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 |
|---|---|---|---|---|---|---|---|---|
| 4868-YJL172W | YJL172W | CPS1 | Gly-Xaa carboxypeptidase | Vacuolar carboxypeptidase S; expression is induced under low-nitrogen conditions | Accessory | Ancestral | NA | NA |
| 4869-YJL173C | YJL173C | RFA3 | RPA14|RPA3 | Subunit of heterotrimeric Replication Protein A (RPA); RPA is a highly conserved single-stranded DNA binding protein complex involved in DNA replication, repair, recombination; RPA protects against inappropriate telomere recombination, and upon telomere uncapping, prevents cell proliferation by a checkpoint-independent pathway; with Sgs1p-Top2p-Rmi1p, stimulates DNA catenation/decatenation activity of Top3p; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4870-YJL174W | YJL174W | KRE9 | NA | Glycoprotein involved in cell wall beta-glucan assembly; null mutation leads to severe growth defects, aberrant multibudded morphology, and mating defects | Accessory | Ancestral | NA | NA |
| 4871-YJL176C_NumOfGenes_2 | YJL176C | SWI3 | HAF2|TYE2 | Subunit of the SWI/SNF chromatin remodeling complex; SWI/SNF regulates transcription by remodeling chromosomes; contains SANT domain that is required for SWI/SNF assembly; is essential for displacement of histone H2A-H2B dimers during ATP-dependent remodeling; required for transcription of many genes, including ADH1, ADH2, GAL1, HO, INO1 and SUC2; relocates to the cytosol under hypoxic conditions | Core | NA | NA | NA |
| 4872-YJL177W | YJL177W | RPL17B | uL22|ribosomal 60S subunit protein L17B|L22|YL17|L20B|L17B | Ribosomal 60S subunit protein L17B; required for processing of 27SB pre-rRNA and formation of stable 66S assembly intermediates; homologous to mammalian ribosomal protein L17 and bacterial L22; RPL17B has a paralog, RPL17A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4873-YJL178C | YJL178C | ATG27 | ETF1 | Type I membrane protein involved in autophagy and the Cvt pathway; may be involved in membrane delivery to the phagophore assembly site | Core | NA | NA | NA |
| 4874-YJL179W | YJL179W | PFD1 | prefolding complex chaperone subunit|GIM6 | Subunit of heterohexameric prefoldin; prefoldin binds cytosolic chaperonin and transfers target proteins to it; involved in the biogenesis of actin and of alpha- and gamma-tubulin; prefoldin complex also localizes to chromatin of actively transcribed genes in the nucleus and facilitates transcriptional elongation | Core | NA | NA | NA |
| 4875-YJL180C | YJL180C | ATP12 | ATP synthase complex assembly protein ATP12 | Assembly factor for F1 sector of mitochondrial F1F0 ATP synthase; conserved protein; required for assembly of alpha and beta subunits into F1 sector of mitochondrial F1F0 ATP synthase; human homolog ATPAF2 can complement yeast atp12 mutant; mutation of human homolog reduces active ATP synthase levels and is associated with the disorder ATPAF2 deficiency | Core | NA | NA | NA |
| 4876-YJL181W | YJL181W | RBH1 | RBH1 | Putative protein of unknown function; expression is cell-cycle regulated as shown by microarray analysis; potential regulatory target of Mbp1p, which binds to the YJL181W promoter region; contains a PH-like domain; RBH1 has a paralog, RBH2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4877-YJL182C | YJL182C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps uncharacterized ORF YJL181W | Core | NA | NA | NA |
| 4878-YJL183W | YJL183W | MNN11 | alpha-1,6-mannosyltransferase | Subunit of a Golgi mannosyltransferase complex; this complex also contains Anp1p, Mnn9p, Mnn10p, and Hoc1p, and mediates elongation of the polysaccharide mannan backbone; has homology to Mnn10p | Core | NA | NA | NA |
| 4879-YJL184W | YJL184W | GON7 | chromatin DNA-binding EKC/KEOPS complex subunit GON7|PCC2|LDB6 | Component of the EKC/KEOPS protein complex; EKC/KEOPS complex is required for t6A tRNA modification and telomeric TG1-3 recombination; may have role in transcription; implicated in osmotic stress response; other complex members are Kae1p, Cgi121p, Pcc1p, and Bud32p | Core | NA | NA | NA |
| 4880-YJL185C | YJL185C | ATG36 | NA | Pex3p interacting protein, required for pexophagy; interacts with Atg8p and Atg11p; mRNA is weakly cell cycle regulated, peaking in G2 phase; YJL185C is a non-essential gene | Core | NA | NA | NA |
| 4881-YJL186W | YJL186W | MNN5 | alpha-1,2-mannosyltransferase MNN5 | Alpha-1,2-mannosyltransferase; responsible for addition of the second alpha-1,2-linked mannose of the branches on the mannan backbone of oligosaccharides, localizes to an early Golgi compartment | Core | NA | NA | NA |
| 4882-YJL187C | YJL187C | SWE1 | tyrosine protein kinase SWE1|WEE1 | Protein kinase that regulates the G2/M transition; negative regulator of the Cdc28p kinase; morphogenesis checkpoint kinase; positive regulator of sphingolipid biosynthesis via Orm2p; phosphorylates a tyrosine residue in the N-terminus of Hsp90 in a cell-cycle associated manner, thus modulating the ability of Hsp90 to chaperone a selected clientele; localizes to the nucleus and to the daughter side of the mother-bud neck; homolog of S. pombe Wee1p; potential Cdc28p substrate | Core | NA | NA | NA |