# refs

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


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


id: PMID:27734801
data:
  {"abstract":"Many eukaryotes assemble a ring-shaped actomyosin network that contracts to drive cytokinesis. Unlike actomyosin in sarcomeres, which cycles through contraction and relaxation, the cytokinetic ring disassembles during contraction through an unknown mechanism. Here we find in  Schizosaccharomyces japonicus  and  Schizosaccharomyces pombe  that, during actomyosin ring contraction, actin filaments associated with actomyosin rings are expelled as micron-scale bundles containing multiple actomyosin ring proteins. Using functional isolated actomyosin rings we show that expulsion of actin bundles does not require continuous presence of cytoplasm. Strikingly, mechanical compression of actomyosin rings results in expulsion of bundles predominantly at regions of high curvature. Our work unprecedentedly reveals that the increased curvature of the ring itself promotes its disassembly. It is likely that such a curvature-induced mechanism may operate in disassembly of other contractile networks.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":2,"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":"Huang J, Chew TG, Gu Y, Palani S, Kamnev A, Martin DS, Carter NJ, Cross RA, Oliferenko S, Balasubramanian MK","authors_abbrev":"Huang J et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-09 15:10:46","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 15:10:46","canto_session_key":"f47401f00ac444e0","canto_session_submitted_date":"2021-07-09 15:10:39","canto_triage_status":"Curatable","citation":"Elife 2016 10 13;5","cv_annotations":{"cellular_component":[{"annotations":[114338],"is_not":false,"summary":null,"term":"GO:0032432"},{"annotations":[114337],"is_not":false,"summary":null,"term":"GO:0005826"}]},"doi":"10.7554/eLife.21383","gene_count":1,"genes_by_uniquename":{"SJAG_04887":null},"genotypes_by_uniquename":{},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2016","pubmed_entrez_date":"2016-10-14","pubmed_publication_date":"13 10 2016","terms_by_termid":{"GO:0005826":null,"GO:0032432":null},"title":"Curvature-induced expulsion of actomyosin bundles during cytokinetic ring contraction.","uniquename":"PMID:27734801"}


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:22641476
data:
  {"abstract":"Measuring relative genetic distances is one of the best ways to locate genetic loci. Here we report the construction of a strains set for genetic mapping in Schizosaccharomyces japonicus, which belongs to the genus Schizosaccharomyces together with the well-studied fission yeast Sz. pombe. We constructed 29 strains that bear a positive-negative selection marker at different loci. The marker was inserted every 500 kb in the genome of Sz. japonicus. Each marker thus becomes a 'scale mark' of a chromosome that behaves like a yardstick. By determining the genetic distances from the inserted markers, the relative location of a genomic mutation can be determined. We also constructed a fosmid library that covers an entire genome of Sz. japonicus. These tools together would facilitate identification and cloning of the gene.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Furuya K, Aoki K, Niki H","authors_abbrev":"Furuya K et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Yeast 2012 Jun;29(6):241-9","cv_annotations":{},"doi":"10.1002/yea.2907","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-05-30","pubmed_publication_date":"Jun 2012","terms_by_termid":{},"title":"Construction of an insertion marker collection of Sz. japonicus (IMACS) for genetic mapping and a fosmid library covering its genome.","uniquename":"PMID:22641476"}


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: 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":null}],"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_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":[114473],"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: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: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: 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_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":[114349],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[114355],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[114352],"is_not":false,"summary":null,"term":"FYPO:0000088"}],"single_locus_phenotype":[{"annotations":[114340,114341,114342,114343,114344,114345,114347,114348],"is_not":false,"summary":null,"term":"FYPO:0007782"},{"annotations":[114366],"is_not":false,"summary":null,"term":"FYPO:0007774"},{"annotations":[114365],"is_not":false,"summary":null,"term":"FYPO:0001690"},{"annotations":[114339,114346],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[114364],"is_not":false,"summary":null,"term":"FYPO:0004693"},{"annotations":[114353,114354,114359,114360,114361],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[114350,114351,114356,114357,114358],"is_not":false,"summary":null,"term":"FYPO:0000088"},{"annotations":[114362,114363],"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","references_by_uniquename":{"PMID:20368354":null,"PMID:23090706":null},"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: PMID:2226803
data:
  {"abstract":"In the fission yeast Schizosaccharomyces pombe, the enzyme RNAse P copurifies with two RNAs, K1- and K2-RNA, which are identical except for their termini [1] and which are encoded by a single gene [2]. We have undertaken the cloning of the K-RNA genes in related organisms in order to gain comparative structural information. Because the K-RNA sequence is poorly conserved across species, we have cloned the K-RNA genes in the Schizosaccharomyces species S. malidevorans, S. japonicus, S. versatilis, and S. octosporus. Of the 4 species, only S. octosporus contains a K-RNA gene different from that in S. pombe; the gene diverges by 20%. Based on the two sequences, nuclease protection data and computer analysis, we have proposed a secondary structure model for the K-RNA. Northern analysis shows the K-RNA genes in all four Schizosaccharomyces species to be expressed as two RNAs, as in S. pombe.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Zimmerly S, Gamulin V, Burkard U, Söll D","authors_abbrev":"Zimmerly S et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"FEBS Lett 1990 Oct 01;271(1-2):189-93","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1990","pubmed_entrez_date":"1990-10-01","pubmed_publication_date":"01 Oct 1990","terms_by_termid":{},"title":"The RNA component of RNase P in Schizosaccharomyces species.","uniquename":"PMID:2226803"}


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


id: PMID:21905090
data:
  {"abstract":"The construction of diploid cells eases genetic analysis in haploid genetic systems because diploid cells allow for the characterization of essential genes. Here, we report the construction of diploid cells using ade6 point mutants that suppress each other via interallelic complementation in the fission yeast Schizosaccharomyces japonicus var japonicus (Sz. japonicus). We constructed an ade6-domK mutant in addition to the previously described ade6-domE. Phenotypes of both mutants exhibited adenine auxotrophy and red colonies. The mutations complemented the phenotypes in a mutually dependent manner. Diploid zygotes, in which the two mutations were introduced simultaneously into the same cells, were isolated by selecting for adenine independence. Such diploid cells are apparently larger in size than haploid cells, yet have a similar nuclear/cytoplasmic ratio, and thus the nuclear size control that has been reported in Sz. pombe is also present in Sz. japonicus.","alleles_by_uniquename":{"SJAG_01081:allele-1":{"allele_type":"nonsense_mutation","description":"S427>stop","gene_uniquename":"SJAG_01081","name":"ade6-domE","uniquename":"SJAG_01081:allele-1"},"SJAG_01081:allele-2":{"allele_type":"amino_acid_mutation","description":"Q262A","gene_uniquename":"SJAG_01081","name":"ade6-domK","uniquename":"SJAG_01081:allele-2"},"SJAG_01081:allele-3":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01081","name":"ade6delta","uniquename":"SJAG_01081:allele-3"}},"annotation_curators":[{"annotation_count":3,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-23","authors":"Furuya K, Niki H","authors_abbrev":"Furuya K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-23 13:21:47","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-23 13:21:47","canto_session_key":"7c1c894d4ee8d8d3","canto_session_submitted_date":"2022-11-23 13:21:40","canto_triage_status":"Curatable","citation":"Yeast 2011 Oct;28(10):747-54","cv_annotations":{"single_locus_phenotype":[{"annotations":[114369,114370,114371],"is_not":false,"summary":null,"term":"FYPO:0000747"}]},"doi":"10.1002/yea.1898","gene_count":1,"genes_by_uniquename":{"SJAG_01081":null},"genotypes_by_uniquename":{"ade6-domE-S427>stop-nonsense_mutation-expression-not_assayed_or_wild_type":{"display_name":"ade6-domE(S427>stop)","display_uniquename":"ade6-domE-S427>stop-nonsense_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-1","expression":"Not assayed or wild type"}]}]},"ade6-domK-Q262A-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ade6-domK(Q262A aa)","display_uniquename":"ade6-domK-Q262A-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-2","expression":"Not assayed or wild type"}]}]},"ade6delta":{"display_name":"ade6delta","display_uniquename":"ade6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-3","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2011","pubmed_entrez_date":"2011-09-10","pubmed_publication_date":"Oct 2011","terms_by_termid":{"FYPO:0000747":null},"title":"Construction of diploid zygotes by interallelic complementation of ade6 in Schizosaccharomyces japonicus.","uniquename":"PMID:21905090"}


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


id: GO_REF:0000043
data:
  {"alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"canto_curator_role":"JaponicusDB","cv_annotations":{"biological_process":[{"annotations":[67768],"is_not":false,"summary":null,"term":"GO:0009088"}],"cellular_component":[{"annotations":[64343],"is_not":false,"summary":null,"term":"GO:0005794"}],"molecular_function":[{"annotations":[66709],"is_not":false,"summary":null,"term":"GO:0003779"},{"annotations":[69399],"is_not":false,"summary":null,"term":"GO:0004812"},{"annotations":[60052],"is_not":false,"summary":null,"term":"GO:0004190"},{"annotations":[57106,57628,64490],"is_not":false,"summary":null,"term":"GO:0005524"},{"annotations":[67221],"is_not":false,"summary":null,"term":"GO:0008061"},{"annotations":[58117,67386],"is_not":false,"summary":null,"term":"GO:0008483"}]},"gene_count":11,"genes_by_uniquename":{"SJAG_00152":null,"SJAG_00620":null,"SJAG_00691":null,"SJAG_01595":null,"SJAG_01874":null,"SJAG_01953":null,"SJAG_02263":null,"SJAG_02329":null,"SJAG_03420":null,"SJAG_03692":null,"SJAG_03856":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0003779":null,"GO:0004190":null,"GO:0004812":null,"GO:0005524":null,"GO:0005794":null,"GO:0008061":null,"GO:0008483":null,"GO:0009088":null},"uniquename":"GO_REF:0000043"}


id: PMID:7612397
data:
  {"abstract":"The ultrastructure of isolated cell walls of Schizosaccharomyces pombe was studied by electron microscopy after treatment with the following purified enzymes: endo-beta-(1-->3)-glucanase, endo-beta-(-->6)-glucanase, and endo-alpha-(1-->3)-glucanase produced by Bacillus circulans; exo-beta-(1-->3)-glucanase and endo-beta-(1-->3)-glucanase produced by Schizosaccharomyces japonicus var. versatilis. The exo-beta-(1-->3)-glucanase had no detectable effect on the walls, but amorphous wall material was removed by action of the endo-beta-(1-->3)- and endo-beta-(1-->6)-glucanases of B. circulans to reveal a wall component consisting of densely interwoven microfibrils. The fibrils were hydrolyzed by treatment with the Schiz. japonicus endo-beta-(1-->3)-glucanase followed by B. circulans endo-alpha-(1-->3)-glucanase--suggesting that they were composed of -beta-(1-->3)-linked glucan and alpha-(1-->3)-linked glucan. The presence of a fibrillar component in untreated walls was evident after negative staining.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Kopecká M, Fleet GH, Phaff HJ","authors_abbrev":"Kopecká M et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"J Struct Biol 1995 Mar;114(2):140-52","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1995","pubmed_entrez_date":"1995-03-01","pubmed_publication_date":"Mar 1995","terms_by_termid":{},"title":"Ultrastructure of the cell wall of Schizosaccharomyces pombe following treatment with various glucanases.","uniquename":"PMID:7612397"}


