Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
A searchable table of the S. cerevisiae pangenome ORFs defined in Peter et al. (2018) Nature (LINK) is provided below. The listed core/accessory classification and origin assignment are based on the original study. Click on the PanORF ID to find out the detailed presence/absence pattern of the corresponding pangenome ORF in both ScRAPdb and the 1002ScGP strain collections (which were recalculated by ScRAPdb).
| PanORF ID | SGD systematic Name | SGD standard name | Alias | Description | Type | Origin assignment | Mostly likely origin species | NCBI megablast hit |
|---|---|---|---|---|---|---|---|---|
| 4388-YHR131W-A | YHR131W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YHR131C | Accessory | Ancestral | NA | NA |
| 4389-YHR132C | YHR132C | ECM14 | putative metallocarboxypeptidase | Putative metalloprotease with similarity to zinc carboxypeptidases; required for normal cell wall assembly | Core | NA | NA | NA |
| 4390-YHR132W-A | YHR132W-A | IGO2 | phosphatase regulator | Protein required for initiation of G0 program; prevents degradation of nutrient-regulated mRNAs via the 5'-3' mRNA decay pathway; phosphorylated by Rim15p; GFP protein localizes to the cytoplasm and nucleus; IGO2 has a paralog, IGO1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4391-YHR133C | YHR133C | NSG1 | NA | Protein involved in regulation of sterol biosynthesis; specifically stabilizes Hmg2p, one of two HMG-CoA isoenzymes that catalyze the rate-limiting step in sterol biosynthesis; forms foci at the nuclear periphery upon DNA replication stress; relocalizes to the cytosol in response to hypoxia; homolog of mammalian INSIG proteins; NSG1 has a paralog, NSG2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4392-YHR134W | YHR134W | WSS1 | metalloendopeptidase WSS1 | SUMO-ligase and SUMO-targeted metalloprotease; involved in DNA repair; removes DNA-protein crosslinks at stalled replication forks during replication of damaged DNA; clears chromatin-bound sumoylated proteins; localizes to single spot on nuclear periphery of mother cells but not daughters; exhibits vacuolar localization upon genotoxic stress; activated by DNA binding; member of minigluzincins protease family with mammalian DVC1/Spartan | Core | NA | NA | NA |
| 4393-YHR135C | YHR135C | YCK1 | serine/threonine protein kinase YCK1|CKI2 | Palmitoylated plasma membrane-bound casein kinase I (CK1) isoform; shares redundant functions with Yck2p in morphogenesis, proper septin assembly, endocytic trafficking, and glucose sensing; stabilized by Sod1p binding in the presence of glucose and oxygen, causing glucose repression of respiratory metabolism; involved in the phosphorylation and regulation of glucose sensor Rgt2p; YCK1 has a paralog, YCK2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4394-YHR136C | YHR136C | SPL2 | NA | Protein with similarity to cyclin-dependent kinase inhibitors; downregulates low-affinity phosphate transport during phosphate limitation by targeting Pho87p to the vacuole; upstream region harbors putative hypoxia response element (HRE) cluster; overproduction suppresses a plc1 null mutation; promoter shows an increase in Snf2p occupancy after heat shock; GFP-fusion protein localizes to the cytoplasm | Core | NA | NA | NA |
| 4395-YHR137W_NumOfGenes_2 | YHR137W | ARO9 | aromatic-amino-acid:2-oxoglutarate transaminase | Aromatic aminotransferase II; catalyzes the first step of tryptophan, phenylalanine, and tyrosine catabolism | Core | NA | NA | NA |
| 4396-YHR138C | YHR138C | NA | NA | Protein of unknown function; similar to Pbi2p; double null mutant lacking Pbi2p and Yhr138cp exhibits highly fragmented vacuoles; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4397-YHR139C | YHR139C | SPS100 | NA | Protein required for spore wall maturation; expressed during sporulation; may be a component of the spore wall; expression also induced in cells treated with the mycotoxin patulin; SPS100 has a paralog, YGP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4398-YHR139C-A | YHR139C-A | NA | NA | Putative protein of unknown function; conserved across S. cerevisiae strains | Core | NA | NA | NA |
| 4399-YHR140W | YHR140W | NA | NA | Putative integral membrane protein of unknown function | Core | NA | NA | NA |
| 4400-YHR141C | YHR141C | RPL42B | eL42|ribosomal 60S subunit protein L42B|L44e|YP44|YL27|L42B|L41B|MAK18 | Ribosomal 60S subunit protein L42B; required for propagation of the killer toxin-encoding M1 double-stranded RNA satellite of the L-A double-stranded RNA virus; homologous to mammalian ribosomal protein L36A, no bacterial homolog; RPL42B has a paralog, RPL42A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4401-YHR142W | YHR142W | CHS7 | NA | Protein of unknown function; may be involved in chitin biosynthesis by regulation of Chs3p export from the ER; relocalizes from bud neck to ER upon DNA replication stress | Core | NA | NA | NA |
| 4402-YHR143W | YHR143W | DSE2 | NA | Daughter cell-specific secreted protein with similarity to glucanases; degrades cell wall from the daughter side causing daughter to separate from mother; expression is repressed by cAMP | Core | NA | NA | NA |