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 |
|---|---|---|---|---|---|---|---|---|
| 2288-YBR297W | YBR297W | MAL33 | transcription factor MAL33|MALR|MAL3R | MAL-activator protein; part of complex locus MAL3; nonfunctional in genomic reference strain S288C | Accessory | Ancestral | NA | NA |
| 2289-YBR298C_NumOfGenes_2 | YBR298C | MAL31 | maltose permease|MALT|MAL3T | Maltose permease; high-affinity maltose transporter (alpha-glucoside transporter); encoded in the MAL3 complex locus; member of the 12 transmembrane domain superfamily of sugar transporters; functional in genomic reference strain S288C | Accessory | Ancestral | NA | NA |
| 2290-YCL001W | YCL001W | RER1 | protein retrieval receptor | Protein involved in retention of membrane proteins; including Sec12p, in the ER; localized to Golgi; functions as a retrieval receptor in returning membrane proteins to the ER | Accessory | Ancestral | NA | NA |
| 2291-YCL001W-A | YCL001W-A | NA | NA | Putative protein of unknown function; YCL001W-A gene has similarity to DOM34 and is present in a region duplicated between chromosomes XIV and III | Accessory | Unknown | NA | NA |
| 2292-YCL001W-B | YCL001W-B | NA | NA | Putative protein of unknown function; present in a region duplicated between chromosomes XIV and III; YCL001W-B has a paralog, DOM34, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2293-YCL002C | YCL002C | NA | NA | Putative protein of unknown function; YCL002C is not an essential gene | Accessory | Ancestral | NA | NA |
| 2294-YCL004W | YCL004W | PGS1 | CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase|YCL003W|PEL1 | Phosphatidylglycerolphosphate synthase; catalyzes the synthesis of phosphatidylglycerolphosphate from CDP-diacylglycerol and sn-glycerol 3-phosphate in the first committed and rate-limiting step of cardiolipin biosynthesis | Accessory | Ancestral | NA | NA |
| 2295-YCL005W | YCL005W | LDB16 | NA | Protein involved in lipid droplet (LD) assembly; forms a complex with Sei1p at ER-LD contact sites, stabilizing contact sites; ensures that LDs bud from the ER towards the cytosolic side of the membrane; null mutants have decreased net negative cell surface charge and localized accumulation of phosphatidic acid (PA) marker proteins; GFP-fusion protein expression is induced in response to MMS; null mutant can be complemented by the human seipin, BSCL2 | Accessory | Ancestral | NA | NA |
| 2296-YCL005W-A_NumOfGenes_2 | YCL005W-A | VMA9 | H(+)-transporting V0 sector ATPase subunit e|LDB10|CWH36 | Vacuolar H+ ATPase subunit e of the V-ATPase V0 subcomplex; essential for vacuolar acidification; interacts with the V-ATPase assembly factor Vma21p in the ER; involved in V0 biogenesis | Accessory | Ancestral | NA | NA |
| 2297-YCL008C_NumOfGenes_2 | YCL008C | STP22 | ubiquitin-binding ESCRT-I subunit protein STP22|AGS1|VPL15|VPS23 | Component of the ESCRT-I complex; ESCRT-I is involved in ubiquitin-dependent sorting of proteins into the endosome; prevents polyubiquitination of the arrestin-related protein Rim8p, thereby directing its monoubiquitination by Rsp5p; homologous to the mouse and human Tsg101 tumor susceptibility gene; mutants exhibit a Class E Vps phenotype; | Accessory | Ancestral | NA | NA |
| 2298-YCL009C_NumOfGenes_2 | YCL009C | ILV6 | acetolactate synthase regulatory subunit | Regulatory subunit of acetolactate synthase; acetolactate synthase catalyzes the first step of branched-chain amino acid biosynthesis; enhances activity of the Ilv2p catalytic subunit, localizes to mitochondria | Accessory | Ancestral | NA | NA |
| 2299-YCL010C_NumOfGenes_2 | YCL010C | SGF29 | NA | Component of the HAT/Core module of the SAGA, SLIK, and ADA complexes; HAT/Core module also contains Gcn5p, Ngg1p, and Ada2p; binds methylated histone H3K4; involved in transcriptional regulation through SAGA and TBP recruitment to target promoters and H3 acetylation | Core | NA | NA | NA |
| 2300-YCL011C_NumOfGenes_2 | YCL011C | GBP2 | single-stranded telomeric DNA-binding/mRNA-binding protein|RLF6 | Poly(A+) RNA-binding protein; key surveillance factor for the selective export of spliced mRNAs from the nucleus to the cytoplasm; preference for intron-containing genes; similar to Npl3p; also binds single-stranded telomeric repeat sequence in vitro; relocalizes to the cytosol in response to hypoxia; GBP2 has a paralog, HRB1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2301-YCL012C | YCL012C | NA | YCL011C-A | Protein of unknown function; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum and vacuole respectively; orthologs are present in S. bayanus, S. paradoxus and Ashbya gossypii; YCL012C is not an essential gene | Core | NA | NA | NA |
| 2302-YCL014W | YCL014W | BUD3 | YCL012W | Guanine nucleotide exchange factor (GEF) for Cdc42p; activates Cdc42p in early G1, accounting for the first stage of biphasic activation, with Cdc24p accounting for the second stage in late G1; involved in the Cdc42p-mediated assembly of the axial landmark that dictates the site for the next round of budding, resulting in the axial budding pattern observed in haploids; localizes with septins to the bud neck contractile ring in mitosis | Core | NA | NA | NA |