id: PMID:21802294
data:
  {"abstract":"Eukaryotes segregate chromosomes in \"open\" or \"closed\" mitosis, depending on whether their nuclear envelopes (NEs) break down or remain intact. Here we show that the control of the nuclear surface area may determine the choice between these two modes. The dividing nucleus does not expand its surface in the fission yeast Schizosaccharomyces japonicus, confining the mitotic spindle and causing it to buckle. The NE ruptures in anaphase, releasing the compressive stress and allowing chromosome segregation. Blocking the NE expansion in the related species Schizosaccharomyces pombe that undergoes closed mitosis induces spindle buckling and collapse in the absence of an intrinsic NE rupture mechanism. We propose that scaling considerations could have shaped the evolution of eukaryotic mitosis by necessitating either nuclear surface expansion or the NE breakdown.","alleles_by_uniquename":{"SJAG_01330:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01330","name":"mad2delta","uniquename":"SJAG_01330:allele-1"},"SJAG_01745:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01745","name":"lem2delta","uniquename":"SJAG_01745:allele-1"}},"annotation_curators":[{"annotation_count":16,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"},{"annotation_count":1,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-05","authors":"Yam C, He Y, Zhang D, Chiam KH, Oliferenko S","authors_abbrev":"Yam C et al.","canto_added_date":"2021-05-10 02:38:30","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-01 07:44:20","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-05 11:58:24","canto_session_key":"ec486c9b0898d3c4","canto_session_submitted_date":"2021-07-05 12:18:55","canto_triage_status":"Curatable","citation":"Curr Biol 2011 Aug 09;21(15):1314-9","cv_annotations":{"biological_process":[{"annotations":[114611],"is_not":false,"summary":null,"term":"GO:0101024"}],"cellular_component":[{"annotations":[114600],"is_not":false,"summary":null,"term":"GO:0000785"},{"annotations":[114604,114605],"is_not":false,"summary":null,"term":"GO:0005783"},{"annotations":[114606],"is_not":false,"summary":null,"term":"GO:0098826"},{"annotations":[114599],"is_not":false,"summary":null,"term":"GO:0000776"},{"annotations":[114596],"is_not":false,"summary":null,"term":"GO:0005874"},{"annotations":[114601,114602,114603,114607],"is_not":false,"summary":null,"term":"GO:0005643"},{"annotations":[114597,114598],"is_not":false,"summary":null,"term":"GO:0005730"}],"single_locus_phenotype":[{"annotations":[114609],"is_not":false,"summary":null,"term":"FYPO:0003779"},{"annotations":[114608],"is_not":false,"summary":null,"term":"FYPO:0004318"},{"annotations":[114610],"is_not":false,"summary":null,"term":"FYPO:0007772"}]},"doi":"10.1016/j.cub.2011.06.052","gene_count":13,"genes_by_uniquename":{"SJAG_00175":null,"SJAG_00471":null,"SJAG_00684":null,"SJAG_00943":null,"SJAG_01006":null,"SJAG_01330":null,"SJAG_01374":null,"SJAG_01460":null,"SJAG_01745":null,"SJAG_02509":null,"SJAG_02830":null,"SJAG_03299":null,"SJAG_03603":null},"genotypes_by_uniquename":{"lem2delta":{"display_name":"lem2delta","display_uniquename":"lem2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01745:allele-1","expression":"Null"}]}]},"mad2delta":{"display_name":"mad2delta","display_uniquename":"mad2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01330:allele-1","expression":"Null"}]}]}},"ltp_gene_count":13,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2011","pubmed_entrez_date":"2011-08-02","pubmed_publication_date":"09 Aug 2011","terms_by_termid":{"FYECO:0000162":null,"FYPO:0003779":null,"FYPO:0004318":null,"FYPO:0007772":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"GO:0000776":null,"GO:0000785":null,"GO:0005643":null,"GO:0005730":null,"GO:0005783":null,"GO:0005874":null,"GO:0098826":null,"GO:0101024":null},"title":"Divergent strategies for controlling the nuclear membrane satisfy geometric constraints during nuclear division.","uniquename":"PMID:21802294"}


id: PMID:31380845
data:
  {"abstract":"Lipid metabolism and its regulation are of interest to both basic and applied life sciences and biotechnology. In this regard, various yeast species are used as models in lipid metabolic research or for industrial lipid production. Lipid droplets are highly dynamic storage bodies and their cellular content represents a convenient readout of the lipid metabolic state. Fluorescence microscopy is a method of choice for quantitative analysis of cellular lipid droplets, as it relies on widely available equipment and allows analysis of individual lipid droplets. Furthermore, microscopic image analysis can be automated, greatly increasing overall analysis throughput. Here, we describe an experimental and analytical workflow for automated detection and quantitative description of individual lipid droplets in three different model yeast species: the fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus, and the budding yeast Saccharomyces cerevisiae. Lipid droplets are visualized with BODIPY 493/503, and cell-impermeable fluorescent dextran is added to the culture media to help identify cell boundaries. Cells are subjected to 3D epifluorescence microscopy in green and blue channels and the resulting z-stack images are processed automatically by a MATLAB pipeline. The procedure outputs rich quantitative data on cellular lipid droplet content and individual lipid droplet characteristics in a tabular format suitable for downstream analyses in major spreadsheet or statistical packages. We provide example analyses of lipid droplet content under various conditions that affect cellular lipid metabolism.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Princová J, Schätz M, Ťupa O, Převorovský M","authors_abbrev":"Princová J et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"J Vis Exp 2019 07 17;(149)","cv_annotations":{},"doi":"10.3791/59889","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2019","pubmed_entrez_date":"2019-08-06","pubmed_publication_date":"17 07 2019","terms_by_termid":{},"title":"Analysis of Lipid Droplet Content in Fission and Budding Yeasts using Automated Image Processing.","uniquename":"PMID:31380845"}


id: PMID:33837814
data:
  {"abstract":"The capability of RNA isolation with good efficiency and high quality is essential for a downstream application such as RNA sequencing. It requires successful cell culturing and an effective RNA isolation method. Although effective methods are available, production of the homogenous mycelia and extraction of good-quality mycelial RNA from true invasive hyphae, which penetrated into the agar plates, are difficult. To overcome these problems, the aim of this study was to develop technical modifications which allow production of homogenous mycelial biomass without extra stimuli agents and improve quality of the RNA extracted from the fungal hyphae. Our alternative culture medium was suitable for production both yeast-phase cells and hyphae of the Schizosaccharomyces japonicus and other dimorphic species, such as the Candida albicans, Saccharomyces cerevisiae, and Jaminaea angkorensis. To improve quality of the mycelial RNA, we developed an isolation procedure of the hyphal tip, which eliminated the unnecessary vacuoles-containing parts of the hyphae. To increase RNA quantity, we used glass beads in the RNA extraction protocol to achieve stronger breaking of the mycelial walls. All these modifications can also be useful for researchers working with other dimorphic fungi and can contribute to the higher comparability of the transcriptional data coming from yeast-phase cells and hyphae or even from different species.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Papp LA, Ács-Szabó L, Póliska S, Miklós I","authors_abbrev":"Papp LA et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Curr Genet 2021 Oct;67(5):823-830","cv_annotations":{},"doi":"10.1007/s00294-021-01181-4","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-04-10","pubmed_publication_date":"Oct 2021","terms_by_termid":{},"title":"A modified culture medium and hyphae isolation method can increase quality of the RNA extracted from mycelia of a dimorphic fungal species.","uniquename":"PMID:33837814"}


id: PMID:31956022
data:
  {"abstract":"Membrane function is fundamental to life. Each species explores membrane lipid diversity within a genetically predefined range of possibilities. How membrane lipid composition in turn defines the functional space available for evolution of membrane-centered processes remains largely unknown. We address this fundamental question using related fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus. We show that, unlike S. pombe that generates membranes where both glycerophospholipid acyl tails are predominantly 16-18 carbons long, S. japonicus synthesizes unusual \"asymmetrical\" glycerophospholipids where the tails differ in length by 6-8 carbons. This results in stiffer bilayers with distinct lipid packing properties. Retroengineered S. pombe synthesizing the S.-japonicus-type phospholipids exhibits unfolded protein response and downregulates secretion. Importantly, our protein sequence comparisons and domain swap experiments support the hypothesis that transmembrane helices co-evolve with membranes, suggesting that, on the evolutionary scale, changes in membrane lipid composition may necessitate extensive adaptation of the membrane-associated proteome.","alleles_by_uniquename":{"SJAG_01458:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01458","name":"acb1delta","uniquename":"SJAG_01458:allele-1"}},"annotation_curators":[{"annotation_count":4,"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":"Makarova M, Peter M, Balogh G, Glatz A, MacRae JI, Lopez Mora N, Booth P, Makeyev E, Vigh L, Oliferenko S","authors_abbrev":"Makarova M et al.","canto_added_date":"2021-05-10 02:37:19","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-09 13:38:09","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 13:38:09","canto_session_key":"801e82954edbb6c1","canto_session_submitted_date":"2021-07-09 13:38:00","canto_triage_status":"Curatable","citation":"Curr Biol 2020 02 03;30(3):367-380.e8","cv_annotations":{"cellular_component":[{"annotations":[114768],"is_not":false,"summary":null,"term":"GO:0005801"},{"annotations":[114770],"is_not":false,"summary":null,"term":"GO:0005829"}],"single_locus_phenotype":[{"annotations":[114769],"is_not":false,"summary":null,"term":"FYPO:0000719"}]},"doi":"10.1016/j.cub.2019.11.043","gene_count":4,"genes_by_uniquename":{"SJAG_00816":null,"SJAG_01458":null,"SJAG_04107":null,"SJAG_04972":null},"genotypes_by_uniquename":{"acb1delta":{"display_name":"acb1delta","display_uniquename":"acb1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01458:allele-1","expression":"Null"}]}]}},"ltp_gene_count":4,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[{"evidence":"Co-purification","gene_uniquename":"SJAG_04972","interactor_uniquename":"SJAG_04107","reference_uniquename":"PMID:31956022","throughput":"low"}],"publication_year":"2020","pubmed_entrez_date":"2020-01-21","pubmed_publication_date":"03 02 2020","terms_by_termid":{"FYECO:0000126":null,"FYPO:0000719":null,"GO:0005801":null,"GO:0005829":null},"title":"Delineating the Rules for Structural Adaptation of Membrane-Associated Proteins to Evolutionary Changes in Membrane Lipidome.","uniquename":"PMID:31956022"}


