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 |
|---|---|---|---|---|---|---|---|---|
| 3098-YDR406W | YDR406W | PDR15 | ATP-binding cassette multidrug transporter PDR15 | Plasma membrane ATP binding cassette (ABC) transporter; multidrug transporter and general stress response factor implicated in cellular detoxification; regulated by Pdr1p, Pdr3p and Pdr8p; promoter contains a PDR responsive element; PDR15 has a paralog, PDR5, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3099-YDR406W-A | YDR406W-A | NA | YDR406C-A | Dubious open reading frame unlikely to encode a functional protein; identified by fungal homology and RT-PCR | Accessory | Unknown | NA | NA |
| 3100-YDR407C | YDR407C | TRS120 | NA | Component of transport protein particle (TRAPP) complex II; TRAPPII is a multimeric guanine nucleotide-exchange factor for the GTPase Ypt1p, regulating intra-Golgi and endosome-Golgi traffic | Core | NA | NA | NA |
| 3101-YDR408C | YDR408C | ADE8 | phosphoribosylglycinamide formyltransferase | Phosphoribosyl-glycinamide transformylase; catalyzes a step in the 'de novo' purine nucleotide biosynthetic pathway | Core | NA | NA | NA |
| 3102-YDR409W | YDR409W | SIZ1 | SUMO ligase SIZ1|ULL1 | SUMO E3 ligase; promotes attachment of small ubiquitin-related modifier sumo (Smt3p) to primarily cytoplasmic proteins; regulates Rsp5p ubiquitin ligase activity and is in turn itself regulated by Rsp5p; required for sumoylation of septins and histone H3 variant Cse4p, a prerequisite for STUbL-mediated Ub-dependent degradation; localizes to the septin ring; acts as an adapter between E2, Ubc9p and substrates; tends to compensate for survival of DNA damage in absence of Nfi1p | Core | NA | NA | NA |
| 3103-YDR410C | YDR410C | STE14 | protein-S-isoprenylcysteine carboxyl O-methyltransferase | Farnesyl cysteine-carboxyl methyltransferase; mediates the carboxyl methylation step during C-terminal CAAX motif processing of a-factor and RAS proteins in the endoplasmic reticulum, localizes to the ER membrane | Core | NA | NA | NA |
| 3104-YDR411C | YDR411C | DFM1 | NA | Endoplasmic reticulum (ER) localized protein; involved in ER-associated protein degradation (ERAD), ER stress, and homeostasis; interacts with components of ERAD-L and ERAD-C and Cdc48p; derlin-like family member similar to Der1p | Core | NA | NA | NA |
| 3105-YDR412W_NumOfGenes_2 | YDR412W | RRP17 | NA | Component of the pre-60S pre-ribosomal particle; required for cell viability under standard (aerobic) conditions but not under anaerobic conditions; exonuclease required for 5' end processing of pre-60S ribosomal RNA | Core | NA | NA | NA |
| 3106-YDR414C | YDR414C | ERD1 | LDB2 | Predicted membrane protein required for lumenal ER protein retention; mutants secrete the endogenous ER protein, BiP (Kar2p) | Core | NA | NA | NA |
| 3107-YDR415C | YDR415C | NA | putative aminopeptidase | Putative aminopeptidase; SWAT-GFP fusion protein localizes to the endoplasmic reticulum and vacuole, while mCherry fusion localizes to the vacuole | Core | NA | NA | NA |
| 3108-YDR416W | YDR416W | SYF1 | mRNA splicing protein SYF1|NTC90 | Member of the NineTeen Complex (NTC); that contains Prp19p and stabilizes U6 snRNA in catalytic forms of the spliceosome containing U2, U5, and U6 snRNAs; null mutant has splicing defect and arrests in G2/M; relocalizes to the cytosol in response to hypoxia; homologs in human and C. elegans | Core | NA | NA | NA |
| 3109-YDR418W_NumOfGenes_2 | YDR418W | RPL12B | uL11|ribosomal 60S subunit protein L12B|L11|YL23|L15B|L12B | Ribosomal 60S subunit protein L12B; rpl12a rpl12b double mutant exhibits slow growth and slow translation; homologous to mammalian ribosomal protein L12 and bacterial L11; RPL12B has a paralog, RPL12A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3110-YDR419W | YDR419W | RAD30 | DNA-directed DNA polymerase eta|DBH1 | DNA polymerase eta; involved in translesion synthesis during post-replication repair; catalyzes the synthesis of DNA opposite cyclobutane pyrimidine dimers and other lesions; involved in formation of post-replicative damage-induced genome-wide cohesion; may also have a role in protection against mitochondrial mutagenesis; mutations in human pol eta are responsible for XPV | Core | NA | NA | NA |
| 3111-YDR420W | YDR420W | HKR1 | NA | Mucin family member that functions as an osmosensor in the HOG pathway; large, highly glycosylated protein that functions redundantly with Msb2p in Sho1p-mediated osmostresss induction of the HOG signaling pathway; cytoplasmic domain interacts with Ahk1p a scaffold protein that prevents cross talk with the Kss1p MAPK of the filamentous growth pathway; mutant displays defects in beta-1,3 glucan synthesis and bud site selection | Core | NA | NA | NA |
| 3112-YDR421W | YDR421W | ARO80 | NA | Zinc finger transcriptional activator of the Zn2Cys6 family; activates transcription of aromatic amino acid catabolic genes in the presence of aromatic amino acids | Core | NA | NA | NA |