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 |
|---|---|---|---|---|---|---|---|---|
| 7388-YPL038W-A | YPL038W-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Accessory | Unknown | NA | NA |
| 7389-YPL039W | YPL039W | NA | NA | Putative protein of unknown function; YPL039W is not an essential gene | Core | NA | NA | NA |
| 7390-YPL040C | YPL040C | ISM1 | isoleucine--tRNA ligase ISM1 | Mitochondrial isoleucyl-tRNA synthetase; null mutant is deficient in respiratory growth; human homolog IARS2 implicated in mitochondrial diseases, can partially complement yeast null mutant | Core | NA | NA | NA |
| 7391-YPL041C | YPL041C | MRX11 | NA | Protein that associates with mitochondrial ribosome; SWAT-GFP and mCherry fusion proteins localize to the mitochondria; involved in maintenance of telomere length | Core | NA | NA | NA |
| 7392-YPL042C | YPL042C | SSN3 | cyclin-dependent serine/threonine protein kinase SSN3|URR1|SSX7|CDK8|RYE5|UME5|SRB10|NUT7|GIG2 | Cyclin-dependent protein kinase; component of RNA polymerase II holoenzyme; involved in phosphorylation of the RNA polymerase II C-terminal domain; involved in glucose repression | Core | NA | NA | NA |
| 7393-YPL043W_NumOfGenes_2 | YPL043W | NOP4 | mRNA-binding ribosome biosynthesis protein NOP4|NOP77 | Nucleolar protein; essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; contains four RNA recognition motifs (RRMs) | Core | NA | NA | NA |
| 7394-YPL045W | YPL045W | VPS16 | tethering complex subunit VPS16|CVT15|VPT16|VAM9|SVL6 | Subunit of the HOPS and the CORVET complexes; part of the Class C Vps complex essential for membrane docking and fusion at Golgi-to-endosome and endosome-to-vacuole protein transport stages | Core | NA | NA | NA |
| 7395-YPL046C | YPL046C | ELC1 | elongin C | Elongin C, conserved among eukaryotes; forms a complex with Cul3p that polyubiquitylates monoubiquitylated RNA polymerase II to trigger its proteolysis; plays a role in global genomic repair | Core | NA | NA | NA |
| 7396-YPL047W | YPL047W | SGF11 | SAGA histone acetyltransferase complex subunit SGF11 | Integral subunit of SAGA histone acetyltransferase complex; regulates transcription of a subset of SAGA-regulated genes, required for the Ubp8p association with SAGA and for H2B deubiquitylation | Core | NA | NA | NA |
| 7397-YPL048W | YPL048W | CAM1 | translation elongation factor EF1B gamma|CPBP|TEF3 | One of two isoforms of the gamma subunit of eEF1B; stimulates the release of GDP from eEF1A (Tef1p/Tef2p) post association with the ribosomal complex with eEF1Balpha subunit; nuclear protein required for transcription of MXR1; binds the MXR1 promoter in the presence of other nuclear factors; binds calcium and phospholipids | Core | NA | NA | NA |
| 7398-YPL049C | YPL049C | DIG1 | RST1 | MAP kinase-responsive inhibitor of the Ste12p transcription factor; involved in the regulation of mating-specific genes and the invasive growth pathway; related regulators Dig1p and Dig2p bind to Ste12p; DIG1 has a paralog, DIG2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7399-YPL050C | YPL050C | MNN9 | mannosyltransferase complex subunit MNN9 | Subunit of Golgi mannosyltransferase complex; this complex mediates elongation of the polysaccharide mannan backbone; forms a separate complex with Van1p that is also involved in backbone elongation; this complex also contains Anp1p, Mnn10p, Mnn11p, and Hoc1p | Core | NA | NA | NA |
| 7400-YPL051W | YPL051W | ARL3 | Arf family GTPase ARL3 | ARF-like small GTPase of the RAS superfamily; required for recruitment of Arl1p, a GTPase that regulates membrane traffic, to the Golgi apparatus; NatC-catalyzed N-terminal acetylation regulates Golgi membrane association mediated by interaction with membrane receptor, Sys1p; similar to ADP-ribosylation factor and orthologous to mammalian ARFRP1 | Core | NA | NA | NA |
| 7401-YPL052W | YPL052W | OAZ1 | YPL052W-A | Regulator of ornithine decarboxylase Spe1p; antizyme that binds to Spe1p to stimulate ubiquitin-independent degradation by the proteasome; binding of polyamines to nascent Oaz1p during translation stimulates +1 ribosomal frameshifting, allowing translation of full-length Oaz1p | Core | NA | NA | NA |
| 7402-YPL053C | YPL053C | KTR6 | putative mannosyltransferase|MNN6 | Probable mannosylphosphate transferase; involved in the synthesis of core oligosaccharides in protein glycosylation pathway; member of the KRE2/MNT1 mannosyltransferase family; KTR6 has a paralog, KRE2, that arose from the whole genome duplication | Core | NA | NA | NA |