id: PMID:19330769
data:
  {"abstract":"The fission yeast Schizosaccharomyces japonicus var. japonicus belong to the genus Schizosaccharomyces, together with Schizosaccharomyces pombe, which has been well studied as a model organism. In contrast, Sz. japonicus is poorly characterized and genetic tools were yet to be developed. We here report the isolation of the heterothallic haploids NIG2017, NIG2025 and NIG2028, which were derivatives of a Sz. japonicus homothallic strain (NIG2008). Based on the genomic sequence of Sz. japonicus, released by the Broad Institute, we found that Sz. japonicus also possesses orthologues of the mating-type genes of Sz. pombe; two mat-M (-) and two mat-P (+) genes. As expected, heterothallic strains were defective in one of the Sz. japonicus mat genes (mat(sj)). We confirmed that NIG2017 and NIG2025 strains only expressed mRNA from the mat(sj)-P genes, while homothallic strains expressed both mat(sj)-M and mat(sj)-P. Although the NIG2028 strain expressed both gene products, mat(sj)-P was found mutated, which may have conferred the heterothallic phenotype of the mutant. Thus, we concluded that these were stable heterothallic strains. We designated NIG2017 and NIG2025 as h(+) and NIG 2028 as h(-), respectively. We also found additional h(-) strains (NIG5872 and NIG5873) that arose from the cross between NIG2017 and NIG2028 derivatives. In addition to that, we have constructed a ura4(sj)-deleted strain and an ade6(sj)-mutated strain. We used these heterothallic strains and the auxotroph strains to perform spore dissection analysis to determine the genetic distances between several loci, and found that the mating type loci and ade6(sj) locus were linked to centromeres.","alleles_by_uniquename":{"SJAG_01081:allele-1":{"allele_type":"nonsense_mutation","description":"S427>stop","gene_uniquename":"SJAG_01081","name":"ade6-domE","uniquename":"SJAG_01081:allele-1"},"SJAG_03164:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03164","name":"ura4delta","uniquename":"SJAG_03164:allele-1"}},"annotation_curators":[{"annotation_count":2,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-23","authors":"Furuya K, Niki H","authors_abbrev":"Furuya K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-23 13:08:27","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-23 13:08:26","canto_session_key":"386d294cfcac2a63","canto_session_submitted_date":"2022-11-23 13:07:46","canto_triage_status":"Curatable","citation":"Yeast 2009 Apr;26(4):221-33","cv_annotations":{"single_locus_phenotype":[{"annotations":[114367],"is_not":false,"summary":null,"term":"FYPO:0000747"},{"annotations":[114368],"is_not":false,"summary":null,"term":"FYPO:0001012"}]},"doi":"10.1002/yea.1662","gene_count":2,"genes_by_uniquename":{"SJAG_01081":null,"SJAG_03164":null},"genotypes_by_uniquename":{"ade6-domE-S427>stop-nonsense_mutation-expression-not_assayed_or_wild_type":{"display_name":"ade6-domE(S427>stop)","display_uniquename":"ade6-domE-S427>stop-nonsense_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-1","expression":"Not assayed or wild type"}]}]},"ura4delta":{"display_name":"ura4delta","display_uniquename":"ura4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03164:allele-1","expression":"Null"}]}]}},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2009","pubmed_entrez_date":"2009-03-31","pubmed_publication_date":"Apr 2009","terms_by_termid":{"FYPO:0000747":null,"FYPO:0001012":null},"title":"Isolation of heterothallic haploid and auxotrophic mutants of Schizosaccharomyces japonicus.","uniquename":"PMID:19330769"}


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:0000041
data:
  {"alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"canto_curator_role":"JaponicusDB","cv_annotations":{"biological_process":[{"annotations":[65942],"is_not":false,"summary":null,"term":"GO:0006021"},{"annotations":[67546],"is_not":false,"summary":null,"term":"GO:0006782"},{"annotations":[57766],"is_not":false,"summary":null,"term":"GO:0006048"}]},"gene_count":3,"genes_by_uniquename":{"SJAG_00097":null,"SJAG_00519":null,"SJAG_03739":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0006021":null,"GO:0006048":null,"GO:0006782":null},"uniquename":"GO_REF:0000041"}


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_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":[114731,114735],"is_not":false,"summary":null,"term":"FYPO:0007782"},{"annotations":[114730],"is_not":false,"summary":null,"term":"FYPO:0007774"},{"annotations":[114732,114733,114734],"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","references_by_uniquename":{"PMID:20368354":null,"PMID:23090706":null},"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:32265131
data:
  {"abstract":"The N- and O-linked oligosaccharides from fission yeast Schizosaccharomyces pombe not only contain large amounts of d-mannose (Man) but also contain large amounts of d-galactose (Gal). Although the galactomannans of S. pombe are mainly composed of α1,2- or α1,3-linked Gals, some of the terminal α1,2-linked Gals are found to be linked to pyruvylated β1,3-linked galactose (PvGal). We have determined the structural characteristics of the N-glycans and O-glycans in three Schizosaccharomyces species (S. japonicus, S. octosporus, and S. cryophilus) using lectin blot,  1 H NMR spectroscopy, and size-fractionation high performance liquid chromatography (HPLC), and found that the galactosylation of oligosaccharides was a common feature in fission yeasts. In addition, each of the terminal Galα1,2-, Galβ1,3- and non-substituted Man residues exhibited distinct characteristics. A BLAST search of gene databases in Schizosaccharomyces identified genes homologous to pvg1 encoding pyruvyltransferase of S. pombe. These genes, when expressed in an S. pombe pvg1Δ strains, led to the pyruvylation of non-reducing terminal β-linked Gal, suggesting the biosynthetic pathway of PvGal-containing oligosaccharides is highly conserved in fission yeasts.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Fukunaga T, Tanaka N, Furumoto T, Nakakita S, Ohashi T, Higuchi Y, Maekawa H, Takegawa K","authors_abbrev":"Fukunaga T et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"J Biosci Bioeng 2020 Aug;130(2):128-136","cv_annotations":{},"doi":"10.1016/j.jbiosc.2020.03.008","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2020","pubmed_entrez_date":"2020-04-09","pubmed_publication_date":"Aug 2020","terms_by_termid":{},"title":"Characterization of N- and O-linked galactosylated oligosaccharides from fission yeast species.","uniquename":"PMID:32265131"}


id: 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_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":[114504],"is_not":false,"summary":null,"term":"GO:0005730"}],"multi_locus_phenotype":[{"annotations":[114518,114519,114520,114522],"is_not":false,"summary":null,"term":"FYPO:0000674"}],"single_locus_phenotype":[{"annotations":[114505,114506,114507,114521],"is_not":false,"summary":null,"term":"FYPO:0000080"},{"annotations":[114514,114515,114516],"is_not":false,"summary":null,"term":"FYPO:0000618"},{"annotations":[114523,114524,114525],"is_not":false,"summary":null,"term":"FYPO:0001327"},{"annotations":[114511,114512,114513],"is_not":false,"summary":null,"term":"FYPO:0001387"},{"annotations":[114508,114509,114510],"is_not":false,"summary":null,"term":"FYPO:0000324"},{"annotations":[114517],"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 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type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03198:allele-3","expression":"Overexpression"}]}]},"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"}]}]},"cem1delta":{"display_name":"cem1delta","display_uniquename":"cem1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01946:allele-1","expression":"Null"}]}]},"cut23-415-A186T_ts-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cut23-415(A186T ts)","display_uniquename":"cut23-415-A186T_ts-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03351:allele-1","expression":"Not assayed or wild type"}]}]},"nuc2-1051-E405K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"nuc2-1051(E405K ts)","display_uniquename":"nuc2-1051-E405K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01956:allele-1","expression":"Not assayed or wild type"}]}]},"oar2-51-Y189D_cold_sensitive-amino_acid_mutation-expression-overexpression":{"display_name":"oar2-51(Y189D cold sensitive)[Overexpression]","display_uniquename":"oar2-51-Y189D_cold_sensitive-amino_acid_mutation-expression-overexpression","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03198:allele-2","expression":"Overexpression"}]}]},"oar2-dm12-R72A,L75A,R106A,L109A-amino_acid_mutation-expression-overexpression":{"display_name":"oar2-dm12(R72A,L75A,R106A,L109A aa)[Overexpression]","display_uniquename":"oar2-dm12-R72A,L75A,R106A,L109A-amino_acid_mutation-expression-overexpression","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03198:allele-3","expression":"Overexpression"}]}]},"oar2delta":{"display_name":"oar2delta","display_uniquename":"oar2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03198:allele-1","expression":"Null"}]}]}},"ltp_gene_count":6,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2013","pubmed_entrez_date":"2013-06-22","pubmed_publication_date":"Sep 2013","references_by_uniquename":{"PMID:23786411":null},"terms_by_termid":{"FYECO:0000004":null,"FYECO:0000006":null,"FYECO:0000137":null,"FYPO:0000080":null,"FYPO:0000324":null,"FYPO:0000618":null,"FYPO:0000674":null,"FYPO:0001327":null,"FYPO:0001387":null,"FYPO:0004683":null,"FYPO_EXT:0000001":null,"GO:0005730":null},"title":"Regulation of nuclear envelope dynamics via APC/C is necessary for the progression of semi-open mitosis in Schizosaccharomyces japonicus.","uniquename":"PMID:23786411"}


