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 |
|---|---|---|---|---|---|---|---|---|
| 3293-YEL058W_NumOfGenes_2 | YEL058W | PCM1 | phosphoacetylglucosamine mutase PCM1|AGM1 | Essential N-acetylglucosamine-phosphate mutase; converts GlcNAc-6-P to GlcNAc-1-P, which is a precursor for the biosynthesis of chitin and for the formation of N-glycosylated mannoproteins and glycosylphosphatidylinositol anchors | Core | NA | NA | NA |
| 3294-YEL059C-A | YEL059C-A | SOM1 | NA | Subunit of the mitochondrial inner membrane peptidase (IMP); IMP is required for maturation of mitochondrial proteins of the intermembrane space; Som1p facilitates cleavage of a subset of substrates; contains twin cysteine-x9-cysteine motifs | Core | NA | NA | NA |
| 3295-YEL059W | YEL059W | HHY1 | ENV6 | Dubious open reading frame unlikely to encode a functional protein; mutant is hypersensitive to hygromycin B indicative of defects in vacuolar trafficking | Core | NA | NA | NA |
| 3296-YEL060C_NumOfGenes_2 | YEL060C | PRB1 | proteinase B|CVT1 | Vacuolar proteinase B (yscB) with H3 N-terminal endopeptidase activity; serine protease of the subtilisin family; involved in protein degradation in the vacuole and required for full protein degradation during sporulation; activity inhibited by Pbi2p; protein abundance increases in response to DNA replication stress; PRB1 has a paralog, YSP3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3297-YEL061C | YEL061C | CIN8 | kinesin motor protein CIN8|SDS15|KSL2 | Kinesin motor protein; involved in mitotic spindle assembly and chromosome segregation | Core | NA | NA | NA |
| 3298-YEL062W | YEL062W | NPR2 | nitrogen permease regulating protein NPR2 | Subunit of the Iml1p/SEACIT complex; SEACIT (Iml1p-Npr2p-Npr3p) is a subcomplex of the SEA complex, a coatomer-related complex that associates dynamically with the vacuole; Npr2p may have a structural or regulatory role, supporting Iml1p function as a GAP for the Rag family GTPase Gtr1p, and resulting in inhibition of TORC1 signaling in response to amino acid deprivation; SEACIT is required for non-nitrogen-starvation-induced autophagy; homolog of human tumor suppressor NPRL2 | Accessory | Ancestral | NA | NA |
| 3299-YEL063C | YEL063C | CAN1 | arginine permease CAN1 | Plasma membrane arginine permease; requires phosphatidyl ethanolamine (PE) for localization, exclusively associated with lipid rafts; mutation confers canavanine resistance; CAN1 has a paralog, ALP1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3300-YEL064C | YEL064C | AVT2 | NA | Putative transporter; member of a family of seven S. cerevisiae genes (AVT1-7) related to vesicular GABA-glycine transporters | Accessory | Ancestral | NA | NA |
| 3301-YEL065W | YEL065W | SIT1 | siderophore transporter|ARN3 | Ferrioxamine B transporter; member of the ARN family of transporters that specifically recognize siderophore-iron chelates; transcription is induced during iron deprivation and diauxic shift; potentially phosphorylated by Cdc28p | Accessory | Ancestral | NA | NA |
| 3302-YEL066W | YEL066W | HPA3 | D-amino-acid N-acetyltransferase | D-Amino acid N-acetyltransferase that detoxifies D-amino acids; catalyzes N-acetylation of D-amino acids through ordered bi-bi mechanism in which acetyl-CoA is first substrate bound and CoA is last product liberated; acetylates histones and polyamines, also autoacetylates | Accessory | Ancestral | NA | NA |
| 3303-YEL067C | YEL067C | NA | NA | Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Accessory | Ancestral | NA | NA |
| 3304-YEL068C | YEL068C | NA | NA | Protein of unknown function; expressed at both mRNA and protein levels; SWAT-GFP and seamless-GFP fusion proteins localize to the endoplasmic reticulum and mCherry fusion protein localizes to the vacuole | Accessory | Unknown | NA | NA |
| 3305-YEL071W | YEL071W | DLD3 | D-lactate dehydrogenase | 2-hydroxyglutarate transhydrogenase, and minor D-lactate dehydrogenase; converts D-2-hydroxyglutarate (D-2HG), an oncometabolite, to alpha-ketoglutarate in the presence of FAD, with concomitant reduction of pyruvate to D-lactate; minor lactate dehydrogenase activity; component of the retrograde regulon that consists of genes whose expression are stimulated by damage to mitochondria and reduced in cells grown with glutamate as the sole nitrogen source; located in the cytoplasm | Accessory | Ancestral | NA | NA |
| 3306-YEL072W | YEL072W | RMD6 | NA | Protein required for sporulation | Accessory | Introgression | S. paradoxus | NA |
| 3307-YEL073C | YEL073C | NA | NA | Putative protein of unknown function; located adjacent to ARS503 and the telomere on the left arm of chromosome V; regulated by inositol/choline | Accessory | Ancestral | NA | NA |