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 |
|---|---|---|---|---|---|---|---|---|
| 5078-YKL011C | YKL011C | CCE1 | cruciform cutting endonuclease|MGT1 | Mitochondrial cruciform cutting endonuclease; cleaves Holliday junctions formed during recombination of mitochondrial DNA; CCE1 has a paralog, MRS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5079-YKL012W | YKL012W | PRP40 | NA | U1 snRNP protein involved in splicing; interacts with the branchpoint-binding protein during the formation of the second commitment complex | Core | NA | NA | NA |
| 5080-YKL013C | YKL013C | ARC19 | NA | Subunit of the ARP2/3 complex; ARP2/3 is required for the motility and integrity of cortical actin patches; mutation is functionally complemented by human ARPC4 | Core | NA | NA | NA |
| 5081-YKL014C | YKL014C | URB1 | NPA1 | Protein required for the normal accumulation of 25S and 5.8S rRNAs; nucleolar protein; associated with the 27SA2 pre-ribosomal particle; proposed to be involved in the biogenesis of the 60S ribosomal subunit | Core | NA | NA | NA |
| 5082-YKL015W | YKL015W | PUT3 | NA | Transcriptional activator; binds specific gene recruitment sequences and is required for DNA zip code-mediated targeting of genes to nuclear periphery; regulates proline utilization genes, constitutively binds PUT1 and PUT2 promoters as a dimer, undergoes conformational change to form active state; binds other promoters only under activating conditions; differentially phosphorylated in presence of different nitrogen sources; has a Zn(2)-Cys(6) binuclear cluster domain | Core | NA | NA | NA |
| 5083-YKL016C | YKL016C | ATP7 | F1F0 ATP synthase subunit d | Subunit d of the stator stalk of mitochondrial F1F0 ATP synthase; F1F0 ATP synthase is a large, evolutionarily conserved enzyme complex required for ATP synthesis | Core | NA | NA | NA |
| 5084-YKL017C | YKL017C | HCS1 | ATP-dependent 5'-3' DNA helicase HCS1|DIP1 | Hexameric DNA polymerase alpha-associated DNA helicase A; involved in lagging strand DNA synthesis; contains single-stranded DNA stimulated ATPase and dATPase activities; replication protein A stimulates helicase and ATPase activities | Core | NA | NA | NA |
| 5085-YKL018C-A | YKL018C-A | NA | NA | Putative protein of unknown function; identified by homology; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm | Core | NA | NA | NA |
| 5086-YKL018W | YKL018W | SWD2 | WD-repeat containing protein SWD2|SAF37|CPS35 | Subunit of the COMPASS (Set1C) histone H3K4 methyltransferase complex; required for Set1C stability and optimal activity; COMPASS methylates histone H3 on lys 4 and is involved in telomeric silencing; subunit of CPF (cleavage and polyadenylation factor), a complex involved in RNAP II transcription termination | Core | NA | NA | NA |
| 5087-YKL019W | YKL019W | RAM2 | bifunctional protein farnesyltransferase/protein geranylgeranyltransferase | Alpha subunit of farnesyltransferase and geranylgeranyltransferase-I; farnesyltransferase (Ram2p-Ram1p heterodimer) catalyzes the addition of 15-carbon isoprenoid farnesyl to substrate proteins containing a CAAX consensus motif; type I geranylgeranyltransferase (Ram2p-Cdc43p heterodimer) catalyzes the addition of the 20-carbon isoprenoid geranylgeranyl to substrate proteins containing a CaaL consensus motif; required for membrane localization of Ras proteins and a-factor | Core | NA | NA | NA |
| 5088-YKL020C | YKL020C | SPT23 | NA | ER membrane protein involved in regulation of OLE1 transcription; inactive ER form dimerizes and one subunit is then activated by ubiquitin/proteasome-dependent processing followed by nuclear targeting; SPT23 has a paralog, MGA2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5089-YKL021C | YKL021C | MAK11 | NA | Protein involved in an early step of 60S ribosomal subunit biogenesis; essential for cell growth and replication of killer M1 dsRNA virus; contains four beta-transducin repeats | Core | NA | NA | NA |
| 5090-YKL022C | YKL022C | CDC16 | anaphase promoting complex subunit CDC16 | Subunit of the anaphase-promoting complex/cyclosome (APC/C); which is a ubiquitin-protein ligase required for degradation of anaphase inhibitors, including mitotic cyclins, during the metaphase/anaphase transition; required for sporulation; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 5091-YKL023C-A | YKL023C-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 5092-YKL023W | YKL023W | NA | NA | Putative protein of unknown function; predicted by computational methods to be involved in mRNA degradation; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm | Core | NA | NA | NA |