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


id: PMID:25866389
data:
  {"abstract":"Strategies to position the division apparatus exhibit a bewildering diversity [1], but how these mechanisms evolve remains virtually unknown. Here, we explore the plasticity of division site positioning in fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus. We demonstrate that, whereas both species divide in the middle, only S. pombe uses the anillin Mid1 as a primary nucleus-derived cue to assemble the actomyosin ring at the equatorial cortex. We trace this variance to the divergence in subcellular targeting of Mid1 and show that duplication of an ancestral anillin early in the Schizosaccharomyces lineage may have led to subfunctionalization of the Mid1 orthologs. In contrast to S. pombe, medial assembly of the actomyosin ring in mitotic S. japonicus relies on the cortical anchor protein Cdc15 regulated by the tip-localized kinase Pom1. Our data suggest that division site placement is determined by cortical positioning of the actomyosin-plasma membrane linkers and that both identity of the linker and control of its subcellular targeting are highly modular.","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"},"SJAG_01143:allele-2":{"allele_type":"partial_amino_acid_deletion","description":"711-723","gene_uniquename":"SJAG_01143","name":"mid1-delta(711-723 a.a.)","uniquename":"SJAG_01143:allele-2"},"SJAG_02392:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02392","name":"pom1delta","uniquename":"SJAG_02392:allele-1"},"SJAG_03596:allele-1":{"allele_type":"amino_acid_mutation","description":"L264P,P442T","gene_uniquename":"SJAG_03596","name":"cdc15-A","uniquename":"SJAG_03596:allele-1"},"SJAG_04332:allele-1":{"allele_type":"amino_acid_mutation","description":"I30T,T572P","gene_uniquename":"SJAG_04332","name":"cdc25-D9","uniquename":"SJAG_04332:allele-1"}},"annotation_curators":[{"annotation_count":3,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"},{"annotation_count":34,"community_curator":true,"file_name":null,"file_type":null,"name":"Ying Gu","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-05-12","authors":"Gu Y, Yam C, Oliferenko S","authors_abbrev":"Gu Y et al.","canto_added_date":"2021-05-10 02:37:54","canto_annotation_status":"APPROVED","canto_approved_date":"2021-05-16 08:31:49","canto_curator_name":"Ying Gu","canto_curator_role":"community","canto_first_approved_date":"2021-05-12 14:24:14","canto_session_key":"bc986e831d627df1","canto_session_submitted_date":"2021-05-14 13:43:22","canto_triage_status":"Curatable","citation":"Curr Biol 2015 May 04;25(9):1187-94","cv_annotations":{"biological_process":[{"annotations":[114656],"is_not":false,"summary":null,"term":"GO:1902408"},{"annotations":[114657],"is_not":false,"summary":null,"term":"GO:1903617"},{"annotations":[114655],"is_not":true,"summary":null,"term":"GO:1902408"}],"cellular_component":[{"annotations":[114663,114664],"is_not":false,"summary":null,"term":"GO:0051286"},{"annotations":[114659,114661,114666,114668],"is_not":false,"summary":null,"term":"GO:1990753"},{"annotations":[114660,114662,114665,114667,114669],"is_not":false,"summary":null,"term":"GO:0110085"}],"multi_locus_phenotype":[{"annotations":[114647],"is_not":false,"summary":null,"term":"FYPO:0000231"},{"annotations":[114651],"is_not":false,"summary":null,"term":"FYPO:0005503"},{"annotations":[114653],"is_not":false,"summary":null,"term":"FYPO:0007177"},{"annotations":[114652],"is_not":false,"summary":null,"term":"FYPO:0000729"},{"annotations":[114649],"is_not":false,"summary":null,"term":"FYPO:0003946"},{"annotations":[114648],"is_not":false,"summary":null,"term":"FYPO:0000118"}],"qualitative_gene_expression":[{"annotations":[114639,114658],"is_not":false,"summary":null,"term":"PomGeneEx:0000011"}],"single_locus_phenotype":[{"annotations":[114640],"is_not":false,"summary":null,"term":"FYPO:0000231"},{"annotations":[114671,114672],"is_not":false,"summary":null,"term":"FYPO:0000731"},{"annotations":[114645],"is_not":false,"summary":null,"term":"FYPO:0005503"},{"annotations":[114642,114643,114650,114654],"is_not":false,"summary":null,"term":"FYPO:0007177"},{"annotations":[114673],"is_not":false,"summary":null,"term":"FYPO:0002026"},{"annotations":[114670],"is_not":false,"summary":null,"term":"FYPO:0003535"},{"annotations":[114641],"is_not":false,"summary":null,"term":"FYPO:0000729"},{"annotations":[114644],"is_not":false,"summary":null,"term":"FYPO:0007701"},{"annotations":[114637,114638],"is_not":false,"summary":null,"term":"FYPO:0000118"},{"annotations":[114646],"is_not":false,"summary":null,"term":"FYPO:0000644"}]},"doi":"10.1016/j.cub.2015.02.056","gene_count":8,"genes_by_uniquename":{"SJAG_00118":null,"SJAG_01143":null,"SJAG_01665":null,"SJAG_02392":null,"SJAG_03596":null,"SJAG_03703":null,"SJAG_04332":null,"SJAG_04498":null},"genotypes_by_uniquename":{"cdc15-A-L264P,P442T-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cdc15-A(L264P,P442T aa)","display_uniquename":"cdc15-A-L264P,P442T-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03596:allele-1","expression":"Not assayed or wild type"}]}]},"cdc15-A-L264P,P442T-amino_acid_mutation-expression-not_assayed_or_wild_type__mid1delta":{"display_name":"cdc15-A(L264P,P442T aa) mid1delta","display_uniquename":"cdc15-A-L264P,P442T-amino_acid_mutation-expression-not_assayed_or_wild_type__mid1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03596:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_01143:allele-1","expression":"Null"}]}]},"cdc25-D9-I30T,T572P-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cdc25-D9(I30T,T572P aa)","display_uniquename":"cdc25-D9-I30T,T572P-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04332:allele-1","expression":"Not assayed or wild type"}]}]},"mid1-delta(711-723_a.a.)-711-723-partial_amino_acid_deletion-expression-not_assayed_or_wild_type":{"display_name":"mid1-delta(711-723 a.a.)(aa)","display_uniquename":"mid1-delta(711-723_a.a.)-711-723-partial_amino_acid_deletion-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01143:allele-2","expression":"Not assayed or wild type"}]}]},"mid1delta":{"display_name":"mid1delta","display_uniquename":"mid1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01143:allele-1","expression":"Null"}]}]},"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"}]}]},"mid1delta__pom1delta":{"display_name":"mid1delta pom1delta","display_uniquename":"mid1delta__pom1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01143:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_02392:allele-1","expression":"Null"}]}]},"mid2delta":{"display_name":"mid2delta","display_uniquename":"mid2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00118:allele-1","expression":"Null"}]}]},"pom1delta":{"display_name":"pom1delta","display_uniquename":"pom1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02392:allele-1","expression":"Null"}]}]}},"ltp_gene_count":8,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2015","pubmed_entrez_date":"2015-04-14","pubmed_publication_date":"04 May 2015","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000005":null,"FYECO:0000137":null,"FYECO:0000162":null,"FYPO:0000118":null,"FYPO:0000231":null,"FYPO:0000644":null,"FYPO:0000729":null,"FYPO:0000731":null,"FYPO:0002026":null,"FYPO:0003535":null,"FYPO:0003946":null,"FYPO:0005503":null,"FYPO:0007177":null,"FYPO:0007701":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"GO:0000085":null,"GO:0000087":null,"GO:0051286":null,"GO:0051325":null,"GO:0051329":null,"GO:0110085":null,"GO:1902408":null,"GO:1903617":null,"GO:1990753":null,"PomGeneEx:0000011":null},"title":"Rewiring of cellular division site selection in evolution of fission yeasts.","uniquename":"PMID:25866389"}


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


id: PMID:28954740
data:
  {"abstract":"After mitosis, nuclear reorganization occurs together with decondensation of mitotic chromosomes and reformation of the nuclear envelope, thereby restoring the Ran-GTP gradient between the nucleus and cytoplasm. The Ran-GTP gradient is dependent on Pim1/RCC1. Interestingly, a defect in Pim1/RCC1 in  Schizosaccharomyces pombe  causes postmitotic condensation of chromatin, namely hypercondensation, suggesting a relationship between the Ran-GTP gradient and chromosome decondensation. However, how Ran-GTP interacts with chromosome decondensation is unresolved. To examine this interaction, we used  Schizosaccharomyces japonicus , which is known to undergo partial breakdown of the nuclear membrane during mitosis. We found that Pim1/RCC1 was localized on nuclear pores, but this localization failed in a temperature-sensitive mutant of Pim1/RCC1. The mutant cells exhibited hypercondensed chromatin after mitosis due to prolonged association of condensin on the chromosomes. Conceivably, a condensin-dephosphorylation defect might cause hypercondensed chromatin, since chromosomal localization of condensin is dependent on phosphorylation by cyclin-dependent kinase (CDK). Indeed, CDK-phospho-mimic mutation of condensin alone caused untimely condensin localization, resulting in hypercondensed chromatin. Together, these results suggest that dephosphorylation of CDK sites of condensin might require the Ran-GTP gradient produced by nuclear pore-localized Pim1/RCC1.","alleles_by_uniquename":{"SJAG_00871:allele-1":{"allele_type":"amino_acid_mutation","description":"cut3-T19E","gene_uniquename":"SJAG_00871","name":"cut3-T19E","uniquename":"SJAG_00871:allele-1"},"SJAG_04284:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04284","name":"nup61delta","uniquename":"SJAG_04284:allele-1"},"SJAG_04464:allele-1":{"allele_type":"amino_acid_mutation","description":"R152C","gene_uniquename":"SJAG_04464","name":"pim1-R152C","synonyms":[{"name":"Inferred CDK-phospho-mimic mutation","reference":"PMID:28954740","type":"exact"}],"uniquename":"SJAG_04464:allele-1"}},"annotation_curators":[{"annotation_count":12,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-23","authors":"Aoki K, Niki H","authors_abbrev":"Aoki K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-23 15:00:26","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-23 15:00:26","canto_session_key":"7c26b8235c98c3eb","canto_session_submitted_date":"2022-11-23 15:00:18","canto_triage_status":"Curatable","citation":"Biol Open 2017 Nov 15;6(11):1614-1628","cv_annotations":{"biological_process":[{"annotations":[114279],"is_not":false,"summary":null,"term":"GO:0101024"},{"annotations":[114284],"is_not":false,"summary":null,"term":"GO:0006998"}],"cellular_component":[{"annotations":[114283],"is_not":false,"summary":null,"term":"GO:0120321"}],"multi_locus_phenotype":[{"annotations":[114286],"is_not":false,"summary":null,"term":"FYPO:0000619"},{"annotations":[114285],"is_not":false,"summary":null,"term":"FYPO:0001489"}],"single_locus_phenotype":[{"annotations":[114287],"is_not":false,"summary":null,"term":"FYPO:0000619"},{"annotations":[114281],"is_not":false,"summary":null,"term":"FYPO:0003738"},{"annotations":[114288],"is_not":false,"summary":null,"term":"FYPO:0000815"},{"annotations":[114280],"is_not":false,"summary":null,"term":"FYPO:0000082"},{"annotations":[114282],"is_not":false,"summary":null,"term":"FYPO:0003976"},{"annotations":[114278],"is_not":false,"summary":null,"term":"FYPO:0001387"}]},"doi":"10.1242/bio.027193","gene_count":4,"genes_by_uniquename":{"SJAG_00471":null,"SJAG_00871":null,"SJAG_04284":null,"SJAG_04464":null},"genotypes_by_uniquename":{"cut3-T19E-cut3-T19E-amino_acid_mutation-expression-not_assayed_or_wild_type__pim1-R152C-R152C-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cut3-T19E(aa) pim1-R152C(aa)","display_uniquename":"cut3-T19E-cut3-T19E-amino_acid_mutation-expression-not_assayed_or_wild_type__pim1-R152C-R152C-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00871:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04464:allele-1","expression":"Not assayed or wild type"}]}]},"nup61delta":{"display_name":"nup61delta","display_uniquename":"nup61delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04284:allele-1","expression":"Null"}]}]},"pim1-R152C-R152C-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"pim1-R152C(aa)","display_uniquename":"pim1-R152C-R152C-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04464:allele-1","expression":"Not assayed or wild type"}]}]}},"ltp_gene_count":4,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[{"evidence":"Affinity Capture-Western","gene_uniquename":"SJAG_04464","interactor_uniquename":"SJAG_00471","reference_uniquename":"PMID:28954740","throughput":"low"}],"publication_year":"2017","pubmed_entrez_date":"2017-09-29","pubmed_publication_date":"15 Nov 2017","references_by_uniquename":{"PMID:28954740":null},"terms_by_termid":{"FYECO:0000004":null,"FYECO:0000005":null,"FYECO:0000137":null,"FYPO:0000082":null,"FYPO:0000619":null,"FYPO:0000815":null,"FYPO:0001387":null,"FYPO:0001489":null,"FYPO:0003738":null,"FYPO:0003976":null,"FYPO_EXT:0000001":null,"GO:0006998":null,"GO:0101024":null,"GO:0120321":null},"title":"Release of condensin from mitotic chromosomes requires the Ran-GTP gradient in the reorganized nucleus.","uniquename":"PMID:28954740"}


