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 |
|---|---|---|---|---|---|---|---|---|
| 3713-YGL066W | YGL066W | SGF73 | deubiquitination module subunit SGF73|SCA7 | Subunit of DUBm module of SAGA and SLIK; has roles in anchoring deubiquitination module (DUBm) into SAGA and SLIK complexes, maintaining organization and ubiquitin-binding conformation of Ubp8p, thereby contributing to overall DUBm activity; involved in preinitiation complex assembly at promoters; relocalizes to cytosol under hypoxia; human homolog ATXN7 implicated in spinocerebellar ataxia, and can complement yeast null mutant | Core | NA | NA | NA |
| 3714-YGL067W | YGL067W | NPY1 | NAD(+) diphosphatase | NADH diphosphatase (pyrophosphatase); hydrolyzes the pyrophosphate linkage in NADH and related nucleotides; localizes to peroxisomes; nudix hydrolase family member | Core | NA | NA | NA |
| 3715-YGL068W_NumOfGenes_2 | YGL068W | MNP1 | mitochondrial nucleoid protein MNP1 | Mitochondrial ribosomal protein of the large subunit; has similarity to E. coli L7/L12 and human MRPL7 ribosomal proteins; associates with the mitochondrial nucleoid; required for normal respiratory growth | Core | NA | NA | NA |
| 3716-YGL070C | YGL070C | RPB9 | DNA-directed RNA polymerase II core subunit RPB9|B12.6|SSU73|SHI | RNA polymerase II subunit B12.6; contacts DNA; mutations affect transcription start site selection and fidelity of transcription | Core | NA | NA | NA |
| 3717-YGL071W | YGL071W | AFT1 | DNA-binding transcription factor AFT1|RCS1 | Transcription factor involved in iron utilization and homeostasis; binds consensus site PyPuCACCCPu and activates transcription in response to changes in iron availability; in iron-replete conditions localization is regulated by Grx3p, Grx4p, and Fra2p, and promoter binding is negatively regulated via Grx3p-Grx4p binding; AFT1 has a paralog, AFT2, that arose from the whole genome duplication; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 3718-YGL072C | YGL072C | 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 HSF1; null mutant displays increased resistance to antifungal agents gliotoxin, cycloheximide and H2O2 | Accessory | Ancestral | NA | NA |
| 3719-YGL073W | YGL073W | HSF1 | stress-responsive transcription factor HSF1|MAS3|EXA3 | Trimeric heat shock transcription factor; activates multiple genes in response to highly diverse stresses; recognizes variable heat shock elements (HSEs) consisting of inverted NGAAN repeats; monitors translational status of cell through an RQC (Ribosomal Quality Control)-mediated translation-stress signal; involved in diauxic shift; posttranslationally regulated; human homolog HSF1 with linker region mutations can complement yeast hsf1 mutant | Core | NA | NA | NA |
| 3720-YGL074C | YGL074C | NA | NA | Dubious open reading frame unlikely to encode a functional protein; overlaps 5' end of essential HSF1 gene encoding heat shock transcription factor | Core | NA | NA | NA |
| 3721-YGL075C | YGL075C | MPS2 | MMC1 | Essential membrane protein localized at nuclear envelope and SPBs; required for insertion of the newly duplicated spindle pole body into the nuclear envelope; potentially phosphorylated by Cdc28p; MPS2 has a paralog, CSM4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3722-YGL077C | YGL077C | HNM1 | CTR1 | Plasma membrane transporter for choline, ethanolamine, and carnitine; involved in the uptake of nitrogen mustard and the uptake of glycine betaine during hypersaline stress; co-regulated with phospholipid biosynthetic genes and negatively regulated by choline and myo-inositol | Core | NA | NA | NA |
| 3723-YGL078C | YGL078C | DBP3 | RNA-dependent ATPase DBP3 | RNA-Dependent ATPase, member of DExD/H-box family; involved in cleavage of site A3 within the ITS1 spacer during rRNA processing; not essential for growth, but deletion causes severe slow-growth phenotype | Core | NA | NA | NA |
| 3724-YGL079W | YGL079W | KXD1 | KIB1 | Subunit of the BLOC-1 complex involved in endosomal maturation; null mutant is sensitive to drug inducing secretion of vacuolar cargo; GFP-fusion protein localizes to the endosome | Core | NA | NA | NA |
| 3725-YGL080W | YGL080W | MPC1 | pyruvate transporter MPC1|FMP37 | Highly conserved subunit of mitochondrial pyruvate carrier (MPC); MPC is a mitochondrial inner membrane complex that mediates pyruvate uptake and comprises Mpc1p and Mpc2p during fermentative growth, or Mcp1p and Mpc3p during respiratory growth; null mutant displays slow growth that is complemented by expression of human or mouse ortholog; mutation in human ortholog MPC1 is associated with lactic acidosis and hyperpyruvatemia | Core | NA | NA | NA |
| 3726-YGL081W | YGL081W | NA | NA | Putative protein of unknown function; non-essential gene; interacts genetically with CHS5, a gene involved in chitin biosynthesis | Core | NA | NA | NA |
| 3727-YGL082W | YGL082W | NA | NA | Putative protein of unknown function; predicted prenylation/proteolysis target of Afc1p and Rce1p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; not an essential gene; YGL082W has a paralog, YPL191C, that arose from the whole genome duplication | Core | NA | NA | NA |