control of cell fates including differentiation, cell death pathway or some combination of these. The responses to DNA damage differ from species to species. Here we aim to delineate the checkpoint pathway in the dimorphic fission yeast Schizosaccharomyces japonicus, where DNA damage can trigger a differentiation pathway that is a switch from a bidirectional yeast growth mode to an apical hyphal growth mode, and the switching is regulated via a checkpoint kinase, Chk1. This Chk1-dependent switch to hyphal growth is activated with even low doses of agents that damage DNA; therefore, we reasoned that this switch may depend on other genes orthologous to the components of the classical Sz. pombe Chk1-dependent DNA checkpoint pathway. As an initial test of this hypothesis, we assessed the effects of mutations in Sz. japonicus orthologs of Sz. pombe checkpoint genes on this switch from bidirectional to hyphal growth. The same set of DNA checkpoint genes was confirmed in Sz. japonicus. We tested the effect of each DNA checkpoint mutants on hyphal differentiation by DNA damage. We found that the Sz. japonicus hyphal differentiation pathway was dependent on Sz. japonicus orthologs of Sz. pombe checkpoint genes-(SP)rad3, (SP)rad26, (SP)rad9, (SP)rad1, (SP)rad24, (SP)rad25, (SP)crb2, and (SP)chk1-that function in the DNA damage checkpoint pathway, but was not dependent on orthologs of two Sz. pombe genes-(SP)cds1 or (SP)mrc1-that function in the DNA replication checkpoint pathway. These findings indicated that although the role of each component of the DNA damage checkpoint and DNA replication checkpoint is mostly same between the two fission yeasts, the DNA damage checkpoint was the only pathway that governed DNA damage-dependent hyphal growth. We also examined whether DNA damage checkpoint signaling engaged in functional crosstalk with other hyphal differentiation pathways because hyphal differentiation can also be triggered by nutritional stress. Here, we discovered genetic interactions that indicated that the cAMP pathway engaged in crosstalk with Chk1-dependent signaling.","alleles_by_uniquename":{"SJAG_00364:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00364","name":"rad3delta","uniquename":"SJAG_00364:allele-1"},"SJAG_00429:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00429","name":"rad26delta","uniquename":"SJAG_00429:allele-1"},"SJAG_01205:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01205","name":"crb2delta","uniquename":"SJAG_01205:allele-1"},"SJAG_01605:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01605","name":"rad9delta","uniquename":"SJAG_01605:allele-1"},"SJAG_01680:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01680","name":"chk1delta","uniquename":"SJAG_01680:allele-1"},"SJAG_01680:allele-2":{"allele_type":"amino_acid_mutation","description":"P470L","gene_uniquename":"SJAG_01680","name":"chk1-P470L","synonyms":[{"name":"chk1- hyperactive (chk1-hyp)","reference":"PMID:23090706","type":"exact"},{"name":"chk1-hyperactive (chk1-hyp)","reference":"PMID:20368354","type":"exact"}],"uniquename":"SJAG_01680:allele-2"},"SJAG_02266:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02266","name":"rad24delta","uniquename":"SJAG_02266:allele-1"},"SJAG_02576:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02576","name":"rad25delta","uniquename":"SJAG_02576:allele-1"},"SJAG_02771:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02771","name":"rad1delta","uniquename":"SJAG_02771:allele-1"},"SJAG_03720:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03720","name":"tel1delta","uniquename":"SJAG_03720:allele-1"},"SJAG_04287:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04287","name":"cds1delta","uniquename":"SJAG_04287:allele-1"},"SJAG_04671:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04671","name":"mrc1delta","uniquename":"SJAG_04671:allele-1"}},"annotation_curators":[{"annotation_count":28,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-21","authors":"Furuya K, Niki H","authors_abbrev":"Furuya K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-21 17:21:20","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-21 17:21:20","canto_session_key":"5f68f94ee65a99b7","canto_session_submitted_date":"2022-11-21 17:21:13","canto_triage_status":"Curatable","citation":"Curr Genet 2012 Dec;58(5-6):291-303","cv_annotations":{"multi_locus_phenotype":[{"annotations":[115375],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115381],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[115378],"is_not":false,"summary":null,"term":"FYPO:0000088"}],"single_locus_phenotype":[{"annotations":[115366,115367,115368,115369,115370,115371,115373,115374],"is_not":false,"summary":null,"term":"FYPO:0007782"},{"annotations":[115392],"is_not":false,"summary":null,"term":"FYPO:0007774"},{"annotations":[115391],"is_not":false,"summary":null,"term":"FYPO:0001690"},{"annotations":[115365,115372],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115390],"is_not":false,"summary":null,"term":"FYPO:0004693"},{"annotations":[115379,115380,115385,115386,115387],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[115376,115377,115382,115383,115384],"is_not":false,"summary":null,"term":"FYPO:0000088"},{"annotations":[115388,115389],"is_not":false,"summary":null,"term":"FYPO:0001234"}]},"doi":"10.1007/s00294-012-0384-4","gene_count":11,"genes_by_uniquename":{"SJAG_00364":null,"SJAG_00429":null,"SJAG_01205":null,"SJAG_01605":null,"SJAG_01680":null,"SJAG_02266":null,"SJAG_02576":null,"SJAG_02771":null,"SJAG_03720":null,"SJAG_04287":null,"SJAG_04671":null},"genotypes_by_uniquename":{"cds1delta":{"display_name":"cds1delta","display_uniquename":"cds1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04287:allele-1","expression":"Null"}]}]},"chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type__rad24delta":{"display_name":"chk1-P470L(aa) rad24delta","display_uniquename":"chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type__rad24delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-2","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_02266:allele-1","expression":"Null"}]}]},"chk1delta":{"display_name":"chk1delta","display_uniquename":"chk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-1","expression":"Null"}]}]},"chk1delta__crb2delta":{"display_name":"chk1delta crb2delta","display_uniquename":"chk1delta__crb2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_01205:allele-1","expression":"Null"}]}]},"crb2delta":{"display_name":"crb2delta","display_uniquename":"crb2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01205:allele-1","expression":"Null"}]}]},"mrc1delta":{"display_name":"mrc1delta","display_uniquename":"mrc1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04671:allele-1","expression":"Null"}]}]},"rad1delta":{"display_name":"rad1delta","display_uniquename":"rad1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02771:allele-1","expression":"Null"}]}]},"rad24delta":{"display_name":"rad24delta","display_uniquename":"rad24delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02266:allele-1","expression":"Null"}]}]},"rad25delta":{"display_name":"rad25delta","display_uniquename":"rad25delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02576:allele-1","expression":"Null"}]}]},"rad26delta":{"display_name":"rad26delta","display_uniquename":"rad26delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00429:allele-1","expression":"Null"}]}]},"rad3delta":{"display_name":"rad3delta","display_uniquename":"rad3delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00364:allele-1","expression":"Null"}]}]},"rad9delta":{"display_name":"rad9delta","display_uniquename":"rad9delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01605:allele-1","expression":"Null"}]}]},"tel1delta":{"display_name":"tel1delta","display_uniquename":"tel1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03720:allele-1","expression":"Null"}]}]}},"ltp_gene_count":11,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-10-24","pubmed_publication_date":"Dec 2012","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYECO:0000314":null,"FYPO:0000085":null,"FYPO:0000088":null,"FYPO:0001234":null,"FYPO:0001690":null,"FYPO:0004693":null,"FYPO:0007774":null,"FYPO:0007782":null,"FYPO:0007790":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"FYPO_EXT:0000003":null},"title":"Hyphal differentiation induced via a DNA damage checkpoint-dependent pathway engaged in crosstalk with nutrient stress signaling in Schizosaccharomyces japonicus.","uniquename":"PMID:23090706"}