id: PMID:29566183
data:
  {"abstract":"Dimorphic yeasts transform into filamentous cells or hyphae in response to environmental cues. The mechanisms for the hyphal transition of dimorphic yeasts have mainly been studied in Candida albicans, an opportunistic human fungal pathogen. The Ras1-MAPK pathway is a major signal transduction pathway for hyphal transition in C. albicans. Recently, the non-pathogenic dimorphic yeast Schizosaccharomyces japonicus has also been used for genetic analyses of hyphal induction. We confirmed that Ras1-MAPK and other MAPK pathways exist in Sz. japonicus. To examine how hyphal transition is induced by environmental stress-triggered signal transduction, we studied the hyphal transition of deletion mutants of MAPK pathways in Sz. japonicus. We found that the MAPK pathways are not involved in hyphal induction, although the mating response is dependent on these pathways. However, only Ras1 deletion caused a severe defect in hyphal development via both DNA damage and environmental stressors. In fact, genes on the Cdc42 branch of the Ras1 (Ras1-Cdc42) pathway, efc25Sj, scd1Sj and scd2Sj, are required for hyphal development. Cell morphology analysis indicated that the apical growth of hyphal cells was inhibited in Ras1-Cdc42-pathway deletion mutants. Thus, the control of cell polarity by the Ras1-Cdc42 pathway is crucial for hyphal development.","alleles_by_uniquename":{"SJAG_00514:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00514","name":"scd1delta","uniquename":"SJAG_00514:allele-1"},"SJAG_00993:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00993","name":"byr1delta","uniquename":"SJAG_00993:allele-1"},"SJAG_01181:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01181","name":"pek1delta","uniquename":"SJAG_01181:allele-1"},"SJAG_01718:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01718","name":"byr2delta","uniquename":"SJAG_01718:allele-1"},"SJAG_01794:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01794","name":"scd2delta","uniquename":"SJAG_01794:allele-1"},"SJAG_02342:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02342","name":"wis1delta","uniquename":"SJAG_02342:allele-1"},"SJAG_02379:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02379","name":"gap1delta","uniquename":"SJAG_02379:allele-1"},"SJAG_02486:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02486","name":"ste6delta","uniquename":"SJAG_02486:allele-1"},"SJAG_02592:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02592","name":"sty1delta","uniquename":"SJAG_02592:allele-1"},"SJAG_02819:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02819","name":"efc25delta","uniquename":"SJAG_02819:allele-1"},"SJAG_02923:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02923","name":"spk1delta","uniquename":"SJAG_02923:allele-1"},"SJAG_03384:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03384","name":"wis4delta","uniquename":"SJAG_03384:allele-1"},"SJAG_03453:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03453","name":"ras1delta","uniquename":"SJAG_03453:allele-1"},"SJAG_03753:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03753","name":"mkh1delta","uniquename":"SJAG_03753:allele-1"},"SJAG_04009:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04009","name":"ste11delta","uniquename":"SJAG_04009:allele-1"},"SJAG_04551:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04551","name":"pmk1delta","uniquename":"SJAG_04551:allele-1"},"SJAG_04777:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04777","name":"win1delta","uniquename":"SJAG_04777:allele-1"}},"annotation_curators":[{"annotation_count":38,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-18","authors":"Nozaki S, Furuya K, Niki H","authors_abbrev":"Nozaki S et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-18 13:44:52","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-18 13:44:52","canto_session_key":"18862c3d67da0cb0","canto_session_submitted_date":"2022-11-18 13:44:26","canto_triage_status":"Curatable","citation":"FEMS Yeast Res 2018 06 01;18(4)","cv_annotations":{"single_locus_phenotype":[{"annotations":[114392],"is_not":false,"summary":null,"term":"FYPO:0007773"},{"annotations":[114375,114376,114385,114407,114408],"is_not":false,"summary":null,"term":"FYPO:0007789"},{"annotations":[114404],"is_not":false,"summary":null,"term":"FYPO:0000584"},{"annotations":[114374,114378,114382],"is_not":false,"summary":null,"term":"FYPO:0001355"},{"annotations":[114406],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[114373,114379,114380,114384,114387,114389,114390,114403,114405],"is_not":false,"summary":null,"term":"FYPO:0000280"},{"annotations":[114381,114386,114388,114391,114393,114394,114395,114396,114397,114398,114399,114400,114401,114402],"is_not":false,"summary":null,"term":"FYPO:0000124"},{"annotations":[114372,114377,114383,114409],"is_not":false,"summary":null,"term":"FYPO:0002380"}]},"doi":"10.1093/femsyr/foy031","gene_count":17,"genes_by_uniquename":{"SJAG_00514":null,"SJAG_00993":null,"SJAG_01181":null,"SJAG_01718":null,"SJAG_01794":null,"SJAG_02342":null,"SJAG_02379":null,"SJAG_02486":null,"SJAG_02592":null,"SJAG_02819":null,"SJAG_02923":null,"SJAG_03384":null,"SJAG_03453":null,"SJAG_03753":null,"SJAG_04009":null,"SJAG_04551":null,"SJAG_04777":null},"genotypes_by_uniquename":{"byr1delta":{"display_name":"byr1delta","display_uniquename":"byr1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00993:allele-1","expression":"Null"}]}]},"byr2delta":{"display_name":"byr2delta","display_uniquename":"byr2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01718:allele-1","expression":"Null"}]}]},"efc25delta":{"display_name":"efc25delta","display_uniquename":"efc25delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02819:allele-1","expression":"Null"}]}]},"gap1delta":{"display_name":"gap1delta","display_uniquename":"gap1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02379:allele-1","expression":"Null"}]}]},"mkh1delta":{"display_name":"mkh1delta","display_uniquename":"mkh1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03753:allele-1","expression":"Null"}]}]},"pek1delta":{"display_name":"pek1delta","display_uniquename":"pek1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01181:allele-1","expression":"Null"}]}]},"pmk1delta":{"display_name":"pmk1delta","display_uniquename":"pmk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04551:allele-1","expression":"Null"}]}]},"ras1delta":{"display_name":"ras1delta","display_uniquename":"ras1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03453:allele-1","expression":"Null"}]}]},"scd1delta":{"display_name":"scd1delta","display_uniquename":"scd1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00514:allele-1","expression":"Null"}]}]},"scd2delta":{"display_name":"scd2delta","display_uniquename":"scd2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01794:allele-1","expression":"Null"}]}]},"spk1delta":{"display_name":"spk1delta","display_uniquename":"spk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02923:allele-1","expression":"Null"}]}]},"ste11delta":{"display_name":"ste11delta","display_uniquename":"ste11delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04009:allele-1","expression":"Null"}]}]},"ste6delta":{"display_name":"ste6delta","display_uniquename":"ste6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02486:allele-1","expression":"Null"}]}]},"sty1delta":{"display_name":"sty1delta","display_uniquename":"sty1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02592:allele-1","expression":"Null"}]}]},"win1delta":{"display_name":"win1delta","display_uniquename":"win1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04777:allele-1","expression":"Null"}]}]},"wis1delta":{"display_name":"wis1delta","display_uniquename":"wis1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02342:allele-1","expression":"Null"}]}]},"wis4delta":{"display_name":"wis4delta","display_uniquename":"wis4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03384:allele-1","expression":"Null"}]}]}},"ltp_gene_count":17,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2018","pubmed_entrez_date":"2018-03-23","pubmed_publication_date":"01 06 2018","terms_by_termid":{"FYECO:0000137":null,"FYPO:0000124":null,"FYPO:0000280":null,"FYPO:0000584":null,"FYPO:0001355":null,"FYPO:0002380":null,"FYPO:0007773":null,"FYPO:0007789":null,"FYPO:0007790":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null},"title":"The Ras1-Cdc42 pathway is involved in hyphal development of Schizosaccharomyces japonicus.","uniquename":"PMID:29566183"}


