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 |
|---|---|---|---|---|---|---|---|---|
| 6623-YNL234W | YNL234W | NA | NA | Protein of unknown function with similarity to globins; has a functional heme-binding domain; mutant has aneuploidy tolerance; transcription induced by stress conditions; may be involved in glucose signaling or metabolism; regulated by Rgt1 | Core | NA | NA | NA |
| 6624-YNL235C | YNL235C | 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 SIN4/YNL236W, a subunit of the mediator complex | Accessory | Ancestral | NA | NA |
| 6625-YNL236W | YNL236W | SIN4 | SSX3|MED16|RYE1|TSF3|SSN4|SSF5|SDI3|GAL22|BEL2 | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; contributes to both postive and negative transcriptional regulation; dispensible for basal transcription | Core | NA | NA | NA |
| 6626-YNL237W | YNL237W | YTP1 | NA | Probable type-III integral membrane protein of unknown function; has regions of similarity to mitochondrial electron transport proteins | Core | NA | NA | NA |
| 6627-YNL238W | YNL238W | KEX2 | kexin KEX2|yscF|SRB1|VMA45|QDS1 | Kexin, a subtilisin-like protease (proprotein convertase); a calcium-dependent serine protease involved in the activation of proproteins of the secretory pathway | Core | NA | NA | NA |
| 6628-YNL239W | YNL239W | LAP3 | bleomycin hydrolase|YCP1|GAL6|BLH1 | Cysteine aminopeptidase with homocysteine-thiolactonase activity; protects cells against homocysteine toxicity; has bleomycin hydrolase activity in vitro; transcription is regulated by galactose via Gal4p; orthologous to human BLMH | Core | NA | NA | NA |
| 6629-YNL240C | YNL240C | NAR1 | NA | Subunit of the cytosolic iron-sulfur (FeS) protein assembly machinery; required for maturation of cytosolic and nuclear FeS proteins and for normal resistance to oxidative stress; deficiency results in shortened lifespan and sensitivity to paraquat; homologous to human Narf | Core | NA | NA | NA |
| 6630-YNL241C | YNL241C | ZWF1 | glucose-6-phosphate dehydrogenase|POS10|MET19 | Glucose-6-phosphate dehydrogenase (G6PD); catalyzes the first step of the pentose phosphate pathway; involved in adapting to oxidative stress; protein abundance increases in response to DNA replication stress; homolog of human G6PD which is deficient in patients with hemolytic anemia; human G6PD can complement yeast zwf1 null mutant | Core | NA | NA | NA |
| 6631-YNL242W | YNL242W | ATG2 | APG2|AUT8|SPO72 | Peripheral membrane protein required for autophagic vesicle formation; also required for vesicle formation during pexophagy and the cytoplasm-to-vaucole targeting (Cvt) pathway; involved in Atg9p cycling between the phagophore assembly site and mitochondria; contains an APT1 domain that binds phosphatidylinositol-3-phosphate; essential for cell cycle progression from G2/M to G1 under nitrogen starvation; forms cytoplasmic foci upon DNA replication stress | Core | NA | NA | NA |
| 6632-YNL243W | YNL243W | SLA2 | MOP2|END4 | Adaptor protein that links actin to clathrin and endocytosis; involved in membrane cytoskeleton assembly and cell polarization; present in the actin cortical patch of the emerging bud tip; dimer in vivo | Core | NA | NA | NA |
| 6633-YNL244C | YNL244C | SUI1 | translation initiation factor eIF1|RFR1|MOF2 | Translation initiation factor eIF1; component of a complex involved in recognition of the initiator codon; modulates translation accuracy at the initiation phase | Core | NA | NA | NA |
| 6634-YNL245C | YNL245C | CWC25 | U2-type spliceosomal complex subunit CWC25 | Splicing factor required for the first step of pre-mRNA splicing; binding to the spliceosome requires Prp2p and Yju2p; heat-stable protein; has similarity to S. pombe Cwf25p | Core | NA | NA | NA |
| 6635-YNL246W | YNL246W | VPS75 | NA | NAP family histone chaperone; binds to histones and Rtt109p, stimulating histone acetyltransferase activity; possesses nucleosome assembly activity in vitro; proposed role in vacuolar protein sorting and in double-strand break repair; protein abundance increases in response to DNA replication stress; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 6636-YNL247W | YNL247W | NA | cysteine--tRNA ligase | Cysteinyl-tRNA synthetase; may interact with ribosomes, based on co-purification experiments; human gene CARS allows growth of the yeast haploid null mutant after sporulation of a heterozygous diploid | Core | NA | NA | NA |
| 6637-YNL248C | YNL248C | RPA49 | DNA-directed RNA polymerase I subunit RPA49|A49 | RNA polymerase I subunit A49; essential for nucleolar assembly and for high polymerase loading rate; required for nucleolar localization of Rpa34p | Core | NA | NA | NA |