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


id: GO_REF:0000024
data:
  {"abstract":"Method for transferring manual annotations to an entry based on a curator's judgment of its similarity to a putative ortholog that has annotations that are supported with experimental evidence. Annotations are created when a curator judges that the sequence of a protein shows high similarity to another protein that has annotation(s) supported by experimental evidence (and therefore display one of the evidence codes EXP, IDA, IGI, IMP, IPI or IEP). Annotations resulting from the transfer of GO terms display the 'ISS' evidence code and include an accession for the protein from which the annotation was projected in the 'with' field (column 8). This field can contain either a UniProtKB accession or an IPI (International Protein Index) identifier. Only annotations with an experimental evidence code and which do not have the 'NOT' qualifier are transferred. Putative orthologs are chosen using information combined from a variety of complementary sources. Potential orthologs are initially identified using sequence similarity search programs such as BLAST. Orthology relationships are then verified manually using a combination of resources including sequence analysis tools, phylogenetic and comparative genomics databases such as Ensembl Compara, INPARANOID and OrthoMCL, as well as other specialised databases such as species-specific collections (e.g. HGNC's HCOP). In all cases curators check each alignment and use their experience to assess whether similarity is considered to be strong enough to infer that the two proteins have a common function so that they can confidently project an annotation. While there is no fixed cut-off point in percentage sequence similarity, generally proteins which have greater than 30% identity that covers greater than 80% of the length of both proteins are examined further. For mammalian proteins this cut-off tends to be higher, with an average of 80% identity over 90% of the length of both proteins. Strict orthologs are desirable but not essential. In general, when there is evidence of multiple paralogs for a single species, annotations using less specific GO terms are transferred to the paralogs, however, annotations using more specific GO terms may be transferred to the most similar paralog in each species, this decision is taken on a case by case basis and may be influenced by statements by researchers in the field. Further detailed information on this procedure, including how ISS annotations are made to protein isoforms, can be found at: http://www.ebi.ac.uk/GOA/ISS_method.html.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"AgBase, BHF-UCL, Parkinson's UK-UCL, dictyBase, HGNC, Roslin Institute, FlyBase and UniProtKB curators.","canto_curator_role":"JaponicusDB","cv_annotations":{"biological_process":[{"annotations":[79165],"is_not":false,"summary":null,"term":"GO:0000122"}],"cellular_component":[{"annotations":[79162],"is_not":false,"summary":null,"term":"GO:0005869"}],"molecular_function":[{"annotations":[79163],"is_not":false,"summary":null,"term":"GO:0001227"},{"annotations":[79164],"is_not":false,"summary":null,"term":"GO:0000978"}]},"gene_count":2,"genes_by_uniquename":{"SJAG_00124":null,"SJAG_01739":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0000122":null,"GO:0000978":null,"GO:0001227":null,"GO:0005869":null},"title":"Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity.","uniquename":"GO_REF:0000024"}


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


id: PMID:23934997
data:
  {"abstract":"Both budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccahromyces pombe have been very popular organisms used for biological research with eukaryotes for many decades. Judging from the fission yeast Schizosaccharomyces japonicus DNA sequence determined 2 years ago, this species is evolutionarily very much unrelated to the commonly used yeasts for research. Indicating evolutionary divergence, the S. japonicus makes 8-spored asci and mitosis occurs with a partial breakdown of nuclear membrane whereas the other yeasts make 4-spored asci and cells divide without nuclear breakdown. The commonly used yeast species exhibit a generation time between 1.5 and 2.0 hr, and their genetic cross takes a period of more than 7 working d. As described here, a generation time of only 63 min and meiotic analysis completed in just 2.5 d, the S. japonicus fission yeast is predicted to become a choice organism for future research on the biology of eukaryotes. ","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Klar AJ","authors_abbrev":"Klar AJ","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"G3 (Bethesda) 2013 Oct 03;3(10):1869-73","cv_annotations":{},"doi":"10.1534/g3.113.007187","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":"2013-08-13","pubmed_publication_date":"03 Oct 2013","terms_by_termid":{},"title":"Schizosaccharomyces japonicus yeast poised to become a favorite experimental organism for eukaryotic research.","uniquename":"PMID:23934997"}


id: PMID:33947067
data:
  {"abstract":"The fission yeast  Schizosaccharomyces japonicus , comprising  S. japonicus  var.  japonicus  and  S. japonicus  var.  versatilis  varieties, has unique characteristics such as striking hyphal growth not seen in other  Schizosaccharomyces  species; however, information on its diversity and evolution, in particular mating and sporulation, remains limited. Here we compared the growth and mating phenotypes of 17 wild strains of  S. japonicus , including eight  S. japonicus  var.  japonicus  strains newly isolated from an insect ( Drosophila ). Unlike existing wild strains isolated from fruits/plants, the strains isolated from  Drosophila  sporulated at high frequency even under nitrogen-abundant conditions. In addition, one of the strains from  Drosophila  was stained by iodine vapor, although the type strain of  S. japonicus  var.  japonicus  is not stained. Sequence analysis further showed that the nucleotide and amino acid sequences of pheromone-related genes have diversified among the eight strains from  Drosophila , suggesting crossing between  S. japonicus  cells of different genetic backgrounds occurs frequently in this insect. Much of yeast ecology remains unclear, but our findings suggest that insects such as  Drosophila  might be a good niche for mating and sporulation, and will provide a basis for the understanding of sporulation mechanisms via signal transduction, as well as the ecology and evolution of yeast.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Seike T, Sakata N, Matsuda F, Furusawa C","authors_abbrev":"Seike T et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"J Fungi (Basel) 2021 Apr 29;7(5)","cv_annotations":{},"doi":"10.3390/jof7050350","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":"2021-05-05","pubmed_publication_date":"29 Apr 2021","terms_by_termid":{},"title":"Elevated Sporulation Efficiency in Fission Yeast  Schizosaccharomyces japonicus  Strains Isolated from  Drosophila .","uniquename":"PMID:33947067"}