id: PMID: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_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":[114774],"is_not":false,"summary":null,"term":"MOD:00696"}],"single_locus_phenotype":[{"annotations":[114773],"is_not":false,"summary":null,"term":"FYPO:0002998"},{"annotations":[114771,114772],"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: PMID:35693892
data:
  {"abstract":"The S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 catalyzes biosynthesis of 4-demethylwyosine (imG-14), the precursor for wyosine, the hypermodified guanine-derived nucleotide present at position 37 of phenylalanine tRNAs of archaea and eukarya. Eukaryotic TYW1 enzymes contain N-terminal flavodoxin-like and C-terminal radical-SAM domains. We determined co-crystal structures of the flavodoxin-like domain of the putative Tyw1 from  Schizosaccharomyces japonicus  in complex with flavin mononucleotide (FMN), exploiting an unexpected anomalous scatterer present in the recombinant protein. Our results show how eukaryotic TYW1 enzymes bind the coenzyme FMN and will help further elucidation of the structural enzymology of 4-demethylwyosine synthesis.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Sjekloća L, Ferré-D'Amaré AR","authors_abbrev":"Sjekloća L et al.","canto_added_date":"2023-05-04 00:40:03","canto_curator_role":"JaponicusDB","canto_triage_status":"Structure","citation":"MicroPubl Biol 2022;2022","cv_annotations":{},"doi":"10.17912/micropub.biology.000570","gene_count":1,"genes_by_uniquename":{"SJAG_04265":null},"genotypes_by_uniquename":{},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"pdb_entries":[{"entry_authors":"Sjekloca L,Ferre D'Amare AR","entry_authors_abbrev":"Sjekloca L et al.","experimental_method":"X-ray","gene_chains":[{"chain":"A","gene_uniquename":"SJAG_04265","position":"76-251"}],"pdb_id":"6pup","reference_uniquename":"PMID:35693892","resolution":"1.89","title":"1.9 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN"},{"entry_authors":"Sjekloca L,Ferre-D'Amare AR","entry_authors_abbrev":"Sjekloca L et al.","experimental_method":"X-ray","gene_chains":[{"chain":"A","gene_uniquename":"SJAG_04265","position":"30-251"}],"pdb_id":"6puq","reference_uniquename":"PMID:35693892","resolution":"1.56","title":"1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN"}],"physical_interactions":[],"publication_year":"2022","pubmed_entrez_date":"2022-06-13","pubmed_publication_date":"2022","terms_by_termid":{},"title":"Biochemical and structural characterization of the flavodoxin-like domain of the  Schizosaccharomyces japonicus  putative tRNA  Phe  4-demethylwyosine synthase Tyw1 in complex with FMN.","uniquename":"PMID:35693892"}


id: PMID:22586155
data:
  {"abstract":"tRNA genes are interspersed throughout eukaryotic DNA, contributing to genome architecture and evolution in addition to translation of the transcriptome. Codon use correlates with tRNA gene copy number in noncomplex organisms including yeasts. Synonymous codons impact translation with various outcomes, dependent on relative tRNA abundances. Availability of whole-genome sequences allowed us to examine tRNA gene copy number variation (tgCNV) and codon use in four Schizosaccharomyces species and Saccharomyces cerevisiae. tRNA gene numbers vary from 171 to 322 in the four Schizosaccharomyces despite very high similarity in other features of their genomes. In addition, we performed whole-genome sequencing of several related laboratory strains of Schizosaccharomyces pombe and found tgCNV at a cluster of tRNA genes. We examined for the first time effects of wobble rules on correlation of tRNA gene number and codon use and showed improvement for S. cerevisiae and three of the Schizosaccharomyces species. In contrast, correlation in Schizosaccharomyces japonicus is poor due to markedly divergent tRNA gene content, and much worsened by the wobble rules. In japonicus, some tRNA iso-acceptor genes are absent and others are greatly reduced relative to the other yeasts, while genes for synonymous wobble iso-acceptors are amplified, indicating wobble use not apparent in any other eukaryote. We identified a subset of japonicus-specific wobbles that improves correlation of codon use and tRNA gene content in japonicus. We conclude that tgCNV is high among Schizo species and occurs in related laboratory strains of S. pombe (and expectedly other species), and tRNAome-codon analyses can provide insight into species-specific wobble decoding.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Iben JR, Maraia RJ","authors_abbrev":"Iben JR et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"RNA 2012 Jul;18(7):1358-72","cv_annotations":{},"doi":"10.1261/rna.032151.111","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-05-16","pubmed_publication_date":"Jul 2012","terms_by_termid":{},"title":"tRNAomics: tRNA gene copy number variation and codon use provide bioinformatic evidence of a new anticodon:codon wobble pair in a eukaryote.","uniquename":"PMID:22586155"}


id: PMID:12527786
data:
  {"abstract":"The fission yeasts are members of the fungal order Schizosaccharomycetales, a candidate deep-diverging group within Ascomycota. Although a great deal of molecular information is available from Schizosaccharomyces pombe, a model eukaryote, very little is available from other members of this group. In order to better characterize mitochondrial genome evolution in this fungal lineage, the mitochondrial DNA (mtDNA) of two additional fission yeasts, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus var. japonicus, was sequenced. Whereas the mtDNA of S.pombe is only 19 431 bp, the mtDNA of S.octosporus is 44 227 bp, and that of S.japonicus var. japonicus is over 80 kb. The size variation of these mtDNAs is due largely to non-coding regions. The gene content in the latter two mtDNAs is almost identical to that of the completely sequenced S.pombe mtDNA, which encodes 25 tRNA species, the large and small mitochondrial ribosomal RNAs (rnl and rns), the RNA component of mitochondrial RNaseP (rnpB), mitochondrial small subunit ribosomal protein 3 (rps3), cytochrome oxidase subunits 1, 2 and 3 (cox1, cox2 and cox3) and ATP-synthase subunits 6, 8 and 9 (atp6, atp8 and atp9). However, trnI2(cau) (C modified to lysidine) is absent in the S.octosporus mtDNA, as are corresponding ATA codons in its protein-coding genes, and rps3 and rnpB are not found in the mtDNA of S.japonicus var. japonicus. The mtDNA of S.octosporus contains five double hairpin elements, the first report of these elements in an ascomycete. This study provides further evidence in favor of the mobility of these elements, and supports their role in mitochondrial genome rearrangement. The results of our phylogenetic analysis support the monophyly of the Schizosaccharomycetales, but question their grouping within the Archiascomycota.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Bullerwell CE, Leigh J, Forget L, Lang BF","authors_abbrev":"Bullerwell CE et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Nucleic Acids Res 2003 Jan 15;31(2):759-68","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":"2003-01-16","pubmed_publication_date":"15 Jan 2003","terms_by_termid":{},"title":"A comparison of three fission yeast mitochondrial genomes.","uniquename":"PMID:12527786"}


id: PMID:32915139
data:
  {"abstract":"Cytokinesis, which enables the physical separation of daughter cells once mitosis has been completed, is executed in fungal and animal cells by a contractile actin- and myosin-based ring (CAR). In the fission yeast  Schizosaccharomyces pombe,  the formin For3 nucleates actin cables and also co-operates for CAR assembly during cytokinesis. Mitogen-activated protein kinases (MAPKs) regulate essential adaptive responses in eukaryotic organisms to environmental changes. We show that the stress-activated protein kinase pathway (SAPK) and its effector, MAPK Sty1, downregulates CAR assembly in  S. pombe  when its integrity becomes compromised during cytoskeletal damage and stress by reducing For3 levels. Accurate control of For3 levels by the SAPK pathway may thus represent a novel regulatory mechanism of cytokinesis outcome in response to environmental cues. Conversely, SAPK signaling favors CAR assembly and integrity in its close relative  Schizosaccharomyces japonicus,  revealing a remarkable evolutionary divergence of this response within the fission yeast clade.","alleles_by_uniquename":{"SJAG_00266:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00266","name":"atf1delta","uniquename":"SJAG_00266:allele-1"},"SJAG_02592:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02592","name":"sty1delta","uniquename":"SJAG_02592:allele-1"}},"annotation_curators":[{"annotation_count":5,"community_curator":true,"file_name":null,"file_type":null,"name":"Elisa Gómez Gil","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-05-13","authors":"Gómez-Gil E, Martín-García R, Vicente-Soler J, Franco A, Vázquez-Marín B, Prieto-Ruiz F, Soto T, Pérez P, Madrid M, Cansado J","authors_abbrev":"Gómez-Gil E et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2023-06-24 05:18:12","canto_curator_name":"Elisa Gómez Gil","canto_curator_role":"community","canto_first_approved_date":"2021-05-13 16:19:42","canto_session_key":"382ba25ae62a1134","canto_session_submitted_date":"2021-05-13 14:28:51","canto_triage_status":"Curatable","citation":"Elife 2020 09 11;9","cv_annotations":{"PSI-MOD":[{"annotations":[114778],"is_not":false,"summary":null,"term":"MOD:00696"}],"biological_process":[{"annotations":[114779],"is_not":false,"summary":null,"term":"GO:1903499"}],"single_locus_phenotype":[{"annotations":[114777],"is_not":false,"summary":null,"term":"FYPO:0002998"},{"annotations":[114775,114776],"is_not":false,"summary":null,"term":"FYPO:0000107"}]},"doi":"10.7554/eLife.57951","gene_count":2,"genes_by_uniquename":{"SJAG_00266":null,"SJAG_02592":null},"genotypes_by_uniquename":{"atf1delta":{"display_name":"atf1delta","display_uniquename":"atf1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00266:allele-1","expression":"Null"}]}]},"sty1delta":{"display_name":"sty1delta","display_uniquename":"sty1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02592:allele-1","expression":"Null"}]}]}},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2020","pubmed_entrez_date":"2020-09-11","pubmed_publication_date":"11 09 2020","terms_by_termid":{"FYECO:0000137":null,"FYECO:0000248":null,"FYPO:0000107":null,"FYPO:0002998":null,"FYPO_EXT:0000001":null,"GO:0120306":null,"GO:1903499":null,"MOD:00696":null},"title":"Stress-activated MAPK signaling controls fission yeast actomyosin ring integrity by modulating formin For3 levels.","uniquename":"PMID:32915139"}


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


id: GO_REF:0000044
data:
  {"alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"canto_curator_role":"JaponicusDB","cv_annotations":{"cellular_component":[{"annotations":[66193],"is_not":false,"summary":null,"term":"GO:0001725"},{"annotations":[67371],"is_not":false,"summary":null,"term":"GO:0031982"}]},"gene_count":2,"genes_by_uniquename":{"SJAG_01739":null,"SJAG_03357":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0001725":null,"GO:0031982":null},"uniquename":"GO_REF:0000044"}


