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 |
|---|---|---|---|---|---|---|---|---|
| 5873-YLR414C_NumOfGenes_2 | YLR414C | PUN1 | NA | Plasma membrane protein with a role in cell wall integrity; co-localizes with Sur7p in punctate membrane patches; null mutant displays decreased thermotolerance; transcription induced upon cell wall damage and metal ion stress | Core | NA | NA | NA |
| 5874-YLR415C_NumOfGenes_3 | YLR415C | NA | NA | Putative protein of unknown function; YLR415C is not an essential gene | Core | NA | NA | NA |
| 5875-YLR417W_NumOfGenes_2 | YLR417W | VPS36 | ESCRT-II subunit protein VPS36|VPL11|VAC3|GRD12 | Component of the ESCRT-II complex; contains the GLUE (GRAM Like Ubiquitin binding in EAP45) domain which is involved in interactions with ESCRT-I and ubiquitin-dependent sorting of proteins into the endosome; plays a role in the formation of mutant huntingtin (Htt) aggregates in yeast | Core | NA | NA | NA |
| 5876-YLR418C_NumOfGenes_2 | YLR418C | CDC73 | NA | Component of the Paf1p complex; binds to and modulates the activity of RNA polymerases I and II; required for expression of certain genes, modification of some histones, and telomere maintenance; involved in transcription elongation as demonstrated by the G-less-based run-on (GLRO) assay; protein abundance increases in response to DNA replication stress; human homolog, parafibromin, is a tumour suppressor linked to breast, renal and gastric cancers | Core | NA | NA | NA |
| 5877-YLR419W_NumOfGenes_2 | YLR419W | NA | putative helicase | Putative helicase with limited sequence similarity to human Rb protein; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YLR419W is not an essential gene | Core | NA | NA | NA |
| 5878-YLR420W_NumOfGenes_2 | YLR420W | URA4 | dihydroorotase | Dihydroorotase; catalyzes the third enzymatic step in the de novo biosynthesis of pyrimidines, converting carbamoyl-L-aspartate into dihydroorotate | Core | NA | NA | NA |
| 5879-YLR421C_NumOfGenes_2 | YLR421C | RPN13 | proteasome regulatory particle lid subunit RPN13 | Subunit of the 19S regulatory particle of the 26S proteasome lid; acts as a ubiquitin receptor for the proteasome; null mutants accumulate ubiquitinated Gcn4p and display decreased 26S proteasome stability; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5880-YLR422W | YLR422W | DCK1 | NA | Dock family protein (Dedicator Of CytoKinesis), homolog of human DOCK1; upstream component for regulation through the small GTPase Rho5p; may form a complex with Lmo1p that acts as a GEF for Rho5p; interacts with Ino4p; cytoplasmic protein that relocates to mitochondria under oxidative stress; implicated in mitophagy; not an essential protein; DOCK proteins act as guanine nucleotide exchange factors | Core | NA | NA | NA |
| 5881-YLR423C | YLR423C | ATG17 | protein kinase regulatory subunit ATG17|APG17 | Scaffold protein responsible for phagophore assembly site organization; regulatory subunit of an autophagy-specific complex that includes Atg1p and Atg13p; stimulates Atg1p kinase activity; human ortholog RB1CC1/FIP200 interacts with p53, which inhibits autophagy in human cells | Core | NA | NA | NA |
| 5882-YLR424W | YLR424W | SPP382 | mRNA splicing protein SPP382|NTR1|CCF8 | Essential protein that forms a dimer with Ntr2p; also forms a trimer, with Ntr2p and Prp43p, that is involved in spliceosome disassembly; found also in a multisubunit complex with the splicing factor Clf1p; suppressor of prp38-1 mutation | Core | NA | NA | NA |
| 5883-YLR425W | YLR425W | TUS1 | Rho family guanine nucleotide exchange factor TUS1|SOP10 | Guanine nucleotide exchange factor (GEF) that modulates Rho1p activity; involved in the cell integrity signaling pathway; interacts with Rgl1p; localization of Tus1p to the bed neck is regulated by Rgl1p; multicopy suppressor of tor2 mutation and ypk1 ypk2 double mutation; potential Cdc28p substrate | Core | NA | NA | NA |
| 5884-YLR426W | YLR426W | TDA5 | NA | Putative protein of unknown function; detected in highly purified mitochondria in high-throughput studies; proposed to be involved in resistance to mechlorethamine and streptozotocin; null mutant sensitive to expression of top1-T722A allele | Core | NA | NA | NA |
| 5885-YLR427W | YLR427W | MAG2 | NA | Cytoplasmic protein of unknown function; induced in response to mycotoxin patulin; ubiquitinated protein similar to the human ring finger motif protein RNF10; predicted to be involved in repair of alkylated DNA due to interaction with MAG1 | Core | NA | NA | NA |
| 5886-YLR428C | YLR428C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF CRN1 | Core | NA | NA | NA |
| 5887-YLR429W | YLR429W | CRN1 | NA | Coronin; cortical actin cytoskeletal component that associates with the Arp2p/Arp3p complex to regulate its activity; plays a role in regulation of actin patch assembly | Core | NA | NA | NA |