id: PMID:23786411
data:
  {"abstract":"Three types of mitosis, which are open, closed or semi-open mitosis, function in eukaryotic cells, respectively. The open mitosis involves breakage of the nuclear envelope before nuclear division, whereas the closed mitosis proceeds with an intact nuclear envelope. To understand the mechanism and significance of three types of mitotic division in eukaryotes, we investigated the process of semi-open mitosis, in which the nuclear envelope is only partially broken, in the fission yeast Schizosaccharomyces japonicus. In anaphase-promoting complex/cyclosome (APC/C) mutants of Sz. japonicus, the nuclear envelope remained relatively intact during anaphase, resulting in impaired semi-open mitosis. As a suppressor of apc2 mutant, a mutation of Oar2, which was a 3-oxoacyl-[acyl carrier protein] reductase, was obtained. The level of the Oar2, which had two destruction-box motifs recognized by APC/C, was increased in APC/C mutants. Furthermore, the defective semi-open mitosis observed in an apc2 mutant was restored by mutated oar2+. Based on these findings, we propose that APC/C regulates the dynamics of the nuclear envelope through degradation of Oar2 dependent on APC/C during the metaphase-to-anaphase transition of semi-open mitosis in Sz. japonicus.","alleles_by_uniquename":{"SJAG_01946:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01946","name":"cem1delta","uniquename":"SJAG_01946:allele-1"},"SJAG_01956:allele-1":{"allele_type":"amino_acid_mutation","description":"E405K ts","gene_uniquename":"SJAG_01956","name":"nuc2-1051","uniquename":"SJAG_01956:allele-1"},"SJAG_03198:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03198","name":"oar2delta","uniquename":"SJAG_03198:allele-1"},"SJAG_03198:allele-2":{"allele_type":"amino_acid_mutation","description":"Y189D cold sensitive","gene_uniquename":"SJAG_03198","name":"oar2-51","uniquename":"SJAG_03198:allele-2"},"SJAG_03198:allele-3":{"allele_type":"amino_acid_mutation","description":"R72A,L75A,R106A,L109A","gene_uniquename":"SJAG_03198","name":"oar2-dm12","synonyms":[{"name":"destruction box mutations","reference":"PMID:23786411","type":"exact"}],"uniquename":"SJAG_03198:allele-3"},"SJAG_03351:allele-1":{"allele_type":"amino_acid_mutation","description":"A186T ts","gene_uniquename":"SJAG_03351","name":"cut23-415","uniquename":"SJAG_03351: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_curators":[{"annotation_count":22,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-21","authors":"Aoki K, Shiwa Y, Takada H, Yoshikawa H, Niki H","authors_abbrev":"Aoki K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-21 18:57:14","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-21 18:57:14","canto_session_key":"a0c3e1394f326db9","canto_session_submitted_date":"2022-11-21 18:57:00","canto_triage_status":"Curatable","citation":"Genes Cells 2013 Sep;18(9):733-52","cv_annotations":{"cellular_component":[{"annotations":[115467],"is_not":false,"summary":null,"term":"GO:0005730"}],"multi_locus_phenotype":[{"annotations":[115481,115482,115483,115485],"is_not":false,"summary":null,"term":"FYPO:0000674"}],"single_locus_phenotype":[{"annotations":[115468,115469,115470,115484],"is_not":false,"summary":null,"term":"FYPO:0000080"},{"annotations":[115477,115478,115479],"is_not":false,"summary":null,"term":"FYPO:0000618"},{"annotations":[115486,115487,115488],"is_not":false,"summary":null,"term":"FYPO:0001327"},{"annotations":[115474,115475,115476],"is_not":false,"summary":null,"term":"FYPO:0001387"},{"annotations":[115471,115472,115473],"is_not":false,"summary":null,"term":"FYPO:0000324"},{"annotations":[115480],"is_not":false,"summary":null,"term":"FYPO:0004683"}]},"doi":"10.1111/gtc.12072","gene_count":6,"genes_by_uniquename":{"SJAG_00259":null,"SJAG_01946":null,"SJAG_01956":null,"SJAG_03198":null,"SJAG_03351":null,"SJAG_03575":null},"genotypes_by_uniquename":{"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"apc2-361(E548K ts)","display_uniquename":"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03575:allele-1","expression":"Not assayed or wild type"}]}]},"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"}]}]},"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":{"display_name":"apc2-361(E548K ts) oar2-51(Y189D cold sensitive)","display_uniquename":"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","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03575:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03198:allele-2","expression":"Not assayed or wild type"}]}]},"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2-dm12-R72A,L75A,R106A,L109A-amino_acid_mutation-expression-overexpression":{"display_name":"apc2-361(E548K ts) oar2-dm12(R72A,L75A,R106A,L109A aa)[Overexpression]","display_uniquename":"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2-dm12-R72A,L75A,R106A,L109A-amino_acid_mutation-expression-overexpression","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03575:allele-1","expression":"Not assayed or wild 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id: GO_REF:0000079
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id: GO_REF:0000078
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id: GO_REF:0000033
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id: PMID:33791858
data:
  {"abstract":"Mitogen-activated protein kinase (MAPK) signalling pathways regulate multiple cellular functions in eukaryotic organisms in response to environmental cues, including the dynamic remodeling of the actin cytoskeleton. The fission yeast S. pombe is an optimal model to investigate the conserved regulatory mechanisms of cytokinesis, which relies in an actomyosin-based contractile ring (CAR) that prompts the physical separation of daughter cells during cellular division. Our group has recently shown that p38 MAPK ortholog Sty1, the core component of the stress-activated pathway (SAPK), negatively modulates CAR assembly and integrity in S. pombe during actin cytoskeletal damage induced with Latrunculin A and in response to environmental stress. This response involves downregulation of protein levels of the formin For3, which assembles actin filaments for cables and the CAR, likely through an ubiquitin-mediated degradation mechanism. Contrariwise, Sty1 function positively reinforces CAR assembly during stress in the close relative dimorphic fission yeast S. japonicus. The opposite effect of SAPK signaling on CAR integrity may represent an evolutionary refined adaptation to cope with the marked differences in cytokinesis onset in both fission yeast species.","alleles_by_uniquename":{"SJAG_00266:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00266","name":"atf1delta","uniquename":"SJAG_00266:allele-1"},"SJAG_02592:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02592","name":"sty1delta","uniquename":"SJAG_02592:allele-1"}},"annotation_curators":[{"annotation_count":4,"community_curator":true,"file_name":null,"file_type":null,"name":"Elisa Gómez Gil","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-09-14","authors":"Madrid M, Gómez-Gil E, Cansado J","authors_abbrev":"Madrid M et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-14 21:24:28","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Elisa Gómez Gil","canto_curator_role":"community","canto_first_approved_date":"2021-09-14 21:24:28","canto_session_key":"84ac20b0ff20a3cd","canto_session_submitted_date":"2021-09-14 16:45:32","canto_triage_status":"Curatable","citation":"Curr Genet 2021 Oct;67(5):715-721","cv_annotations":{"PSI-MOD":[{"annotations":[115567],"is_not":false,"summary":null,"term":"MOD:00696"}],"single_locus_phenotype":[{"annotations":[115566],"is_not":false,"summary":null,"term":"FYPO:0002998"},{"annotations":[115564,115565],"is_not":false,"summary":null,"term":"FYPO:0000107"}]},"doi":"10.1007/s00294-021-01155-6","gene_count":2,"genes_by_uniquename":{"SJAG_00266":null,"SJAG_02592":null},"genotypes_by_uniquename":{"atf1delta":{"display_name":"atf1delta","display_uniquename":"atf1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00266:allele-1","expression":"Null"}]}]},"sty1delta":{"display_name":"sty1delta","display_uniquename":"sty1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02592:allele-1","expression":"Null"}]}]}},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-04-01","pubmed_publication_date":"Oct 2021","terms_by_termid":{"FYECO:0000248":null,"FYPO:0000107":null,"FYPO:0002998":null,"FYPO_EXT:0000001":null,"GO:0120306":null,"MOD:00696":null},"title":"Negative control of cytokinesis by stress-activated MAPK signaling.","uniquename":"PMID:33791858"}


