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 |
|---|---|---|---|---|---|---|---|---|
| 7028-YOR061W | YOR061W | CKA2 | casein kinase 2 catalytic subunit CKA2|YOR29-12 | Alpha' catalytic subunit of casein kinase 2 (CK2); CK2 is a Ser/Thr protein kinase with roles in cell growth and proliferation; CK2, comprised of CKA1, CKA2, CKB1 and CKB2, has many substrates including transcription factors and all RNA polymerases; protein abundance increases in response to DNA replication stress; regulates Fkh1p-mediated donor preference during mating-type switching | Core | NA | NA | NA |
| 7029-YOR062C | YOR062C | NA | YOR29-13 | Protein of unknown function; similar to Reg1p; expression regulated by glucose and Rgt1p; GFP-fusion protein is induced in response to the DNA-damaging agent MMS; YOR062C has a paralog, YKR075C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7030-YOR063W | YOR063W | RPL3 | uL3|ribosomal 60S subunit protein L3|rp1|YL1|L3|YOR29-14|TCM1|MAK8 | Ribosomal 60S subunit protein L3; homologous to mammalian ribosomal protein L3 and bacterial L3; plays an important role in function of eIF5B in stimulating 3' end processing of 18S rRNA in context of 80S ribosomes that have not yet engaged in translation; involved in replication and maintenance of killer double stranded RNA virus | Core | NA | NA | NA |
| 7031-YOR064C | YOR064C | YNG1 | YOR29-15 | Subunit of the NuA3 histone acetyltransferase complex; this complex acetylates histone H3; contains PHD finger domain that interacts with methylated histone H3; shares significant sequence identity with the human candidate tumor suppressor p33-ING1 in C-terminal region | Core | NA | NA | NA |
| 7032-YOR065W | YOR065W | CYT1 | ubiquinol--cytochrome-c reductase catalytic subunit CYT1|YOR29-16|CTC1 | Cytochrome c1; component of the mitochondrial respiratory chain; expression is regulated by the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex | Core | NA | NA | NA |
| 7033-YOR066W | YOR066W | MSA1 | YOR29-17 | Activator of G1-specific transcription factors MBF and SBF; involved in regulation of the timing of G1-specific gene transcription and cell cycle initiation; localization is cell-cycle dependent and regulated by Cdc28p phosphorylation; MSA1 has a paralog, MSA2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7034-YOR067C | YOR067C | ALG8 | dolichyl-P-Glc:Glc1Man(9)GlcNAc(2)-PP-dolichol alpha-1,3-glucosyltransferase|YOR29-18 | Glucosyl transferase; involved in N-linked glycosylation; adds glucose to the dolichol-linked oligosaccharide precursor prior to transfer to protein during lipid-linked oligosaccharide biosynthesis; similar to Alg6p; human homolog ALG8 can complement yeast null mutant | Core | NA | NA | NA |
| 7035-YOR068C_NumOfGenes_2 | YOR068C | VAM10 | YOR29-19 | Protein involved in vacuole morphogenesis; acts at an early step of homotypic vacuole fusion that is required for vacuole tethering | Core | NA | NA | NA |
| 7036-YOR070C | YOR070C | GYP1 | YOR29-21 | Cis-golgi GTPase-activating protein (GAP) for yeast Rabs; the Rab family members are Ypt1p (in vivo) and for Ypt1p, Sec4p, Ypt7p, and Ypt51p (in vitro); involved in vesicle docking and fusion | Core | NA | NA | NA |
| 7037-YOR071C | YOR071C | NRT1 | nicotinamide riboside transporter|THI71|YOR29-22 | High-affinity nicotinamide riboside transporter; also transports thiamine with low affinity; major transporter for 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranoside (acadesine) uptake; shares sequence similarity with Thi7p and Thi72p; proposed to be involved in 5-fluorocytosine sensitivity | Core | NA | NA | NA |
| 7038-YOR072W | YOR072W | NA | YOR29-23 | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the dubious gene YOR072W-A; diploid deletion strains are methotrexate, paraquat and wortmannin sensitive | Core | NA | NA | NA |
| 7039-YOR072W-A | YOR072W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YOR072W; originally identified by fungal homology and RT-PCR | Core | NA | NA | NA |
| 7040-YOR072W-B | YOR072W-B | NA | NA | Putative protein of unknown function; identified by expression profiling and mass spectrometry | Accessory | Unknown | NA | NA |
| 7041-YOR073W | YOR073W | SGO1 | YOR29-24 | Component of the spindle checkpoint; involved in sensing lack of tension on mitotic chromosomes; protects centromeric Rec8p at meiosis I; required for accurate chromosomal segregation at meiosis II and for mitotic chromosome stability; recruits condensin to the pericentric region of chromosomes during meiosis; dissociates from pericentromeres when sister kinetochores are under tension | Core | NA | NA | NA |
| 7042-YOR074C_NumOfGenes_2 | YOR074C | CDC21 | thymidylate synthase|YOR29-25|TMP1|CRT9 | Thymidylate synthase; required for de novo biosynthesis of pyrimidine deoxyribonucleotides; expression is induced at G1/S; human homolog TYMSOS can complement yeast cdc21 temperature-sensitive mutant at restrictive temperature | Core | NA | NA | NA |