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


id: 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"}


# genotypes

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":[114407],"is_not":false,"summary":null,"term":"FYPO:0007789"},{"annotations":[114405],"is_not":false,"summary":null,"term":"FYPO:0000280"},{"annotations":[114401],"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: ned1-5E-S499E__S538E__T620E__T638E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
  {"alleles_by_uniquename":{"SJAG_02763:allele-5":{"allele_type":"amino_acid_mutation","description":"S499E; S538E; T620E; T638E; S651E","gene_uniquename":"SJAG_02763","name":"ned1-5E","uniquename":"SJAG_02763:allele-5"}},"annotation_count":3,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114762],"is_not":false,"summary":null,"term":"FYPO:0006054"},{"annotations":[114761],"is_not":false,"summary":null,"term":"FYPO:0001784"},{"annotations":[114760],"is_not":false,"summary":null,"term":"FYPO:0001556"}]},"display_name":"ned1-5E(S499E; S538E; T620E; T638E; S651E aa)","display_uniquename":"ned1-5E-S499E__S538E__T620E__T638E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type","genes_by_uniquename":{"SJAG_02763":null},"genotypes_by_uniquename":{"ned1-5E-S499E__S538E__T620E__T638E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1-5E(S499E; S538E; T620E; T638E; S651E aa)","display_uniquename":"ned1-5E-S499E__S538E__T620E__T638E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-5","expression":"Not assayed or wild type"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-5","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: oar2-51-Y189D_cold_sensitive-amino_acid_mutation-expression-overexpression
data:
  {"alleles_by_uniquename":{"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"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114507],"is_not":false,"summary":null,"term":"FYPO:0000080"}]},"display_name":"oar2-51(Y189D cold sensitive)[Overexpression]","display_uniquename":"oar2-51-Y189D_cold_sensitive-amino_acid_mutation-expression-overexpression","genes_by_uniquename":{"SJAG_03198":null},"genotypes_by_uniquename":{"oar2-51-Y189D_cold_sensitive-amino_acid_mutation-expression-overexpression":{"display_name":"oar2-51(Y189D cold sensitive)[Overexpression]","display_uniquename":"oar2-51-Y189D_cold_sensitive-amino_acid_mutation-expression-overexpression","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03198:allele-2","expression":"Overexpression"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03198:allele-2","expression":"Overexpression"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:23786411":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000006":null,"FYECO:0000137":null,"FYPO:0000080":null,"FYPO_EXT:0000001":null}}


id: leo1delta
data:
  {"alleles_by_uniquename":{},"annotation_count":0,"annotation_details":{},"comment":null,"cv_annotations":{},"display_name":"leo1delta","display_uniquename":"leo1delta","genes_by_uniquename":{},"genotypes_by_uniquename":{},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03118:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{},"taxonid":4897,"terms_by_termid":{}}


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":[114671,114672],"is_not":false,"summary":null,"term":"FYPO:0000731"},{"annotations":[114645],"is_not":false,"summary":null,"term":"FYPO:0005503"},{"annotations":[114673],"is_not":false,"summary":null,"term":"FYPO:0002026"},{"annotations":[114670],"is_not":false,"summary":null,"term":"FYPO:0003535"},{"annotations":[114588],"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: wee1delta
data:
  {"alleles_by_uniquename":{},"annotation_count":0,"annotation_details":{},"comment":null,"cv_annotations":{},"display_name":"wee1delta","display_uniquename":"wee1delta","genes_by_uniquename":{},"genotypes_by_uniquename":{},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-3","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{},"taxonid":4897,"terms_by_termid":{}}


id: wis1delta
data:
  {"alleles_by_uniquename":{"SJAG_02342:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02342","name":"wis1delta","uniquename":"SJAG_02342:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114402],"is_not":false,"summary":null,"term":"FYPO:0000124"}]},"display_name":"wis1delta","display_uniquename":"wis1delta","genes_by_uniquename":{"SJAG_02342":null},"genotypes_by_uniquename":{"wis1delta":{"display_name":"wis1delta","display_uniquename":"wis1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02342:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02342:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:29566183":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000137":null,"FYPO:0000124":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":[114678],"is_not":false,"summary":null,"term":"FYPO:0000356"},{"annotations":[114677],"is_not":false,"summary":null,"term":"FYPO:0006433"},{"annotations":[114680],"is_not":false,"summary":null,"term":"FYPO:0004695"},{"annotations":[114679],"is_not":false,"summary":null,"term":"FYPO:0002227"},{"annotations":[114681],"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: gef1delta
data:
  {"alleles_by_uniquename":{"SJAG_03581:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03581","name":"gef1delta","uniquename":"SJAG_03581:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114621],"is_not":false,"summary":null,"term":"FYPO:0001877"}]},"display_name":"gef1delta","display_uniquename":"gef1delta","genes_by_uniquename":{"SJAG_03581":null},"genotypes_by_uniquename":{"gef1delta":{"display_name":"gef1delta","display_uniquename":"gef1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03581:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03581:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:30664646":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYPO:0001877":null,"FYPO_EXT:0000002":null}}


id: acb1delta
data:
  {"alleles_by_uniquename":{"SJAG_01458:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01458","name":"acb1delta","uniquename":"SJAG_01458:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114769],"is_not":false,"summary":null,"term":"FYPO:0000719"}]},"display_name":"acb1delta","display_uniquename":"acb1delta","genes_by_uniquename":{"SJAG_01458":null},"genotypes_by_uniquename":{"acb1delta":{"display_name":"acb1delta","display_uniquename":"acb1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01458:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01458:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:31956022":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000126":null,"FYPO:0000719":null}}


id: alx1delta
data:
  {"alleles_by_uniquename":{"SJAG_03891:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03891","name":"alx1delta","uniquename":"SJAG_03891:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114302],"is_not":false,"summary":null,"term":"FYPO:0007772"}]},"display_name":"alx1delta","display_uniquename":"alx1delta","genes_by_uniquename":{"SJAG_03891":null},"genotypes_by_uniquename":{"alx1delta":{"display_name":"alx1delta","display_uniquename":"alx1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03891:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03891:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:32243490":null},"taxonid":4897,"terms_by_termid":{"FYPO:0007772":null,"FYPO_EXT:0000003":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":7,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114315],"is_not":false,"summary":null,"term":"FYPO:0004205"},{"annotations":[114317],"is_not":false,"summary":null,"term":"FYPO:0004982"},{"annotations":[114319],"is_not":false,"summary":null,"term":"FYPO:0000595"},{"annotations":[114316],"is_not":false,"summary":null,"term":"FYPO:0004574"},{"annotations":[114312],"is_not":false,"summary":null,"term":"FYPO:0002061"},{"annotations":[114320],"is_not":false,"summary":null,"term":"FYPO:0006989"},{"annotations":[114318],"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:0004574":null,"FYPO:0004982":null,"FYPO:0006989":null,"FYPO_EXT:0000001":null}}


id: clr4delta
data:
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id: pck1delta
data:
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id: mdh1delta
data:
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id: pyk1-A343T-A343T-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: pim1-R152C-R152C-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: win1delta
data:
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id: wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: nur1delta
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id: clr4delta__leo1delta
data:
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id: ras1delta
data:
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id: arb1delta
data:
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id: man1delta
data:
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id: for3delta
data:
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id: rga4delta__rga6delta
data:
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id: cem1delta
data:
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id: Man1DHEH-man1DHEH-partial_amino_acid_deletion-expression-not_assayed_or_wild_type
data:
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id: cdc15-A-L264P,P442T-amino_acid_mutation-expression-not_assayed_or_wild_type__mid1delta
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id: oar2-dm12-R72A,L75A,R106A,L109A-amino_acid_mutation-expression-overexpression
data:
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id: rad26delta
data:
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id: rip1delta
data:
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id: lem2delta
data:
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id: dcr1delta__frameshift-aa61->stop-nonsense_mutation-expression-not_assayed_or_wild_type
data:
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id: mid1delta__pom1delta
data:
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id: SJAG_00124delta
data:
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id: vps28delta
data:
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id: vps25delta
data:
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id: rad51delta
data:
  {"alleles_by_uniquename":{"SJAG_01410:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01410","name":"rad51delta","uniquename":"SJAG_01410:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114734],"is_not":false,"summary":null,"term":"FYPO:0000085"}]},"display_name":"rad51delta","display_uniquename":"rad51delta","genes_by_uniquename":{"SJAG_01410":null},"genotypes_by_uniquename":{"rad51delta":{"display_name":"rad51delta","display_uniquename":"rad51delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01410:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01410:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:20368354":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYECO:0000314":null,"FYPO:0000085":null,"FYPO_EXT:0000001":null}}


id: ade6-domK-Q262A-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
  {"alleles_by_uniquename":{"SJAG_01081:allele-2":{"allele_type":"amino_acid_mutation","description":"Q262A","gene_uniquename":"SJAG_01081","name":"ade6-domK","uniquename":"SJAG_01081:allele-2"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114371],"is_not":false,"summary":null,"term":"FYPO:0000747"}]},"display_name":"ade6-domK(Q262A aa)","display_uniquename":"ade6-domK-Q262A-amino_acid_mutation-expression-not_assayed_or_wild_type","genes_by_uniquename":{"SJAG_01081":null},"genotypes_by_uniquename":{"ade6-domK-Q262A-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ade6-domK(Q262A aa)","display_uniquename":"ade6-domK-Q262A-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-2","expression":"Not assayed or wild type"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-2","expression":"Not assayed or wild type"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:21905090":null},"taxonid":4897,"terms_by_termid":{"FYPO:0000747":null}}


id: rim20E308V-E308V-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: vps24delta
data:
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id: vps32delta
data:
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id: stc1delta
data:
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id: nuc2-1051-E405K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id:
  Pmk1Sp(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: ste11delta
data:
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id: gms1delta
data:
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id: fum1delta
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: sep1delta
data:
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id: ned1delta
data:
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id: Pmk1Sp-Pmk1_from_S._pombe-other-expression-not_assayed_or_wild_type
data:
  {"alleles_by_uniquename":{"SJAG_04551:allele-3":{"allele_type":"other","description":"Pmk1 from S. pombe","gene_uniquename":"SJAG_04551","name":"Pmk1Sp","uniquename":"SJAG_04551:allele-3"}},"annotation_count":3,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114566],"is_not":false,"summary":null,"term":"FYPO:0007776"},{"annotations":[114567],"is_not":false,"summary":null,"term":"FYPO:0007780"},{"annotations":[114565],"is_not":false,"summary":null,"term":"FYPO:0007521"}]},"display_name":"Pmk1Sp(Pmk1 from S. pombe)","display_uniquename":"Pmk1Sp-Pmk1_from_S._pombe-other-expression-not_assayed_or_wild_type","genes_by_uniquename":{"SJAG_04551":null},"genotypes_by_uniquename":{"Pmk1Sp-Pmk1_from_S._pombe-other-expression-not_assayed_or_wild_type":{"display_name":"Pmk1Sp(Pmk1 from S. pombe)","display_uniquename":"Pmk1Sp-Pmk1_from_S._pombe-other-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04551:allele-3","expression":"Not assayed or wild type"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04551:allele-3","expression":"Not assayed or wild type"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:34198697":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000314":null,"FYPO:0007521":null,"FYPO:0007776":null,"FYPO:0007780":null,"FYPO_EXT:0000002":null}}