id: GO_REF:0000089
data:
  {"abstract":"We have created a standard template for classes describing the single-organism and multi-organism biological processes. The underlying equivalence axiom templates are \"P and 'bearer_of' some PATO:0002487\" (single-organism) and \"P and 'bearer_of' some PATO:0002486\" (multi-organism), where P is a biological process.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of single-organism and multi-organism biological processes in the Gene Ontology","uniquename":"GO_REF:0000089"}


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


id: PMID: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":[115335,115336],"is_not":false,"summary":null,"term":"GO:0071483"}],"molecular_function":[{"annotations":[115334],"is_not":false,"summary":null,"term":"GO:0009882"}],"single_locus_phenotype":[{"annotations":[115337,115338],"is_not":false,"summary":null,"term":"FYPO:0008031"},{"annotations":[115339,115340],"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:19473263
data:
  {"abstract":"Schizosaccharomyces cells divide by medial septation, followed by enzymatic degradation of parts of the septum (septum cleavage) to allow the sister cells to separate from each other. In a previous study we found that the cell separation mutant sep9-307 was defective in a gene that encodes a protein highly similar in sequence to the Saccharomyces cerevisiae protein Spt8, a subunit of the SAGA complex. Here, we show that the sep9-307 mutation causes a frameshift in translation. The deletion of sep9(+) is not lethal but abolishes normal septum cleavage by reducing the activity of ace2(+), a gene coding for a transcription factor of numerous genes producing proteins for septum cleavage. Indirect evidence indicates that Sep9 might also act directly in the transcription of certain target genes (e.g. eng1(+)) of this regulator. sep9-307 is synthetically lethal with mutations in the cell separation genes sep11/med18(+) and sep15/med8(+), which encode subunits of the general transcription factor mediator. Heterologous expression of SPT8 and the putative Schizosaccharomyces japonicus sep9(+) orthologue cannot substitute for sep9(+). Both Spt8 and the fission yeast proteins have highly acidic (74-76 amino-acid long) N-terminal regions with no sequence conservation.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Batta G, Szilagyi Z, Laczik M, Sipiczki M","authors_abbrev":"Batta G et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"FEMS Yeast Res 2009 Aug;9(5):757-67","cv_annotations":{},"doi":"10.1111/j.1567-1364.2009.00522.x","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2009","pubmed_entrez_date":"2009-05-29","pubmed_publication_date":"Aug 2009","terms_by_termid":{},"title":"The involvement of the Schizosaccharomyces pombe sep9/spt8 gene in the regulation of septum cleavage.","uniquename":"PMID:19473263"}


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


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


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


id: PMID: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"}


# genotypes

id: mrc1delta
data:
  {"alleles_by_uniquename":{"SJAG_04671:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04671","name":"mrc1delta","uniquename":"SJAG_04671:allele-1"}},"annotation_count":3,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115365],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115385],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[115382],"is_not":false,"summary":null,"term":"FYPO:0000088"}]},"display_name":"mrc1delta","display_uniquename":"mrc1delta","genes_by_uniquename":{"SJAG_04671":null},"genotypes_by_uniquename":{"mrc1delta":{"display_name":"mrc1delta","display_uniquename":"mrc1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04671:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04671:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:23090706":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYPO:0000085":null,"FYPO:0000088":null,"FYPO:0007790":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null}}


id: rad9delta
data:
  {"alleles_by_uniquename":{"SJAG_01605:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01605","name":"rad9delta","uniquename":"SJAG_01605:allele-1"}},"annotation_count":3,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115368,115647],"is_not":false,"summary":null,"term":"FYPO:0007782"},{"annotations":[115645],"is_not":false,"summary":null,"term":"FYPO:0000085"}]},"display_name":"rad9delta","display_uniquename":"rad9delta","genes_by_uniquename":{"SJAG_01605":null},"genotypes_by_uniquename":{"rad9delta":{"display_name":"rad9delta","display_uniquename":"rad9delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01605:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01605:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:20368354":null,"PMID:23090706":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYECO:0000314":null,"FYPO:0000085":null,"FYPO:0007782":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null}}


id: rad1delta
data:
  {"alleles_by_uniquename":{"SJAG_02771:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02771","name":"rad1delta","uniquename":"SJAG_02771:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115369],"is_not":false,"summary":null,"term":"FYPO:0007782"}]},"display_name":"rad1delta","display_uniquename":"rad1delta","genes_by_uniquename":{"SJAG_02771":null},"genotypes_by_uniquename":{"rad1delta":{"display_name":"rad1delta","display_uniquename":"rad1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02771:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02771:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:23090706":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000137":null,"FYECO:0000314":null,"FYPO:0007782":null,"FYPO_EXT:0000001":null}}


