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 |
|---|---|---|---|---|---|---|---|---|
| 1778-YAL013W | YAL013W | DEP1 | Rpd3L histone deacetylase complex subunit DEP1|FUN54 | Component of the Rpd3L histone deacetylase complex; required for diauxic shift-induced histone H2B deposition onto rDNA genes; transcriptional modulator involved in regulation of structural phospholipid biosynthesis genes and metabolically unrelated genes, as well as maintenance of telomeres, mating efficiency, and sporulation | Core | NA | NA | NA |
| 1779-YAL014C | YAL014C | SYN8 | syntaxin|SLT2|UIP2 | Endosomal SNARE related to mammalian syntaxin 8 | Core | NA | NA | NA |
| 1780-YAL015C | YAL015C | NTG1 | bifunctional N-glycosylase/AP lyase NTG1|ogg2|SCR1|FUN33 | DNA N-glycosylase and apurinic/apyrimidinic (AP) lyase; involved in base excision repair; acts in both nucleus and mitochondrion; creates a double-strand break at mtDNA origins that stimulates replication in response to oxidative stress; required for maintaining mitochondrial genome integrity; NTG1 has a paralog, NTG2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1781-YAL016C-A | YAL016C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps ORF TPD3/YAL016W | Accessory | Unknown | NA | NA |
| 1782-YAL016C-B | YAL016C-B | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Unknown | NA | NA |
| 1783-YAL016W | YAL016W | TPD3 | protein phosphatase 2A structural subunit TPD3|FUN32 | Regulatory subunit A of the heterotrimeric PP2A complex; the heterotrimeric protein phosphatase 2A (PP2A) complex also contains regulatory subunit Cdc55p and either catalytic subunit Pph21p or Pph22p; required for cell morphogenesis and transcription by RNA polymerase III | Core | NA | NA | NA |
| 1784-YAL017W | YAL017W | PSK1 | serine/threonine protein kinase PSK1|FUN31 | PAS domain-containing serine/threonine protein kinase; coordinately regulates protein synthesis and carbohydrate metabolism and storage in response to a unknown metabolite that reflects nutritional status; PSK1 has a paralog, PSK2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1785-YAL018C | YAL018C | LDS1 | NA | Protein Involved in spore wall assembly; localizes to lipid droplets found on or outside of the prospore membrane; shares similarity with Lds2p and Rrt8p, and a strain mutant for all 3 genes exhibits reduced dityrosine fluorescence relative to the single mutants | Core | NA | NA | NA |
| 1786-YAL019W | YAL019W | FUN30 | DNA-dependent ATPase FUN30 | Snf2p family member with ATP-dependent chromatin remodeling activity; has a role in silencing at the mating type locus, telomeres and centromeres; enriched at centromeres and is required for correct chromatin structure around centromeres, as well as at the boundary element of the silent HMR; recruited to DNA double-strand breaks (DSBs) where it promotes 5' strand resection of DSBs; potential Cdc28p substrate | Core | NA | NA | NA |
| 1787-YAL019W-A | YAL019W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps ORF ATS1/YAL020C | Accessory | Ancestral | NA | NA |
| 1788-YAL020C | YAL020C | ATS1 | KTI13|FUN28 | Protein required for modification of wobble nucleosides in tRNA; acts with Elongator complex, Kti11p, and Kti12p; has a potential role in regulatory interactions between microtubules and the cell cycle; forms a stable heterodimer with Kti11p | Accessory | Ancestral | NA | NA |
| 1789-YAL021C | YAL021C | CCR4 | CCR4-NOT core exoribonuclease subunit CCR4|NUT21|FUN27 | Component of the CCR4-NOT transcriptional complex; CCR4-NOT is involved in regulation of gene expression; component of the major cytoplasmic deadenylase, which is involved in mRNA poly(A) tail shortening | Core | NA | NA | NA |
| 1790-YAL022C | YAL022C | FUN26 | nucleoside transmembrane transporter FUN26 | High affinity, broad selectivity, nucleoside/nucleobase transporter; vacuolar membrane localized transporter which may regulate the balance of nicotinamide riboside (NmR) levels between the cytosol and vacuole, contributing to salvage of NmR for use in cytosolic NAD+ synthesis; equilibrative nucleoside transporter (ENT) family member | Core | NA | NA | NA |
| 1791-YAL023C | YAL023C | PMT2 | dolichyl-phosphate-mannose-protein mannosyltransferase PMT2|FUN25 | Protein O-mannosyltransferase of the ER membrane; transfers mannose residues from dolichyl phosphate-D-mannose to protein serine/threonine residues; involved in ER quality control; acts in a complex with Pmt1p, can instead interact with Pmt5p; antifungal drug target; PMT2 has a paralog, PMT3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1792-YAL024C | YAL024C | LTE1 | mitotic regulator LTE1|MSI2 | Protein similar to GDP/GTP exchange factors; without detectable GEF activity; required for asymmetric localization of Bfa1p at daughter-directed spindle pole bodies and for mitotic exit at low temperatures | Core | NA | NA | NA |