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 |
|---|---|---|---|---|---|---|---|---|
| 5303-YKR010C_NumOfGenes_2 | YKR010C | TOF2 | NA | Protein required for rDNA silencing and mitotic rDNA condensation; stimulates Cdc14p phosphatase activity and biphasic release to promote rDNA repeat segregation; required for condensin recruitment to the replication fork barrier site; TOF2 has a paralog, NET1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5304-YKR011C_NumOfGenes_2 | YKR011C | NA | TOS5 | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nucleus; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5305-YKR012C | YKR012C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene PRY2 | Core | NA | NA | NA |
| 5306-YKR013W_NumOfGenes_2 | YKR013W | PRY2 | sterol-binding protein|YFW12 | Sterol binding protein involved in the export of acetylated sterols; secreted glycoprotein and member of the CAP protein superfamily (cysteine-rich secretory proteins (CRISP), antigen 5, and pathogenesis related 1 proteins); sterol export function is redundant with that of PRY1; may be involved in detoxification of hydrophobic compounds; PRY2 has a paralog, PRY1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5307-YKR014C_NumOfGenes_2 | YKR014C | YPT52 | Rab family GTPase YPT52 | Endosomal Rab family GTPase; required for vacuolar protein sorting, endocytosis and multivesicular body (MVB) biogenesis and sorting; required for localization of the CORVET complex to endosomes; involved in autophagy and ionic stress tolerance; similar to Vps21p and Ypt53p; mammalian Rab5 homolog; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5308-YKR015C_NumOfGenes_2 | YKR015C | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 5309-YKR016W_NumOfGenes_2 | YKR016W | MIC60 | FCJ1|AIM28|FMP13 | Component of the MICOS complex; MICOS (formerly MINOS or MitOS) is a mitochondrial inner membrane complex that extends into the intermembrane space and has a role in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane; Mic60p is also involved in import of intermembrane space (IMS) proteins, probably by positioning Mia40p relative to the TOM complex to receive incoming proteins; ortholog of mammalian mitofilin | Core | NA | NA | NA |
| 5310-YKR017C_NumOfGenes_2 | YKR017C | HEL1 | E3 ubiquitin-protein ligase HEL1 | RING finger ubiquitin ligase (E3); involved in ubiquitination and degradation of excess histones; interacts with Ubc4p and Rad53p; null mutant sensitive to hydroxyurea (HU) | Core | NA | NA | NA |
| 5311-YKR018C_NumOfGenes_2 | YKR018C | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; protein abundance increases in response to DNA replication stress; YKR018C has a paralog, IML2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5312-YKR019C_NumOfGenes_2 | YKR019C | IRS4 | NA | EH domain-containing protein; involved in regulating phosphatidylinositol 4,5-bisphosphate levels and autophagy; Irs4p and Tax4p bind and activate the PtdIns phosphatase Inp51p; Irs4p and Tax4p are involved in localizing Atg17p to the PAS; IRS4 has a paralog, TAX4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5313-YKR020W_NumOfGenes_2 | YKR020W | VPS51 | VPS67|API3|WHI6 | Component of the GARP (Golgi-associated retrograde protein) complex; GARP is required for the recycling of proteins from endosomes to the late Golgi, and for mitosis after DNA damage induced checkpoint arrest; links the (VFT/GARP) complex to the SNARE Tlg1p; members of the GARP complex are Vps51p-Vps52p-Vps53p-Vps54p | Core | NA | NA | NA |
| 5314-YKR021W_NumOfGenes_2 | YKR021W | ALY1 | ART6 | Alpha arrestin, substrate of calcineurin; controls nutrient-mediated intracellular sorting of permease Gap1p; interacts with AP-1 subunit Apl4p; dephosphorylation of Aly1p required for the endocytosis of Dip5p; may regulate endocytosis of plasma membrane proteins by recruiting ubiquitin ligase Rsp5p to plasma membrane targets; ALY1 has a paralog, ALY2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5315-YKR022C_NumOfGenes_2 | YKR022C | NTR2 | NA | Essential protein that forms a dimer with Ntr1p; also forms a trimer, with Ntr2p and the DExD/H-box RNA helicase Prp43p, that is involved in spliceosome disassembly | Core | NA | NA | NA |
| 5316-YKR023W_NumOfGenes_2 | YKR023W | NA | NA | Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 5317-YKR024C_NumOfGenes_2 | YKR024C | DBP7 | putative ATP-dependent RNA helicase | Putative ATP-dependent RNA helicase of the DEAD-box family; involved in ribosomal biogenesis; required at post-transcriptional step for efficient retrotransposition; essential for growth under anaerobic conditions | Core | NA | NA | NA |