id: atf1delta
data:
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id: apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__cem1delta
data:
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id: gms1delta
data:
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id: wee1delta
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id: dcr1delta__mpe1-R77W-R77W-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: ned1-5A-S499A__S538A__T620A__T638A__S651A-amino_acid_mutation-expression-not_assayed_or_wild_type
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id: nup132delta
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id: ned1S235A_S651-S235A__S651-amino_acid_mutation-expression-not_assayed_or_wild_type
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id: byr1delta
data:
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id: wis4delta
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id: gpd1delta
data:
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id: acb1delta
data:
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id: mkh1delta
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: rad3delta
data:
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id: vps4delta
data:
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id: tip1delta
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id: pim1-R152C-R152C-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: rga4delta
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: rad51delta
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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: chp1delta
data:
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id: sep1delta
data:
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id: nde1delta
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id: nem2delta
data:
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id: lem2delta
data:
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id: ned1delta
data:
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id: apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: pmk1delta
data:
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id: sst4delta
data:
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id: ste11delta
data:
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id: rga4delta__rga6delta
data:
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id: wis1delta
data:
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id: SJAG_00124delta
data:
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id: Pmk1Sp-Pmk1_from_S._pombe-other-expression-not_assayed_or_wild_type
data:
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id: rad25delta
data:
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id: vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: rim20E308V-E308V-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: gef1delta
data:
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id: rga6delta
data:
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id: wcs2delta
data:
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id: wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: pck2delta
data:
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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":[115410],"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: cdc2-1w-G146D-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: SJAG_00124delta__sty1delta
data:
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id: tel1delta
data:
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id: scd1delta
data:
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id: chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: nur1delta__vps4delta
data:
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id: wcs1delta
data:
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id: mid1delta
data:
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id: dcr1delta__frameshift-aa61->stop-nonsense_mutation-expression-not_assayed_or_wild_type
data:
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id: rga4delta__wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
  {"alleles_by_uniquename":{"SJAG_04280:allele-2":{"allele_type":"amino_acid_mutation","description":"G788E","gene_uniquename":"SJAG_04280","name":"wee1-G788E","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":1,"annotation_details":{},"comment":null,"cv_annotations":{"multi_locus_phenotype":[{"annotations":[115553],"is_not":false,"summary":null,"term":"FYPO:0004293"}]},"display_name":"rga4delta wee1-G788E(aa)","display_uniquename":"rga4delta__wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type","genes_by_uniquename":{"SJAG_04280":null,"SJAG_04522":null},"genotypes_by_uniquename":{"rga4delta__wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"rga4delta wee1-G788E(aa)","display_uniquename":"rga4delta__wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04522:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-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,"FYPO:0004293":null,"FYPO_EXT:0000001":null}}


id: cdc15-A-L264P,P442T-amino_acid_mutation-expression-not_assayed_or_wild_type__mid1delta
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: efc25delta
data:
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id: pck1delta__pmk1delta
data:
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id: dcr1delta__leo1delta
data:
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id: for3delta
data:
  {"alleles_by_uniquename":{"SJAG_04703:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04703","name":"for3delta","uniquename":"SJAG_04703:allele-1"}},"annotation_count":3,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115356],"is_not":false,"summary":null,"term":"FYPO:0003315"},{"annotations":[115357],"is_not":false,"summary":null,"term":"FYPO:0001355"},{"annotations":[115355],"is_not":false,"summary":null,"term":"FYPO:0001956"}]},"display_name":"for3delta","display_uniquename":"for3delta","genes_by_uniquename":{"SJAG_04703":null},"genotypes_by_uniquename":{"for3delta":{"display_name":"for3delta","display_uniquename":"for3delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04703:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04703:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:30726171":null},"taxonid":4897,"terms_by_termid":{"FYPO:0001355":null,"FYPO:0001956":null,"FYPO:0003315":null}}


id: cmp7delta
data:
  {"alleles_by_uniquename":{"SJAG_05207:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_05207","name":"cmp7delta","uniquename":"SJAG_05207:allele-1"}},"annotation_count":7,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115293,115294],"is_not":false,"summary":null,"term":"FYPO:0007771"},{"annotations":[115517],"is_not":false,"summary":null,"term":"FYPO:0000080"},{"annotations":[115292,115513],"is_not":false,"summary":null,"term":"FYPO:0007772"},{"annotations":[115518],"is_not":false,"summary":null,"term":"FYPO:0000714"},{"annotations":[115515],"is_not":false,"summary":null,"term":"FYPO:0001234"}]},"display_name":"cmp7delta","display_uniquename":"cmp7delta","genes_by_uniquename":{"SJAG_01050":null,"SJAG_01745":null,"SJAG_05207":null},"genotypes_by_uniquename":{"cmp7delta":{"display_name":"cmp7delta","display_uniquename":"cmp7delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_05207:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_05207:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:32109380":null,"PMID:32243490":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000006":null,"FYECO:0000137":null,"FYPO:0000080":null,"FYPO:0000714":null,"FYPO:0001234":null,"FYPO:0007771":null,"FYPO:0007772":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null}}


id: chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type__rad24delta
data:
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id: vps25delta
data:
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id: oar2-dm12-R72A,L75A,R106A,L109A-amino_acid_mutation-expression-overexpression
data:
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id: mid2delta
data:
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id: Vps4-EQ-E233Q-amino_acid_mutation-expression-not_assayed_or_wild_type
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:
  lig4::KanMX6-RNA_sequencing_revealed_that_only_the_5'_end_of_the_disrupted_allele_showed_low_RNA_expression_and_coverage-disruption-expression-knockdown

data:
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id: wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
  {"alleles_by_uniquename":{"SJAG_04280:allele-2":{"allele_type":"amino_acid_mutation","description":"G788E","gene_uniquename":"SJAG_04280","name":"wee1-G788E","uniquename":"SJAG_04280:allele-2"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115543],"is_not":false,"summary":null,"term":"FYPO:0000648"}]},"display_name":"wee1-G788E(aa)","display_uniquename":"wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type","genes_by_uniquename":{"SJAG_04280":null},"genotypes_by_uniquename":{"wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"wee1-G788E(aa)","display_uniquename":"wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-2","expression":"Not assayed or wild type"}]}]}},"loci":[{"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,"FYPO:0000648":null,"FYPO_EXT:0000002":null}}


id: ade6delta
data:
  {"alleles_by_uniquename":{"SJAG_01081:allele-3":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01081","name":"ade6delta","uniquename":"SJAG_01081:allele-3"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115363],"is_not":false,"summary":null,"term":"FYPO:0000747"}]},"display_name":"ade6delta","display_uniquename":"ade6delta","genes_by_uniquename":{"SJAG_01081":null},"genotypes_by_uniquename":{"ade6delta":{"display_name":"ade6delta","display_uniquename":"ade6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-3","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-3","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:21905090":null},"taxonid":4897,"terms_by_termid":{"FYPO:0000747":null}}


