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 |
|---|---|---|---|---|---|---|---|---|
| 7013-YOR044W | YOR044W | IRC23 | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion localizes to the ER; null mutant displays increased levels of spontaneous Rad52p foci; IRC23 has a paralog, BSC2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7014-YOR045W | YOR045W | TOM6 | MOM8B|ISP6 | Component of the TOM (translocase of outer membrane) complex; responsible for recognition and initial import steps for all mitochondrially directed proteins; promotes assembly and stability of the TOM complex | Core | NA | NA | NA |
| 7015-YOR046C | YOR046C | DBP5 | ATP-dependent RNA helicase DBP5|RAT8 | Cytoplasmic ATP-dependent RNA helicase of the DEAD-box family; involved in mRNA export from the nucleus, remodeling messenger ribonucleoprotein particles (mRNPs), with ATPase activity stimulated by Gle1p, IP6 and Nup159p; involved in translation termination along with Sup45p (eRF1); role in the cellular response to heat stress | Core | NA | NA | NA |
| 7016-YOR047C | YOR047C | STD1 | SFS3|MSN3 | Protein involved in control of glucose-regulated gene expression; interacts with kinase Snf1p, glucose sensors Snf3p and Rgt2p, TATA-binding Spt15p; regulator of transcription factor Rgt1p; interactions with Pma1p appear to propagate [GAR+]; STD1 has a paralog, MTH1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7017-YOR048C | YOR048C | RAT1 | ssRNA exonuclease RAT1|XRN2|TAP1|HKE1 | Nuclear 5' to 3' single-stranded RNA exonuclease; involved in RNA metabolism, including rRNA and snoRNA processing, as well as poly (A+) dependent and independent mRNA transcription termination; required for cotranscriptional pre-rRNA cleavage; displaces Cdk1p from elongating transcripts, especially as RNAPII reaches the poly(A) site, negatively regulates phosphorylation of the CTD of RNAPII, and inhibits RNAPII transcriptional elongation | Core | NA | NA | NA |
| 7018-YOR049C | YOR049C | RSB1 | phospholipid-translocating ATPase RSB1 | Putative sphingoid long-chain base (LCB) efflux transporter; integral membrane transporter that localizes to the plasma membrane and may transport long chain bases (LCBs) from the cytoplasmic side toward the extracytoplasmic side of the membrane; role in glycerophospholipid translocation; suppressor of the sphingoid LCB sensitivity of an LCB-lyase mutation | Core | NA | NA | NA |
| 7019-YOR050C | YOR050C | NA | YOR29-01 | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; null mutant is viable | Core | NA | NA | NA |
| 7020-YOR051C | YOR051C | ETT1 | NRO1|YOR29-02 | Nuclear protein that inhibits replication of Brome mosaic virus; S. cerevisiae is a model system for studying replication of positive-strand RNA viruses in their natural hosts; deletion increases stop codon readthrough | Core | NA | NA | NA |
| 7021-YOR052C | YOR052C | TMC1 | YOR29-03 | AN1-type zinc finger protein, effector of proteotoxic stress response; stress-inducible transcriptional target of Rpn4p; induced by nitrogen limitation, weak acid, misfolded proteins; short-lived protein, degraded by proteasome; may protect cells from trivalent metalloid induced proteotoxicity; contains PACE promoter element; ortholog of human AIRAP, which stimulates proteasome activity in response to arsenic; protein abundance increases under DNA replication stress | Core | NA | NA | NA |
| 7022-YOR054C_NumOfGenes_3 | YOR054C | VHS3 | phosphopantothenoylcysteine decarboxylase complex subunit VHS3|YOR29-05 | Negative regulatory subunit of protein phosphatase 1 Ppz1p; involved in coenzyme A biosynthesis; subunit of the phosphopantothenoylcysteine decarboxylase (PPCDC; Cab3p, Sis2p, Vhs3p) complex and the CoA-Synthesizing Protein Complex (CoA-SPC: Cab2p, Cab3p, Cab4p, Cab5p, Sis2p and Vhs3p) | Core | NA | NA | NA |
| 7023-YOR056C | YOR056C | NOB1 | rRNA-binding endoribonuclease|YOR29-07 | Protein involved in proteasomal and 40S ribosomal subunit biogenesis; required for cleavage of the 20S pre-rRNA to generate the mature 18S rRNA; cleavage is activated by Fun12p, a GTPase and translation initiation factor; relocalizes from nucleus to nucleolus upon DNA replication stress | Core | NA | NA | NA |
| 7024-YOR057W | YOR057W | SGT1 | co-chaperone SGT1|YOR29-08 | Cochaperone protein; regulates activity of adenylyl cyclase Cyr1p; involved in kinetochore complex assembly; associates with the SCF (Skp1p/Cdc53p/F box protein) ubiquitin ligase complex; acts as a linker between Skp1p and HSP90 complexes; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 7025-YOR058C | YOR058C | ASE1 | YOR29-09 | Mitotic spindle midzone-localized microtubule bundling protein; microtubule-associated protein (MAP) family member; required for spindle elongation and stabilization; undergoes cell cycle-regulated degradation by anaphase promoting complex; potential Cdc28p substrate; relative distribution to microtubules decreases upon DNA replication stress | Core | NA | NA | NA |
| 7026-YOR059C | YOR059C | LPL1 | putative hydrolase|YOR29-10 | Phospholipase; contains lipase specific GXSXG motif; maintains lipid droplet (LD) morphology; induced by transcription factor Rpn4p; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 7027-YOR060C | YOR060C | SLD7 | YOR29-11 | Protein with a role in chromosomal DNA replication; interacts with Sld3p and reduces its affinity for Cdc45p; deletion mutant has aberrant mitochondria | Core | NA | NA | NA |