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 |
|---|---|---|---|---|---|---|---|---|
| 6008-YML086C | YML086C | ALO1 | D-arabinono-1,4-lactone oxidase | D-Arabinono-1,4-lactone oxidase; catalyzes the final step in biosynthesis of dehydro-D-arabinono-1,4-lactone, which is protective against oxidative stress | Accessory | Ancestral | NA | NA |
| 6009-YML087C | YML087C | AIM33 | cytochrome-b5 reductase | Protein of unknown function, highly conserved across species; homolog of human CYB5R4; null mutant displays reduced frequency of mitochondrial genome loss; AIM33 has a paralog, PGA3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6010-YML088W | YML088W | UFO1 | SCF ubiquitin ligase complex subunit UFO1 | F-box receptor protein; subunit of the Skp1-Cdc53-F-box receptor (SCF) E3 ubiquitin ligase complex; binds to phosphorylated Ho endonuclease, allowing its ubiquitination by SCF and subsequent degradation | Core | NA | NA | NA |
| 6011-YML089C | YML089C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; expression induced by calcium shortage | Core | NA | NA | NA |
| 6012-YML090W | YML090W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YML089C; exhibits growth defect on a non-fermentable (respiratory) carbon source | Core | NA | NA | NA |
| 6013-YML091C | YML091C | RPM2 | ribonuclease P | Protein subunit of mitochondrial RNase P; has roles in nuclear transcription, cytoplasmic and mitochondrial RNA processing, and mitochondrial translation; distributed to mitochondria, cytoplasmic processing bodies, and the nucleus | Core | NA | NA | NA |
| 6014-YML092C | YML092C | PRE8 | proteasome core particle subunit alpha 2 | Alpha 2 subunit of the 20S proteasome | Core | NA | NA | NA |
| 6015-YML093W | YML093W | UTP14 | NA | Subunit of U3-containing Small Subunit (SSU) processome complex; involved in production of 18S rRNA and assembly of small ribosomal subunit | Core | NA | NA | NA |
| 6016-YML094W_NumOfGenes_2 | YML094W | GIM5 | PFD5 | Subunit of the heterohexameric cochaperone prefoldin complex; prefoldin binds specifically to cytosolic chaperonin and transfers target proteins to it; prefoldin complex also localizes to chromatin of actively transcribed genes in the nucleus and facilitates transcriptional elongation | Core | NA | NA | NA |
| 6017-YML095C | YML095C | RAD10 | NA | Single-stranded DNA endonuclease (with Rad1p); cleaves single-stranded DNA during nucleotide excision repair and double-strand break repair; subunit of Nucleotide Excision Repair Factor 1 (NEF1); homolog of human ERCC1 protein | Core | NA | NA | NA |
| 6018-YML096W | YML096W | NA | putative asparagine synthase | Putative protein with similarity to asparagine synthetases; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YML096W is not an essential gene and partially overlaps the verified gene RAD10 | Core | NA | NA | NA |
| 6019-YML097C | YML097C | VPS9 | guanine nucleotide exchange factor VPS9|VPT9|VPL31 | Guanine nucleotide exchange factor (GEF) and ubiquitin receptor; involved in vesicle-mediated vacuolar transport, including Golgi-endosome trafficking and sorting through the multivesicular body (MVB); stimulates the intrinsic guanine nucleotide exchange activity of Rab family members (Vps21p/Ypt52p/Ypt53p); partially redundant with GEF MUK1; required for localization of the CORVET complex to endosomes; similar to mammalian ras inhibitors; contains a Ub-interacting CUE domain | Core | NA | NA | NA |
| 6020-YML098W | YML098W | TAF13 | TafII19|TAF19|FUN81 | TFIID subunit (19 kDa); involved in RNA polymerase II transcription initiation, similar to histone H4 with atypical histone fold motif of Spt3-like transcription factors | Core | NA | NA | NA |
| 6021-YML099C | YML099C | ARG81 | ARGRII|ARGR2 | Zinc finger transcription factor involved in arginine-responsive genes; Zn(2)-Cys(6) binuclear cluster domain type; involved in the regulation of arginine-responsive genes; acts with Arg80p and Arg82p | Core | NA | NA | NA |
| 6022-YML099W-A | YML099W-A | NA | YML100W-A | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF ARG81/YML099C | Accessory | Ancestral | NA | NA |