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":[115769],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115763],"is_not":false,"summary":null,"term":"FYPO:0000760"},{"annotations":[115765],"is_not":false,"summary":null,"term":"FYPO:0000579"},{"annotations":[115764],"is_not":false,"summary":null,"term":"FYPO:0000590"},{"annotations":[115761,115762],"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: apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2delta
data:
  {"alleles_by_uniquename":{"SJAG_03198:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03198","name":"oar2delta","uniquename":"SJAG_03198: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":[115483],"is_not":false,"summary":null,"term":"FYPO:0000674"}]},"display_name":"apc2-361(E548K ts) oar2delta","display_uniquename":"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2delta","genes_by_uniquename":{"SJAG_03198":null,"SJAG_03575":null},"genotypes_by_uniquename":{"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2delta":{"display_name":"apc2-361(E548K ts) oar2delta","display_uniquename":"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03575:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03198:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03575:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03198: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: pom1delta
data:
  {"alleles_by_uniquename":{"SJAG_02392:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02392","name":"pom1delta","uniquename":"SJAG_02392:allele-1"}},"annotation_count":6,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115609,115610],"is_not":false,"summary":null,"term":"FYPO:0000731"},{"annotations":[115583],"is_not":false,"summary":null,"term":"FYPO:0005503"},{"annotations":[115611],"is_not":false,"summary":null,"term":"FYPO:0002026"},{"annotations":[115608],"is_not":false,"summary":null,"term":"FYPO:0003535"},{"annotations":[115361],"is_not":false,"summary":null,"term":"FYPO:0007801"}]},"display_name":"pom1delta","display_uniquename":"pom1delta","genes_by_uniquename":{"SJAG_01143":null,"SJAG_01665":null,"SJAG_02392":null,"SJAG_03596":null},"genotypes_by_uniquename":{"pom1delta":{"display_name":"pom1delta","display_uniquename":"pom1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02392:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02392:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:25866389":null,"PMID:30726171":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000137":null,"FYECO:0000162":null,"FYPO:0000731":null,"FYPO:0002026":null,"FYPO:0003535":null,"FYPO:0005503":null,"FYPO:0007801":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null}}


id: vps24delta
data:
  {"alleles_by_uniquename":{"SJAG_03783:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03783","name":"vps24delta","uniquename":"SJAG_03783:allele-1"}},"annotation_count":4,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115326],"is_not":false,"summary":null,"term":"FYPO:0001370"},{"annotations":[115321,115322,115323],"is_not":false,"summary":null,"term":"FYPO:0007771"}]},"display_name":"vps24delta","display_uniquename":"vps24delta","genes_by_uniquename":{"SJAG_01745":null,"SJAG_03783":null,"SJAG_03892":null},"genotypes_by_uniquename":{"vps24delta":{"display_name":"vps24delta","display_uniquename":"vps24delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03783:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03783:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:32109380":null},"taxonid":4897,"terms_by_termid":{"FYPO:0001370":null,"FYPO:0007771":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null}}


id: nur1delta
data:
  {"alleles_by_uniquename":{"SJAG_01050:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01050","name":"nur1delta","uniquename":"SJAG_01050:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115297],"is_not":false,"summary":null,"term":"FYPO:0007073"}]},"display_name":"nur1delta","display_uniquename":"nur1delta","genes_by_uniquename":{"SJAG_01050":null,"SJAG_01745":null},"genotypes_by_uniquename":{"nur1delta":{"display_name":"nur1delta","display_uniquename":"nur1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01050:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01050:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:32109380":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000137":null,"FYPO:0007073":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null}}


id: frameshift-aa61->stop-nonsense_mutation-expression-not_assayed_or_wild_type
data:
  {"alleles_by_uniquename":{},"annotation_count":0,"annotation_details":{},"comment":null,"cv_annotations":{},"display_name":"frameshift(aa61->stop)","display_uniquename":"frameshift-aa61->stop-nonsense_mutation-expression-not_assayed_or_wild_type","genes_by_uniquename":{},"genotypes_by_uniquename":{},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03118:allele-2","expression":"Not assayed or wild type"}]}],"ploidiness":"haploid","references_by_uniquename":{},"taxonid":4897,"terms_by_termid":{}}


id: pek1delta
data:
  {"alleles_by_uniquename":{"SJAG_01181:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01181","name":"pek1delta","uniquename":"SJAG_01181:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115747],"is_not":false,"summary":null,"term":"FYPO:0000124"}]},"display_name":"pek1delta","display_uniquename":"pek1delta","genes_by_uniquename":{"SJAG_01181":null},"genotypes_by_uniquename":{"pek1delta":{"display_name":"pek1delta","display_uniquename":"pek1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01181:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01181:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:29566183":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000137":null,"FYPO:0000124":null}}


id: nem1delta
data:
  {"alleles_by_uniquename":{"SJAG_01906:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01906","name":"nem1delta","uniquename":"SJAG_01906:allele-1"}},"annotation_count":2,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115670],"is_not":false,"summary":null,"term":"FYPO:0001784"},{"annotations":[115669],"is_not":false,"summary":null,"term":"FYPO:0001556"}]},"display_name":"nem1delta","display_uniquename":"nem1delta","genes_by_uniquename":{"SJAG_01906":null},"genotypes_by_uniquename":{"nem1delta":{"display_name":"nem1delta","display_uniquename":"nem1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01906:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01906:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:26774782":null},"taxonid":4897,"terms_by_termid":{"FYPO:0001556":null,"FYPO:0001784":null,"FYPO_EXT:0000001":null}}


id: chk1delta__crb2delta
data:
  {"alleles_by_uniquename":{"SJAG_01205:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01205","name":"crb2delta","uniquename":"SJAG_01205:allele-1"},"SJAG_01680:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01680","name":"chk1delta","uniquename":"SJAG_01680:allele-1"}},"annotation_count":2,"annotation_details":{},"comment":null,"cv_annotations":{"multi_locus_phenotype":[{"annotations":[115381],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[115378],"is_not":false,"summary":null,"term":"FYPO:0000088"}]},"display_name":"chk1delta crb2delta","display_uniquename":"chk1delta__crb2delta","genes_by_uniquename":{"SJAG_01205":null,"SJAG_01680":null},"genotypes_by_uniquename":{"chk1delta__crb2delta":{"display_name":"chk1delta crb2delta","display_uniquename":"chk1delta__crb2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_01205:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_01205:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:23090706":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYPO:0000085":null,"FYPO:0000088":null,"FYPO_EXT:0000002":null}}


