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 |
|---|---|---|---|---|---|---|---|---|
| 1958-YBL087C | YBL087C | RPL23A | uL14|ribosomal 60S subunit protein L23A|L14|YL32|L23A|L17aA | Ribosomal 60S subunit protein L23A; homologous to mammalian ribosomal protein L23 and bacterial L14; RPL23A has a paralog, RPL23B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1959-YBL088C | YBL088C | TEL1 | DNA-binding protein kinase TEL1 | Protein kinase primarily involved in telomere length regulation; contributes to cell cycle checkpoint control in response to DNA damage; acts with Red1p and Mec1p to promote interhomolog recombination by phosphorylation of Hop1; functionally redundant with Mec1p; regulates P-body formation induced by replication stress; homolog of human ataxia-telangiectasia mutated (ATM) gene | Core | NA | NA | NA |
| 1960-YBL089W | YBL089W | AVT5 | amino acid transporter | Putative transporter; member of a family of seven S. cerevisiae genes (AVT1-7) related to vesicular GABA-glycine transporters; AVT5 has a paralog, AVT6, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1961-YBL090W | YBL090W | MRP21 | mitochondrial 37S ribosomal protein MRP21|MRP50 | Mitochondrial ribosomal protein of the small subunit; MRP21 exhibits genetic interactions with mutations in the COX2 and COX3 mRNA 5'-untranslated leader sequences | Core | NA | NA | NA |
| 1962-YBL091C | YBL091C | MAP2 | methionine aminopeptidase | Methionine aminopeptidase; catalyzes the cotranslational removal of N-terminal methionine from nascent polypeptides; function is partially redundant with that of Map1p | Core | NA | NA | NA |
| 1963-YBL091C-A | YBL091C-A | SCS22 | phospholipid metabolism-regulating protein SCS22 | Protein involved in regulation of phospholipid metabolism; one of 6 proteins (Ist2p, Scs2p, Scs22p, Tcb1p, Tcb2p, Tcb3p) that connect the ER and plasma membrane (PM); regulates PM PI4P levels by controlling access of the Sac1p phosphatase to its substrate, PI4P; human VAP homolog; similar to D. melanogaster inturned protein; SWAT-GFP and mCherry fusion proteins localize to the cytosol; SCS22 has a paralog, SCS2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1964-YBL092W | YBL092W | RPL32 | eL32|ribosomal 60S subunit protein L32|L32e|L32 | Ribosomal 60S subunit protein L32; overexpression disrupts telomeric silencing; homologous to mammalian ribosomal protein L32, no bacterial homolog | Core | NA | NA | NA |
| 1965-YBL093C | YBL093C | ROX3 | SSX2|MED19|SSN7|NUT3 | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme | Core | NA | NA | NA |
| 1966-YBL095W_NumOfGenes_2 | YBL095W | MRX3 | NA | Protein that associates with mitochondrial ribosome; likely functions in cristae junction formation; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 1967-YBL096C | YBL096C | NA | NA | Non-essential protein of unknown function | Accessory | Ancestral | NA | NA |
| 1968-YBL097W | YBL097W | BRN1 | condensin subunit BRN1 | Subunit of the condensin complex; required for chromosome condensation and for clustering of tRNA genes at the nucleolus; may influence multiple aspects of chromosome transmission | Core | NA | NA | NA |
| 1969-YBL098W | YBL098W | BNA4 | kynurenine 3-monooxygenase | Kynurenine 3-monooxygenase; required for the de novo biosynthesis of NAD from tryptophan via kynurenine; expression regulated by Hst1p; putative therapeutic target for Huntington disease | Core | NA | NA | NA |
| 1970-YBL099W_NumOfGenes_2 | YBL099W | ATP1 | F1F0 ATP synthase subunit alpha | Alpha subunit of the F1 sector of mitochondrial F1F0 ATP synthase; which is a large, evolutionarily conserved enzyme complex required for ATP synthesis; F1 translationally regulates ATP6 and ATP8 expression to achieve a balanced output of ATP synthase genes encoded in nucleus and mitochondria; phosphorylated; N-terminally propionylated in vivo | Core | NA | NA | NA |
| 1971-YBL100W-C | YBL100W-C | NA | YBL101W-C | Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching | Accessory | Ancestral | NA | NA |
| 1972-YBL101C | YBL101C | ECM21 | ART2 | Protein involved in regulating endocytosis of plasma membrane proteins; identified as a substrate for ubiquitination by Rsp5p and deubiquitination by Ubp2p; promoter contains several Gcn4p binding elements; ECM21 has a paralog, CSR2, that arose from the whole genome duplication | Core | NA | NA | NA |