id: cox6delta
data:
  {"alleles_by_uniquename":{"SJAG_01355:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01355","name":"cox6delta","uniquename":"SJAG_01355:allele-1"}},"annotation_count":6,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114269],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[114265],"is_not":false,"summary":null,"term":"FYPO:0000760"},{"annotations":[114267],"is_not":false,"summary":null,"term":"FYPO:0000579"},{"annotations":[114266],"is_not":false,"summary":null,"term":"FYPO:0000590"},{"annotations":[114259],"is_not":false,"summary":null,"term":"FYPO:0001357"},{"annotations":[114258],"is_not":false,"summary":null,"term":"FYPO:0001234"}]},"display_name":"cox6delta","display_uniquename":"cox6delta","genes_by_uniquename":{"SJAG_01355":null},"genotypes_by_uniquename":{"cox6delta":{"display_name":"cox6delta","display_uniquename":"cox6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01355:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01355: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:0001234":null,"FYPO:0001357":null,"FYPO:0007790":null,"FYPO_EXT:0000003":null}}


id: nde1delta
data:
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id: nem2delta
data:
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id: ned1S235A_S651-S235A__S651-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2delta
data:
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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":[114370],"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: wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type
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id: ned1-5A-S499A__S538A__T620A__T638A__S651A-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: ste6delta
data:
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id: scd1delta
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id: mat-Pc-R47K-R47K-amino_acid_mutation-expression-not_assayed_or_wild_type
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id: chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type__rad24delta
data:
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id: etr1delta
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id: rga4delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: pka1delta
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:
  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: dcr1delta__leo1delta
data:
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id: sty1delta
data:
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id: tel1delta
data:
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id: spk1delta
data:
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id: wcs1delta
data:
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id: pck1delta__pmk1delta
data:
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id: mad2delta
data:
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id: rad3delta
data:
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id: rad25delta
data:
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id: atf1delta
data:
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id: vps4delta
data:
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id: oar2delta
data:
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id: pom152delta
data:
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id: nup132delta
data:
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id: ptp4delta
data:
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id: rga6delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id:
  Pmk1Sj(ins82-105)-82-NITCIYDLDIIINPYNFNEVYIYEE-105-amino_acid_insertion-expression-not_assayed_or_wild_type

data:
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id: vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: pck2delta
data:
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id: wcs2delta
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: nup61delta
data:
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id: mpe1-R77W-R77W-amino_acid_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:
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id: nur1delta__vps4delta
data:
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id: chp1delta
data:
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id: mid1delta__mid2delta
data:
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id: mrc1delta
data:
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id: rad1delta
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:
  {"alleles_by_uniquename":{"SJAG_01143:allele-2":{"allele_type":"partial_amino_acid_deletion","description":"711-723","gene_uniquename":"SJAG_01143","name":"mid1-delta(711-723 a.a.)","uniquename":"SJAG_01143:allele-2"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114646],"is_not":false,"summary":null,"term":"FYPO:0000644"}]},"display_name":"mid1-delta(711-723 a.a.)(aa)","display_uniquename":"mid1-delta(711-723_a.a.)-711-723-partial_amino_acid_deletion-expression-not_assayed_or_wild_type","genes_by_uniquename":{"SJAG_01143":null},"genotypes_by_uniquename":{"mid1-delta(711-723_a.a.)-711-723-partial_amino_acid_deletion-expression-not_assayed_or_wild_type":{"display_name":"mid1-delta(711-723 a.a.)(aa)","display_uniquename":"mid1-delta(711-723_a.a.)-711-723-partial_amino_acid_deletion-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01143:allele-2","expression":"Not assayed or wild type"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01143:allele-2","expression":"Not assayed or wild type"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:25866389":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000137":null,"FYPO:0000644":null}}


id: ned1cat-D422E,D424E-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
  {"alleles_by_uniquename":{"SJAG_02763:allele-2":{"allele_type":"amino_acid_mutation","description":"D422E,D424E","gene_uniquename":"SJAG_02763","name":"ned1cat","synonyms":[{"name":"Catalytic mutant","reference":"PMID:26774782","type":"exact"}],"uniquename":"SJAG_02763:allele-2"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114752],"is_not":false,"summary":null,"term":"FYPO:0001556"}]},"display_name":"ned1cat(D422E,D424E aa)","display_uniquename":"ned1cat-D422E,D424E-amino_acid_mutation-expression-not_assayed_or_wild_type","genes_by_uniquename":{"SJAG_02763":null},"genotypes_by_uniquename":{"ned1cat-D422E,D424E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1cat(D422E,D424E aa)","display_uniquename":"ned1cat-D422E,D424E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-2","expression":"Not assayed or wild type"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-2","expression":"Not assayed or wild type"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:26774782":null},"taxonid":4897,"terms_by_termid":{"FYPO:0001556":null,"FYPO_EXT:0000001":null}}


id: ago1delta
data:
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id: agn1delta
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: man1-1-488-man1-1-488-amino_acid_insertion_and_deletion-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:
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id: byr2delta
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id: pmk1delta
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id: chk1delta
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id: cds1delta
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id: pek1delta
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id: mkh1delta
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id: Vps4-EQ-E233Q-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: gpd1delta
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id: cut3-T19E-cut3-T19E-amino_acid_mutation-expression-not_assayed_or_wild_type
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id: ago1delta__leo1delta
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id: ndi1delta
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id: scd2delta
data:
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id: rdp1delta
data:
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id: cmp7delta
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: apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: pyp1delta
data:
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id: cdc2-1w-G146D-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: dcr1delta__mpe1-R77W-R77W-amino_acid_mutation-expression-not_assayed_or_wild_type
data:
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id: chk1-P470L-P470L-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:
  {"alleles_by_uniquename":{"SJAG_04332:allele-1":{"allele_type":"amino_acid_mutation","description":"I30T,T572P","gene_uniquename":"SJAG_04332","name":"cdc25-D9","uniquename":"SJAG_04332:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114644],"is_not":false,"summary":null,"term":"FYPO:0007701"}]},"display_name":"cdc25-D9(I30T,T572P aa)","display_uniquename":"cdc25-D9-I30T,T572P-amino_acid_mutation-expression-not_assayed_or_wild_type","genes_by_uniquename":{"SJAG_04332":null},"genotypes_by_uniquename":{"cdc25-D9-I30T,T572P-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cdc25-D9(I30T,T572P aa)","display_uniquename":"cdc25-D9-I30T,T572P-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04332:allele-1","expression":"Not assayed or wild type"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04332:allele-1","expression":"Not assayed or wild type"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:25866389":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000004":null,"FYECO:0000137":null,"FYPO:0007701":null,"FYPO_EXT:0000001":null}}


id: nem1delta
data:
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id: rga4delta
data:
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id: rad9delta
data:
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id: ura4delta
data:
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id: arb2delta
data:
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id: sst4delta
data:
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id: 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"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114637],"is_not":false,"summary":null,"term":"FYPO:0000118"}]},"display_name":"mid2delta","display_uniquename":"mid2delta","genes_by_uniquename":{"SJAG_00118":null},"genotypes_by_uniquename":{"mid2delta":{"display_name":"mid2delta","display_uniquename":"mid2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00118:allele-1","expression":"Null"}]}]}},"loci":[{"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: mid1delta
data:
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id: apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__cem1delta
data:
  {"alleles_by_uniquename":{"SJAG_01946:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01946","name":"cem1delta","uniquename":"SJAG_01946:allele-1"},"SJAG_03575:allele-1":{"allele_type":"amino_acid_mutation","description":"E548K ts","gene_uniquename":"SJAG_03575","name":"apc2-361","uniquename":"SJAG_03575:allele-1"}},"annotation_count":1,"annotation_details":{},"comment":null,"cv_annotations":{"multi_locus_phenotype":[{"annotations":[114519],"is_not":false,"summary":null,"term":"FYPO:0000674"}]},"display_name":"apc2-361(E548K ts) cem1delta","display_uniquename":"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__cem1delta","genes_by_uniquename":{"SJAG_01946":null,"SJAG_03575":null},"genotypes_by_uniquename":{"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__cem1delta":{"display_name":"apc2-361(E548K ts) cem1delta","display_uniquename":"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__cem1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03575:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_01946:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03575:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_01946:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:23786411":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000004":null,"FYECO:0000137":null,"FYPO:0000674":null}}


id: ade6-domE-S427>stop-nonsense_mutation-expression-not_assayed_or_wild_type
data:
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id: ace2delta
data:
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id: chk1delta__crb2delta
data:
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id: efc25delta
data:
  {"alleles_by_uniquename":{"SJAG_02819:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02819","name":"efc25delta","uniquename":"SJAG_02819:allele-1"}},"annotation_count":4,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114408],"is_not":false,"summary":null,"term":"FYPO:0007789"},{"annotations":[114404],"is_not":false,"summary":null,"term":"FYPO:0000584"},{"annotations":[114399],"is_not":false,"summary":null,"term":"FYPO:0000124"},{"annotations":[114409],"is_not":false,"summary":null,"term":"FYPO:0002380"}]},"display_name":"efc25delta","display_uniquename":"efc25delta","genes_by_uniquename":{"SJAG_02819":null},"genotypes_by_uniquename":{"efc25delta":{"display_name":"efc25delta","display_uniquename":"efc25delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02819:allele-1","expression":"Null"}]}]}},"loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02819:allele-1","expression":"Null"}]}],"ploidiness":"haploid","references_by_uniquename":{"PMID:29566183":null},"taxonid":4897,"terms_by_termid":{"FYECO:0000137":null,"FYPO:0000124":null,"FYPO:0000584":null,"FYPO:0002380":null,"FYPO:0007789":null,"FYPO_EXT:0000002":null}}


id: SJAG_00124delta__sty1delta
data:
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id: rga6delta
data:
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id: byr1delta
data:
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id: tip1delta
data:
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id: did4delta
data:
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id: rad24delta
data:
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id: sdh3delta
data:
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id: wis4delta
data:
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id: frameshift-aa61->stop-nonsense_mutation-expression-not_assayed_or_wild_type
data:
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id: 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"}},"annotation_count":3,"annotation_details":{},"comment":null,"cv_annotations":{"single_locus_phenotype":[{"annotations":[114344],"is_not":false,"summary":null,"term":"FYPO:0007782"},{"annotations":[114353],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[114350],"is_not":false,"summary":null,"term":"FYPO:0000088"}]},"display_name":"crb2delta","display_uniquename":"crb2delta","genes_by_uniquename":{"SJAG_01205":null},"genotypes_by_uniquename":{"crb2delta":{"display_name":"crb2delta","display_uniquename":"crb2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01205:allele-1","expression":"Null"}]}]}},"loci":[{"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,"FYECO:0000314":null,"FYPO:0000085":null,"FYPO:0000088":null,"FYPO:0007782":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null}}


