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 |
|---|---|---|---|---|---|---|---|---|
| 3398-YER075C | YER075C | PTP3 | tyrosine protein phosphatase PTP3 | Phosphotyrosine-specific protein phosphatase; involved in the inactivation of mitogen-activated protein kinase (MAPK) during osmolarity sensing; dephosporylates Hog1p MAPK and regulates its localization; localized to the cytoplasm | Core | NA | NA | NA |
| 3399-YER076C | YER076C | NA | NA | Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; analysis of HA-tagged protein suggests a membrane localization | Accessory | Ancestral | NA | NA |
| 3400-YER076W-A | YER076W-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 YER076C | Accessory | Unknown | S. paradoxus | NA |
| 3401-YER077C | YER077C | MRX1 | NA | Protein that associates with mitochondrial ribosome; green fluorescent protein (GFP)-fusion protein localizes to the mitochondrion; null mutation results in a decrease in plasma membrane electron transport | Core | NA | NA | NA |
| 3402-YER078C | YER078C | ICP55 | aminopeptidase | Mitochondrial aminopeptidase; cleaves the N termini of at least 38 imported proteins after cleavage by the mitochondrial processing peptidase (MPP), thereby increasing their stability; member of the aminopeptidase P family | Core | NA | NA | NA |
| 3403-YER078W-A | YER078W-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Core | NA | NA | NA |
| 3404-YER079W | YER079W | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 3405-YER080W_NumOfGenes_2 | YER080W | AIM9 | FMP29 | Protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; null mutant displays elevated frequency of mitochondrial genome loss | Core | NA | NA | NA |
| 3406-YER081W | YER081W | SER3 | phosphoglycerate dehydrogenase SER3 | 3-phosphoglycerate dehydrogenase and alpha-ketoglutarate reductase; 3PG dehydrogenase that catalyzes the first step in serine and glycine biosynthesis; also functions as an alpha-ketoglutarate reductase, converting alpha-ketoglutarate to D-2-hydroxyglutarate (D-2HG); localizes to the cytoplasm; SER3 has a paralog, SER33, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3407-YER082C | YER082C | UTP7 | KRE31 | Nucleolar protein; component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA | Core | NA | NA | NA |
| 3408-YER083C | YER083C | GET2 | GET complex subunit GET2|RMD7|HUR2 | Subunit of the GET complex; involved in insertion of proteins into the ER membrane; required for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion and for meiotic nuclear division | Core | NA | NA | NA |
| 3409-YER084W | YER084W | NA | NA | Protein of unknown function; expressed at both mRNA and protein levels | Core | NA | NA | NA |
| 3410-YER085C_NumOfGenes_2 | YER085C | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 3411-YER086W | YER086W | ILV1 | threonine ammonia-lyase ILV1|ISO1 | Threonine deaminase, catalyzes first step in isoleucine biosynthesis; expression is under general amino acid control; ILV1 locus exhibits highly positioned nucleosomes whose organization is independent of known ILV1 regulation | Core | NA | NA | NA |
| 3412-YER087C-B | YER087C-B | SBH1 | Arf family guanine nucleotide exchange factor SBH1|YER087C-A|SEB1 | Beta subunit of Sec61p ER translocation complex (Sec61p-Sss1p-Sbh1p); involved in protein translocation into the endoplasmic reticulum; interacts with the exocyst complex and also with Rtn1p; cotranslationally N-acetylated by NatA; SBH1 has a paralog, SBH2, that arose from the whole genome duplication | Core | NA | NA | NA |