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 |
|---|---|---|---|---|---|---|---|---|
| 5948-YML027W | YML027W | YOX1 | NA | Homeobox transcriptional repressor; binds to Mcm1p and to early cell cycle boxes (ECBs) in the promoters of cell cycle-regulated genes expressed in M/G1 phase; expression is cell cycle-regulated; phosphorylated by Cdc28p; relocalizes from nucleus to cytoplasm upon DNA replication stress; YOX1 has a paralog, YHP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5949-YML028W | YML028W | TSA1 | thioredoxin peroxidase TSA1|cTPxI|TPX1|ZRG14 | Thioredoxin peroxidase; acts as both ribosome-associated and free cytoplasmic antioxidant; self-associates to form high-molecular weight chaperone complex under oxidative stress; chaperone activity essential for growth in zinc deficiency; required for telomere length maintenance; binds and modulates Cdc19p activity; protein abundance increases, forms cytoplasmic foci during DNA replication stress; TSA1 has a paralog, TSA2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5950-YML029W | YML029W | USA1 | NA | Scaffold subunit of the Hrd1p ubiquitin ligase; also promotes ligase oligomerization; involved in ER-associated protein degradation (ERAD); interacts with the U1 snRNP-specific protein, Snp1p | Core | NA | NA | NA |
| 5951-YML030W | YML030W | RCF1 | AIM31 | Cytochrome c oxidase subunit; required for assembly of the Complex III-Complex IV supercomplex, and for assembly of Cox13p and Rcf2p into cytochrome c oxidase; similar to Rcf2p, and either Rcf1p or Rcf2p is required for late-stage assembly of the Cox12p and Cox13p subunits and for cytochrome c oxidase activity; required for growth under hypoxic conditions; member of the hypoxia induced gene family; C. elegans and human orthologs are functional in yeast | Core | NA | NA | NA |
| 5952-YML031C-A | YML031C-A | NA | YML032C-A | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps verified ORF NDC1/YML031W | Accessory | Ancestral | NA | NA |
| 5953-YML031W | YML031W | NDC1 | NA | Subunit of the transmembrane ring of the nuclear pore complex (NPC); contributes to nucleocytoplasmic transport, NPC biogenesis and spindle pole body duplication; homologous to human NDC1 | Core | NA | NA | NA |
| 5954-YML032C | YML032C | RAD52 | recombinase RAD52 | Protein that stimulates strand exchange; stimulates strand exchange by facilitating Rad51p binding to single-stranded DNA; anneals complementary single-stranded DNA; involved in the repair of double-strand breaks in DNA during vegetative growth and meiosis and UV induced sister chromatid recombination | Core | NA | NA | NA |
| 5955-YML034W_NumOfGenes_2 | YML034W | SRC1 | HEH1|YML033W | Inner nuclear membrane protein; highly enriched at telomeres and subtelomeric regions; functions in regulation of subtelomeric genes and is linked to TREX (transcription export) factors; SRC1 produces 2 splice variant proteins with different functions; alternative splicing of SRC1 pre-mRNA is promoted by Hub1p; mutant has aneuploidy tolerance; SEC1 has a paralog, HEH2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5956-YML035C | YML035C | AMD1 | AMP deaminase|AMD3 | AMP deaminase; tetrameric enzyme that catalyzes the deamination of AMP to form IMP and ammonia; thought to be involved in regulation of intracellular purine (adenine, guanine, and inosine) nucleotide pools | Core | NA | NA | NA |
| 5957-YML036W | YML036W | CGI121 | NA | Component of the EKC/KEOPS complex; EKC/KEOPS complex is required for t6A tRNA modification and telomeric TG1-3 recombination; may have role in transcription; Cgi121p is dispensable for tRNA modification; other complex members are Bud32p, Kae1p, Pcc1p, and Gon7p | Core | NA | NA | NA |
| 5958-YML037C | YML037C | NA | NA | Putative protein of unknown function; has some characteristics of a transcriptional activator; may be a target of Dbf2p-Mob1p kinase; GFP-fusion protein co-localizes with clathrin-coated vesicles; YML037C is not an essential gene | Core | NA | NA | NA |
| 5959-YML038C | YML038C | YMD8 | NA | Putative nucleotide sugar transporter; has similarity to Vrg4p | Core | NA | NA | NA |
| 5960-YML041C | YML041C | VPS71 | SWC6 | Nucleosome-binding component of the SWR1 complex; SWR1 exchanges histone variant H2AZ (Htz1p) for chromatin-bound histone H2A; required for vacuolar protein sorting | Core | NA | NA | NA |
| 5961-YML042W | YML042W | CAT2 | carnitine O-acetyltransferase CAT2|YCAT | Carnitine acetyl-CoA transferase; present in both mitochondria and peroxisomes; transfers activated acetyl groups to carnitine to form acetylcarnitine which can be shuttled across membranes | Core | NA | NA | NA |
| 5962-YML043C | YML043C | RRN11 | NA | Component of the core factor (CF) rDNA transcription factor complex; CF is required for transcription of 35S rRNA genes by RNA polymerase I and is composed of Rrn6p, Rrn7p, and Rrn11p | Core | NA | NA | NA |