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 |
|---|---|---|---|---|---|---|---|---|
| 3758-YGL114W | YGL114W | NA | OPT3 | Putative protein of unknown function; predicted member of the oligopeptide transporter (OPT) family of membrane transporters | Core | NA | NA | NA |
| 3759-YGL115W | YGL115W | SNF4 | AMP-activated serine/threonine-protein kinase regulatory subunit SNF4|SCI1|CAT3 | Activating gamma subunit of the AMP-activated Snf1p kinase complex; additional subunits of the complex are Snf1p and a Sip1p/Sip2p/Gal83p family member; activates glucose-repressed genes, represses glucose-induced genes; role in sporulation, and peroxisome biogenesis; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3760-YGL116W | YGL116W | CDC20 | ubiquitin-protein transferase activating protein CDC20|PAC5 | Activator of anaphase-promoting complex/cyclosome (APC/C); APC/C is required for metaphase/anaphase transition; directs ubiquitination of mitotic cyclins, Pds1p, and other anaphase inhibitors; cell-cycle regulated; potential Cdc28p substrate; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 3761-YGL117W | YGL117W | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 3762-YGL118C | YGL118C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YGL118C is not an essential gene | Core | NA | NA | NA |
| 3763-YGL119W | YGL119W | COQ8 | protein kinase COQ8|ABC1 | ATPase required for ubiquinone biosynthesis and respiratory growth; maintains levels of CoQ biosynthetic proteins; binds to CoQ biosynthesis intermediates; UbiB protein kinase-like family member that lacks canonical protein kinase activity; similar to prokaryotic proteins involved in ubiquinone biosynthesis; human homolog ADCK3 complements a coq8 null, is associated with CoQ and respiratory-chain deficiencies, and is mutated in autosomal-recessive cerebellar ataxia type 2 | Core | NA | NA | NA |
| 3764-YGL120C | YGL120C | PRP43 | DEAH-box ATP-dependent RNA helicase PRP43|JA1 | RNA helicase in the DEAH-box family; functions in both RNA polymerase I and polymerase II transcript metabolism; catalyzes removal of U2, U5, and U6 snRNPs from the postsplicing lariat-intron ribonucleoprotein complex; required for efficient biogenesis of both small- and large-subunit rRNAs; acts with Sqs1p to promote 20S to 18S rRNA processing catalyzed by endonuclease Nob1p | Core | NA | NA | NA |
| 3765-YGL121C | YGL121C | GPG1 | NA | Proposed gamma subunit of the heterotrimeric G protein; interacts with the receptor Gpr1p; involved in regulation of pseudohyphal growth; requires Gpb1p or Gpb2p to interact with Gpa2p; overproduction causes prion curing | Core | NA | NA | NA |
| 3766-YGL122C | YGL122C | NAB2 | mRNA-binding protein NAB2 | Nuclear polyadenylated RNA-binding protein; required for nuclear mRNA export and poly(A) tail length control; stimulates RNA polymerase III transcription by enhancing TFIIIB binding to promoters; protects mRNA against decay by the nuclear exosome in a poly(A)-tail-dependent manner; involved in forming export-competent mRNPs in the nucleus; autoregulates mRNA levels; NLS binds Kap104p; protein abundance increases under DNA replication stress; related to human hnRNPs | Core | NA | NA | NA |
| 3767-YGL123W_NumOfGenes_2 | YGL123W | RPS2 | uS5|ribosomal 40S subunit protein S2|rp12|Ys5|S5|S4|S2|SUP138|SUP44|SUP38|RPS4 | Protein component of the small (40S) subunit; essential for control of translational accuracy; phosphorylation by C-terminal domain kinase I (CTDK-I) enhances translational accuracy; methylated on one or more arginine residues by Hmt1p; homologous to mammalian ribosomal protein S2 and bacterial S5 | Core | NA | NA | NA |
| 3768-YGL124C | YGL124C | MON1 | AUT12 | Subunit of a heterodimeric guanine nucleotide exchange factor (GEF); subunit of the Mon1-Ccz1 GEF complex which stimulates nucleotide exchange and activation of Ypt7p, a Rab family GTPase involved in membrane tethering and fusion events at the late endosome and vacuole; GEF activity is stimulated by membrane association and anionic phospholipids; role in localizing Ypt7p to the vacuolar membrane; required for autophagy, the CVT pathway and mitophagy; potential Cdc28 substrate | Core | NA | NA | NA |
| 3769-YGL125W | YGL125W | MET13 | methylenetetrahydrofolate reductase (NAD(P)H) MET13|MRPL45|MET11 | Major isozyme of methylenetetrahydrofolate reductase; catalyzes the reduction of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate in the methionine biosynthesis pathway | Core | NA | NA | NA |
| 3770-YGL126W | YGL126W | SCS3 | FIT2B | Protein required for inositol prototrophy; required for normal ER membrane biosynthesis; ortholog of the FIT family of proteins involved in triglyceride droplet biosynthesis and homologous to human FIT2; disputed role in the synthesis of inositol phospholipids from inositol | Core | NA | NA | NA |
| 3771-YGL127C | YGL127C | SOH1 | MED31 | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; involved in telomere maintenance; conserved with other metazoan MED31 subunits | Core | NA | NA | NA |
| 3772-YGL128C | YGL128C | CWC23 | U2-type spliceosomal complex subunit CWC23 | Component of a complex containing Cef1p; putatively involved in pre-mRNA splicing; has similarity to E. coli DnaJ and other DnaJ-like proteins and to S. pombe Cwf23p | Core | NA | NA | NA |