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 |
|---|---|---|---|---|---|---|---|---|
| 4943-YJR035W | YJR035W | RAD26 | DNA-dependent ATPase RAD26 | Protein involved in transcription-coupled nucleotide excision repair; repairs UV-induced DNA lesions; recruitment to DNA lesions is dependent on an elongating RNA polymerase II; homolog of human CSB protein | Core | NA | NA | NA |
| 4944-YJR036C_NumOfGenes_2 | YJR036C | HUL4 | putative E3 ubiquitin-protein ligase HUL4 | Protein with similarity to hect domain E3 ubiquitin-protein ligases; not essential for viability; found in association with Trf4 in TRAMP complex | Core | NA | NA | NA |
| 4945-YJR038C | YJR038C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 4946-YJR039W | YJR039W | NA | NA | Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 4947-YJR040W | YJR040W | GEF1 | CLC | Voltage-gated chloride channel; localized to the golgi, the endosomal system, and plasma membrane; involved in cation homeostasis; highly homologous to vertebrate voltage-gated chloride channels; modulates TBSV model (+) RNA virus replication by regulating copper metabolism | Core | NA | NA | NA |
| 4948-YJR041C | YJR041C | URB2 | NPA2 | Protein required for normal metabolism of the rRNA primary transcript; nucleolar protein; proposed to be involved in ribosome biogenesis | Core | NA | NA | NA |
| 4949-YJR042W | YJR042W | NUP85 | RAT9 | Subunit of the Nup84p subcomplex of the nuclear pore complex (NPC); contributes to nucleocytoplasmic transport and NPC biogenesis and is involved in establishment of a normal nucleocytoplasmic concentration gradient of the GTPase Gsp1p; also plays roles in several processes that may require localization of genes or chromosomes at the nuclear periphery, including double-strand break repair, transcription and chromatin silencing; homologous to human NUP85 aka NUP75 | Core | NA | NA | NA |
| 4950-YJR043C | YJR043C | POL32 | DNA polymerase delta subunit POL32|REV5 | Third subunit of DNA polymerase delta; involved in chromosomal DNA replication; required for error-prone DNA synthesis in the presence of DNA damage and processivity; forms a complex with Rev3p, Rev7p and Pol31p; interacts with Hys2p, PCNA (Pol30p), and Pol1p | Core | NA | NA | NA |
| 4951-YJR044C | YJR044C | VPS55 | NA | Late endosomal protein involved in late endosome to vacuole transport; functional homolog of human obesity receptor gene-related protein (OB-RGRP) | Core | NA | NA | NA |
| 4952-YJR045C | YJR045C | SSC1 | Hsp70 family ATPase SSC1|mtHSP70|ENS1 | Hsp70 family ATPase; constituent of the import motor component of the Translocase of the Inner Mitochondrial membrane (TIM23 complex); involved in protein translocation and folding; subunit of SceI endonuclease; SSC1 has a paralog, ECM10, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4953-YJR046W | YJR046W | TAH11 | CDT1|SID2 | DNA replication licensing factor; required for pre-replication complex assembly | Core | NA | NA | NA |
| 4954-YJR047C | YJR047C | ANB1 | translation elongation factor eIF-5A|eIF-5A|eIF5A|TIF51B|HYP1 | Translation elongation factor eIF-5A; previously thought to function in translation initiation; undergoes an essential hypusination modification; expressed under anaerobic conditions; ANB1 has a paralog, HYP2, that arose from the whole genome duplication; human EIF5A complements the inviability of the yeast hyp2 anb1 double null mutant | Core | NA | NA | NA |
| 4955-YJR048W | YJR048W | CYC1 | cytochrome c isoform 1 | Cytochrome c, isoform 1; also known as iso-1-cytochrome c; electron carrier of mitochondrial intermembrane space that transfers electrons from ubiquinone-cytochrome c oxidoreductase to cytochrome c oxidase during cellular respiration; CYC1 has a paralog, CYC7, that arose from the whole genome duplication; human homolog CYC1 can complement yeast null mutant; mutations in human CYC1 cause insulin-responsive hyperglycemia | Core | NA | NA | NA |
| 4956-YJR049C | YJR049C | UTR1 | NADH/NAD(+) kinase | ATP-NADH kinase; phosphorylates both NAD and NADH; active as a hexamer; enhances the activity of ferric reductase (Fre1p); UTR1 has a paralog, YEF1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4957-YJR050W | YJR050W | ISY1 | NTC30|UTR3 | Member of the NineTeen Complex (NTC); NTC contains Prp19p and stabilizes U6 snRNA in catalytic forms of spliceosome containing U2, U5, and U6 snRNAs; interacts with Prp16p to modulate splicing fidelity; isy1 syf2 cells have defective spindles | Core | NA | NA | NA |