id: rga4delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
  {"alleles_by_uniquename":{"SJAG_04280:allele-1":{"allele_type":"amino_acid_mutation","description":"T582G","gene_uniquename":"SJAG_04280","name":"wee1-as8","uniquename":"SJAG_04280:allele-1"},"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":[115549],"is_not":false,"summary":null,"term":"FYPO:0007783"},{"annotations":[115551],"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-1","expression":"Not assayed or wild type"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04522:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-1","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: Man1DHEH-man1DHEH-partial_amino_acid_deletion-expression-not_assayed_or_wild_type
data:
  {"alleles_by_uniquename":{"SJAG_03449:allele-2":{"allele_type":"partial_amino_acid_deletion","description":"man1DHEH","gene_uniquename":"SJAG_03449","name":"Man1DHEH","uniquename":"SJAG_03449:allele-2"}},"annotation_count":3,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115657],"is_not":false,"summary":null,"term":"FYPO:0003779"},{"annotations":[115662],"is_not":false,"summary":null,"term":"FYPO:0000671"},{"annotations":[115656],"is_not":false,"summary":null,"term":"FYPO:0004890"}]},"display_name":"Man1DHEH(man1DHEH)","display_uniquename":"Man1DHEH-man1DHEH-partial_amino_acid_deletion-expression-not_assayed_or_wild_type","genes_by_uniquename":{"SJAG_03449":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"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03449:allele-2","expression":"Not assayed or wild type"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:24184107":null},"taxonid":4897,"terms_by_termid":{"FYPO:0000671":null,"FYPO:0003779":null,"FYPO:0004890":null,"FYPO_EXT:0000001":null}}


id: ndi1delta
data:
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id: mdh1delta
data:
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id: ade6-domK-Q262A-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: ura4delta
data:
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id: vps32delta
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: ptp4delta
data:
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id: mad2delta
data:
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id: chk1delta
data:
  {"alleles_by_uniquename":{"SJAG_01680:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01680","name":"chk1delta","uniquename":"SJAG_01680:allele-1"}},"annotation_count":5,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115371,115643],"is_not":false,"summary":null,"term":"FYPO:0007782"},{"annotations":[115380,115644],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[115377],"is_not":false,"summary":null,"term":"FYPO:0000088"}]},"display_name":"chk1delta","display_uniquename":"chk1delta","genes_by_uniquename":{"SJAG_01680":null},"genotypes_by_uniquename":{"chk1delta":{"display_name":"chk1delta","display_uniquename":"chk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:20368354":null,"PMID:23090706":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYECO:0000314":null,"FYPO:0000085":null,"FYPO:0000088":null,"FYPO:0007782":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null}}


id: bbl1-P363S-P363S-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
  {"alleles_by_uniquename":{"SJAG_00426:allele-1":{"allele_type":"amino_acid_mutation","description":"P363S","gene_uniquename":"SJAG_00426","name":"bbl1-P363S","uniquename":"SJAG_00426:allele-1"}},"annotation_count":5,"annotation_details":{},"comment":"Catalytically deficient at restrictive temperature, recessive","cv_annotations":{"single_locus_phenotype":[{"annotations":[115631],"is_not":false,"summary":null,"term":"FYPO:0000356"},{"annotations":[115630],"is_not":false,"summary":null,"term":"FYPO:0006433"},{"annotations":[115633],"is_not":false,"summary":null,"term":"FYPO:0004695"},{"annotations":[115632],"is_not":false,"summary":null,"term":"FYPO:0002227"},{"annotations":[115634],"is_not":false,"summary":null,"term":"FYPO:0001357"}]},"display_name":"bbl1-P363S(aa)","display_uniquename":"bbl1-P363S-P363S-amino_acid_mutation-expression-not_assayed_or_wild_type","genes_by_uniquename":{"SJAG_00426":null},"genotypes_by_uniquename":{"bbl1-P363S-P363S-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"bbl1-P363S(aa)","display_uniquename":"bbl1-P363S-P363S-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00426:allele-1","expression":"Not assayed or wild type"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00426:allele-1","expression":"Not assayed or wild type"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:25318672":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000004":null,"FYECO:0000006":null,"FYECO:0000162":null,"FYPO:0000356":null,"FYPO:0001357":null,"FYPO:0002227":null,"FYPO:0004695":null,"FYPO:0006433":null,"FYPO_EXT:0000001":null}}


id: cds1delta
data:
  {"alleles_by_uniquename":{"SJAG_04287:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04287","name":"cds1delta","uniquename":"SJAG_04287:allele-1"}},"annotation_count":2,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115372],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115383],"is_not":false,"summary":null,"term":"FYPO:0000088"}]},"display_name":"cds1delta","display_uniquename":"cds1delta","genes_by_uniquename":{"SJAG_04287":null},"genotypes_by_uniquename":{"cds1delta":{"display_name":"cds1delta","display_uniquename":"cds1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04287:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04287:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:23090706":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYPO:0000088":null,"FYPO:0007790":null,"FYPO_EXT:0000001":null}}


id: leo1delta
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-1":{"allele_type":"amino_acid_mutation","description":"T582G","gene_uniquename":"SJAG_04280","name":"wee1-as8","uniquename":"SJAG_04280:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"multi_locus_phenotype":[{"annotations":[115554],"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-1","expression":"Not assayed or wild type"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00028:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-1","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: mat-Pc-R47K-R47K-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:
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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: ned1S235E_S651E-S235E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
  {"alleles_by_uniquename":{"SJAG_02763:allele-4":{"allele_type":"amino_acid_mutation","description":"S235E; S651E","gene_uniquename":"SJAG_02763","name":"ned1S235E/S651E","synonyms":[{"name":"phosphomimetic","reference":"PMID:26774782","type":"exact"}],"uniquename":"SJAG_02763:allele-4"}},"annotation_count":3,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115683],"is_not":false,"summary":null,"term":"FYPO:0006054"},{"annotations":[115682],"is_not":false,"summary":null,"term":"FYPO:0001784"},{"annotations":[115681],"is_not":false,"summary":null,"term":"FYPO:0001556"}]},"display_name":"ned1S235E/S651E(S235E; S651E aa)","display_uniquename":"ned1S235E_S651E-S235E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type","genes_by_uniquename":{"SJAG_02763":null},"genotypes_by_uniquename":{"ned1S235E_S651E-S235E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1S235E/S651E(S235E; S651E aa)","display_uniquename":"ned1S235E_S651E-S235E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-4","expression":"Not assayed or wild type"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-4","expression":"Not assayed or wild type"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:26774782":null},"taxonid":4897,"terms_by_termid":{"FYPO:0001556":null,"FYPO:0001784":null,"FYPO:0006054":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null}}


