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 |
|---|---|---|---|---|---|---|---|---|
| 2528-YDL081C | YDL081C | RPP1A | P1A|ribosomal protein P1A|RPLA1 | Ribosomal stalk protein P1 alpha; involved in the interaction between translational elongation factors and the ribosome; free (non-ribosomal) P1 stimulates the phosphorylation of the eIF2 alpha subunit (Sui2p) by Gcn2p; accumulation of P1 in the cytoplasm is regulated by phosphorylation and interaction with the P2 stalk component | Core | NA | NA | NA |
| 2529-YDL082W | YDL082W | RPL13A | eL13|ribosomal 60S subunit protein L13A|L13e|L13A | Ribosomal 60S subunit protein L13A; not essential for viability; homologous to mammalian ribosomal protein L13, no bacterial homolog; RPL13A has a paralog, RPL13B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2530-YDL083C | YDL083C | RPS16B | uS9|ribosomal 40S subunit protein S16B|S9|rp61R|S16B | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S16 and bacterial S9; RPS16B has a paralog, RPS16A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2531-YDL084W | YDL084W | SUB2 | ATP-dependent RNA helicase SUB2 | Component of the TREX complex required for nuclear mRNA export; member of the DEAD-box RNA helicase superfamily and is involved in early and late steps of spliceosome assembly; homolog of the human splicing factor hUAP56; relocalizes from nucleus to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 2532-YDL085C-A | YDL085C-A | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus | Core | NA | NA | NA |
| 2533-YDL085W | YDL085W | NDE2 | NADH-ubiquinone reductase (H(+)-translocating) NDE2|NDH2 | Mitochondrial external NADH dehydrogenase; catalyzes the oxidation of cytosolic NADH; Nde1p and Nde2p are involved in providing the cytosolic NADH to the mitochondrial respiratory chain; NDE2 has a paralog, NDE1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2534-YDL086W_NumOfGenes_2 | YDL086W | NA | carboxymethylenebutenolidase | Putative carboxymethylenebutenolidase; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YDL086W is not an essential gene | Core | NA | NA | NA |
| 2535-YDL087C | YDL087C | LUC7 | EPE1|EXM2 | Essential protein associated with the U1 snRNP complex; splicing factor involved in recognition of 5' splice site; contains two zinc finger motifs; N-terminal zinc finger binds pre-mRNA; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 2536-YDL088C | YDL088C | ASM4 | FG-nucleoporin ASM4|NUP59 | FG-nucleoporin component of central core of nuclear pore complex (NPC); contributes directly to nucleocytoplasmic transport; induces membrane tubulation, which may contribute to nuclear pore assembly; ASM4 has a paralog, NUP53, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2537-YDL089W | YDL089W | NUR1 | NA | Protein involved in regulation of mitotic exit; dephosphorylation target of Cdc14p in anaphase, which promotes timely rDNA segregation and allows mitotic progression; interacts with Csm1p, Lrs4p; required for rDNA repeat stability; null mutant causes increase in unequal sister-chromatid exchange; GFP-fusion protein localizes to the nuclear periphery, possible Cdc28p substrate | Core | NA | NA | NA |
| 2538-YDL090C | YDL090C | RAM1 | protein farnesyltransferase|STE16|SGP2|SCG2|FUS8|DPR1 | Beta subunit of the CAAX farnesyltransferase (FTase); this complex prenylates the a-factor mating pheromone and Ras proteins; required for the membrane localization of Ras proteins and a-factor; homolog of the mammalian FTase beta subunit | Core | NA | NA | NA |
| 2539-YDL091C | YDL091C | UBX3 | NA | Clathrin-coated vesicle component, regulator of endocytosis; copurifies with the DSC ubiquitin ligase complex; UBX (ubiquitin regulatory X) domain-containing protein that interacts with Cdc48p; required for efficient clathrin-mediated endocytosis; ortholog of fission yeast Ucp10 | Core | NA | NA | NA |
| 2540-YDL092W | YDL092W | SRP14 | RNA-binding signal recognition particle subunit SRP14 | Signal recognition particle (SRP) subunit; interacts with the RNA component of SRP to form the Alu domain, which is the region of SRP responsible for arrest of nascent chain elongation during membrane targeting; homolog of mammalian SRP14 | Core | NA | NA | NA |
| 2541-YDL093W | YDL093W | PMT5 | putative dolichyl-phosphate-mannose-protein mannosyltransferase PMT5 | Protein O-mannosyltransferase; transfers mannose residues from dolichyl phosphate-D-mannose to protein serine/threonine residues; acts in a complex with Pmt3p, can instead interact with Pmt2p in some conditions; target for new antifungals | Core | NA | NA | NA |
| 2542-YDL094C | YDL094C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps verfied gene PMT5/YDL093W; YDL094C is not essential | Core | NA | NA | NA |