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 |
|---|---|---|---|---|---|---|---|---|
| 2828-YDR137W | YDR137W | RGP1 | NA | Subunit of a Golgi membrane exchange factor (Ric1p-Rgp1p); this complex catalyzes nucleotide exchange on Ypt6p | Core | NA | NA | NA |
| 2829-YDR138W | YDR138W | HPR1 | TRF1 | Subunit of THO/TREX complexes; this complex couple transcription elongation with mitotic recombination and with mRNA metabolism and export, subunit of an RNA Pol II complex; regulates lifespan; involved in telomere maintenance; similar to Top1p | Core | NA | NA | NA |
| 2830-YDR139C | YDR139C | RUB1 | NEDD8 family protein RUB1 | Ubiquitin-like protein with similarity to mammalian NEDD8; conjugation (neddylation) substrates include the cullins Cdc53p, Rtt101p, and Cul3p; activated by Ula1p and Uba3p (E1 enzyme pair); conjugation mediated by Ubc12p (E2 enzyme) | Core | NA | NA | NA |
| 2831-YDR140W | YDR140W | MTQ2 | S-adenosylmethionine-dependent methyltransferase | S-adenosylmethionine-dependent methyltransferase; subunit of complex with Trm112p that methylates translation release factor Sup45p (eRF1) in the ternary complex eRF1-eRF3-GTP; similar to E.coli PrmC; member of the seven beta-strand family | Core | NA | NA | NA |
| 2832-YDR141C | YDR141C | DOP1 | NA | Golgi-localized, leucine-zipper domain containing protein; involved in endosome to Golgi transport, organization of the ER, establishing cell polarity, and morphogenesis; detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 2833-YDR142C | YDR142C | PEX7 | PEB1|PAS7 | Peroxisomal signal receptor for peroxisomal matrix proteins; recognizes the N-terminal nonapeptide signal (PTS2); WD repeat protein; defects in human homolog cause lethal rhizomelic chondrodysplasia punctata (RCDP) | Core | NA | NA | NA |
| 2834-YDR143C | YDR143C | SAN1 | ubiquitin-protein ligase SAN1 | Ubiquitin-protein ligase; involved in proteasome-dependent degradation of aberrant nuclear proteins; targets substrates with regions of exposed hydrophobicity containing 5 or more contiguous hydrophobic residues; contains intrinsically disordered regions that contribute to substrate recognition; prefers a window of exposed hydrophobicity that causes a particular level of protein insolubility, suggesting that San1p evolved to target highly aggregation-prone proteins | Core | NA | NA | NA |
| 2835-YDR144C | YDR144C | MKC7 | aspartyl protease|YPS2 | GPI-anchored aspartyl protease; member of the yapsin family of proteases involved in cell wall growth and maintenance; shares functions with Yap3p and Kex2p; MKC7 has a paralog, YPS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2836-YDR145W | YDR145W | TAF12 | TafII61|TafII68|TAF68|TAF61 | Subunit (61/68 kDa) of TFIID and SAGA complexes; involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A; overexpression of the human ortholog, TAF12, an oncogene involved in the formation of choroid plexus carcinomas, results in dosage chromosomal instability (dCIN) in a human cell line similar to the dCIN observed in yeast overexpressors | Core | NA | NA | NA |
| 2837-YDR146C | YDR146C | SWI5 | DNA-binding transcription factor SWI5 | Transcription factor that recruits Mediator and Swi/Snf complexes; activates transcription of genes expressed at the M/G1 phase boundary and in G1 phase; required for expression of the HO gene controlling mating type switching; localization to nucleus occurs during G1 and appears to be regulated by phosphorylation by Cdc28p kinase; SWI5 has a paralog, ACE2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2838-YDR147W | YDR147W | EKI1 | bifunctional choline kinase/ethanolamine kinase EKI1 | Ethanolamine kinase; primarily responsible for phosphatidylethanolamine synthesis via the CDP-ethanolamine pathway; exhibits some choline kinase activity, thus contributing to phosphatidylcholine synthesis via the CDP-choline pathway; EKI1 has a paralog, CKI1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2839-YDR148C | YDR148C | KGD2 | alpha-ketoglutarate dehydrogenase KGD2 | Dihydrolipoyl transsuccinylase; component of the mitochondrial alpha-ketoglutarate dehydrogenase complex, which catalyzes the oxidative decarboxylation of alpha-ketoglutarate to succinyl-CoA in the TCA cycle; phosphorylated | Core | NA | NA | NA |
| 2840-YDR150W_NumOfGenes_2 | YDR150W | NUM1 | PAC12 | Protein required for nuclear migration; component of the mitochondria-ER-cortex-ancor (MECA); required for the association of mitochondria with the cell cortex and for accurate distribution of mitochondrial network; interacts with Mdm36p to link the ER and mitochondria at the cortex; localizes to the mother cell cortex and the bud tip; may mediate interactions of dynein and cytoplasmic microtubules with the cell cortex | Core | NA | NA | NA |
| 2841-YDR151C | YDR151C | CTH1 | putative mRNA-binding protein CTH1 | Member of the CCCH zinc finger family; similar to mammalian Tis11 protein, which activates transcription and also has a role in mRNA degradation; may function with Tis11p in iron homeostasis; CTH1 has a paralog, TIS11, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2842-YDR152W | YDR152W | GIR2 | NA | Highly-acidic RWD domain-containing cytoplasmic protein; forms a highly conserved complex with Rbg2p that is responsible for efficient cell growth under amino acid starvation and binds translational activator Gcn1p in dose-dependent manner according to stress level; associates with translating ribosomes; intrinsically unstructured protein whose stability is enhanced upon binding Rbg2p | Core | NA | NA | NA |