id: vps28delta
data:
  {"alleles_by_uniquename":{"SJAG_04349:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04349","name":"vps28delta","uniquename":"SJAG_04349:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115315],"is_not":false,"summary":null,"term":"FYPO:0001440"}]},"display_name":"vps28delta","display_uniquename":"vps28delta","genes_by_uniquename":{"SJAG_04349":null},"genotypes_by_uniquename":{"vps28delta":{"display_name":"vps28delta","display_uniquename":"vps28delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04349:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04349: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: crb2delta
data:
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id: pyp1delta
data:
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id: clr4delta
data:
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id: pyk1-A343T-A343T-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: arb2delta
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: nup61delta
data:
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id: man1delta
data:
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id: pka1delta
data:
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id: sdh3delta
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: stc1delta
data:
  {"alleles_by_uniquename":{"SJAG_02409:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02409","name":"stc1delta","uniquename":"SJAG_02409:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115399],"is_not":false,"summary":null,"term":"FYPO:0002061"}]},"display_name":"stc1delta","display_uniquename":"stc1delta","genes_by_uniquename":{"SJAG_02409":null},"genotypes_by_uniquename":{"stc1delta":{"display_name":"stc1delta","display_uniquename":"stc1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02409:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02409: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: dcr1delta
data:
  {"alleles_by_uniquename":{"SJAG_03689:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03689","name":"dcr1delta","uniquename":"SJAG_03689:allele-1"}},"annotation_count":6,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115400],"is_not":false,"summary":null,"term":"FYPO:0004205"},{"annotations":[115401],"is_not":false,"summary":null,"term":"FYPO:0004982"},{"annotations":[115403],"is_not":false,"summary":null,"term":"FYPO:0000595"},{"annotations":[115397],"is_not":false,"summary":null,"term":"FYPO:0002061"},{"annotations":[115404],"is_not":false,"summary":null,"term":"FYPO:0006989"},{"annotations":[115402],"is_not":false,"summary":null,"term":"FYPO:0000596"}]},"display_name":"dcr1delta","display_uniquename":"dcr1delta","genes_by_uniquename":{"SJAG_03689":null},"genotypes_by_uniquename":{"dcr1delta":{"display_name":"dcr1delta","display_uniquename":"dcr1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03689:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03689:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:35226668":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000162":null,"FYPO:0000595":null,"FYPO:0000596":null,"FYPO:0002061":null,"FYPO:0004205":null,"FYPO:0004982":null,"FYPO:0006989":null,"FYPO_EXT:0000001":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":[115724],"is_not":false,"summary":null,"term":"FYPO:0007789"},{"annotations":[115723],"is_not":false,"summary":null,"term":"FYPO:0001355"},{"annotations":[115722],"is_not":false,"summary":null,"term":"FYPO:0000280"},{"annotations":[115721],"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: gap1delta
data:
  {"alleles_by_uniquename":{"SJAG_02379:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02379","name":"gap1delta","uniquename":"SJAG_02379:allele-1"}},"annotation_count":3,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115756],"is_not":false,"summary":null,"term":"FYPO:0007789"},{"annotations":[115754],"is_not":false,"summary":null,"term":"FYPO:0000280"},{"annotations":[115750],"is_not":false,"summary":null,"term":"FYPO:0000124"}]},"display_name":"gap1delta","display_uniquename":"gap1delta","genes_by_uniquename":{"SJAG_02379":null},"genotypes_by_uniquename":{"gap1delta":{"display_name":"gap1delta","display_uniquename":"gap1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02379:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02379:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:29566183":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000137":null,"FYPO:0000124":null,"FYPO:0000280":null,"FYPO:0007789":null}}


id: spk1delta
data:
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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":[115778],"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: cox6delta
data:
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id: rad24delta
data:
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id: mid1delta__pom1delta
data:
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id: rad26delta
data:
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id: sty1delta
data:
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id: oar2-51-Y189D_cold_sensitive-amino_acid_mutation-expression-overexpression
data:
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id: etr1delta
data:
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id: ste6delta
data:
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id: ace2delta
data:
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id: rdp1delta
data:
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id: mpe1-R77W-R77W-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: cdc25-D9-I30T,T572P-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: ago1delta__leo1delta
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: ned1cat-D422E,D424E-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: oar2delta
data:
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id: ras1delta
data:
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id: pom152delta
data:
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id: alx1delta
data:
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id: cut3-T19E-cut3-T19E-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: agn1delta
data:
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id: cem1delta
data:
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id: ago1delta
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: byr2delta
data:
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id: did4delta
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: mid1delta__mid2delta
data:
  {"alleles_by_uniquename":{"SJAG_00118:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00118","name":"mid2delta","uniquename":"SJAG_00118:allele-1"},"SJAG_01143:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01143","name":"mid1delta","uniquename":"SJAG_01143:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"multi_locus_phenotype":[{"annotations":[115586],"is_not":false,"summary":null,"term":"FYPO:0000118"}]},"display_name":"mid1delta mid2delta","display_uniquename":"mid1delta__mid2delta","genes_by_uniquename":{"SJAG_00118":null,"SJAG_01143":null},"genotypes_by_uniquename":{"mid1delta__mid2delta":{"display_name":"mid1delta mid2delta","display_uniquename":"mid1delta__mid2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01143:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_00118:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01143:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_00118:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:25866389":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYPO:0000118":null}}


id: win1delta
data:
  {"alleles_by_uniquename":{"SJAG_04777:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04777","name":"win1delta","uniquename":"SJAG_04777:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115744],"is_not":false,"summary":null,"term":"FYPO:0000124"}]},"display_name":"win1delta","display_uniquename":"win1delta","genes_by_uniquename":{"SJAG_04777":null},"genotypes_by_uniquename":{"win1delta":{"display_name":"win1delta","display_uniquename":"win1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04777:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04777: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
data:
  {"alleles_by_uniquename":{"SJAG_01787:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01787","name":"pck1delta","uniquename":"SJAG_01787:allele-1"}},"annotation_count":5,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115792],"is_not":false,"summary":null,"term":"FYPO:0007775"},{"annotations":[115793],"is_not":false,"summary":null,"term":"FYPO:0007779"},{"annotations":[115791],"is_not":false,"summary":null,"term":"FYPO:0001038"},{"annotations":[115789],"is_not":false,"summary":null,"term":"FYPO:0005152"},{"annotations":[115790],"is_not":false,"summary":null,"term":"FYPO:0007522"}]},"display_name":"pck1delta","display_uniquename":"pck1delta","genes_by_uniquename":{"SJAG_01787":null,"SJAG_04551":null},"genotypes_by_uniquename":{"pck1delta":{"display_name":"pck1delta","display_uniquename":"pck1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01787:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01787:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:34198697":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000314":null,"FYPO:0001038":null,"FYPO:0005152":null,"FYPO:0007522":null,"FYPO:0007775":null,"FYPO:0007779":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null}}


id: arb1delta
data:
  {"alleles_by_uniquename":{"SJAG_02594:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02594","name":"arb1delta","uniquename":"SJAG_02594:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[115394],"is_not":false,"summary":null,"term":"FYPO:0002061"}]},"display_name":"arb1delta","display_uniquename":"arb1delta","genes_by_uniquename":{"SJAG_02594":null},"genotypes_by_uniquename":{"arb1delta":{"display_name":"arb1delta","display_uniquename":"arb1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02594:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02594: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}}


