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 |
|---|---|---|---|---|---|---|---|---|
| 6803-YOL007C | YOL007C | CSI2 | NA | Protein of unknown function; green fluorescent protein (GFP)- fusion protein localizes to the mother side of the bud neck and the vacuole; YOL007C is not an essential gene | Core | NA | NA | NA |
| 6804-YOL008W | YOL008W | COQ10 | ubiquinone-binding protein COQ10 | Coenzyme Q (ubiquinone) binding protein; functions in the delivery of Q<sub>6</sub> to its proper location for electron transport during respiration; START domain protein with homologs in bacteria and eukaryotes; respiratory growth defect of the null mutant is functionally complemented by human COQ10A | Core | NA | NA | NA |
| 6805-YOL009C | YOL009C | MDM12 | ERMES complex subunit MDM12 | Mitochondrial outer membrane protein, ERMES complex subunit; required for transmission of mitochondria to daughter cells; required for mitophagy; may influence import and assembly of outer membrane beta-barrel proteins; ERMES complex is often co-localized with peroxisomes and with concentrated areas of pyruvate dehydrogenase | Core | NA | NA | NA |
| 6806-YOL010W | YOL010W | RCL1 | rRNA-processing endoribonuclease | Endonuclease that cleaves pre-rRNA at site A2 for 18S rRNA biogenesis; subunit of U3-containing 90S preribosome processome complex involved in small ribosomal subunit assembly; stimulates Bms1p GTPase and U3 binding activity; similar to RNA cyclase-like proteins but no cyclase activity detected | Core | NA | NA | NA |
| 6807-YOL011W | YOL011W | PLB3 | lysophospholipase | Phospholipase B (lysophospholipase) involved in lipid metabolism; hydrolyzes phosphatidylinositol and phosphatidylserine and displays transacylase activity in vitro; PLB3 has a paralog, PLB1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6808-YOL012C | YOL012C | HTZ1 | histone H2AZ|H2AZ|H2A.F/Z|HTA3 | Histone variant H2AZ; exchanged for histone H2A in nucleosomes by the SWR1 complex; involved in transcriptional regulation through prevention of the spread of silent heterochromatin; Htz1p-containing nucleosomes facilitate RNA Pol II passage by affecting correct assembly and modification status of RNA Pol II elongation complexes and by favoring efficient nucleosome remodeling | Core | NA | NA | NA |
| 6809-YOL013C | YOL013C | HRD1 | E3 ubiquitin-protein ligase HRD1|DER3 | Ubiquitin-protein ligase involved in ER-associated degradation (ERAD) of misfolded proteins; upon autoubiquitination triggers retrotranslocation of misfolded proteins to cytosol for degradation; genetically linked to the unfolded protein response (UPR); regulated through association with Hrd3p; contains an H2 ring finger; likely plays a general role in targeting proteins that persistently associate with and potentially obstruct the ER-localized translocon | Core | NA | NA | NA |
| 6810-YOL013W-A | YOL013W-A | NA | YOL013W-B | Putative protein of unknown function; identified by SAGE | Accessory | Ancestral | NA | NA |
| 6811-YOL013W-B | YOL013W-B | NA | YOL013W-A | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; completely overlaps the long terminal repeat (LTR) of a Ty1 element | Core | NA | NA | NA |
| 6812-YOL014W | YOL014W | NA | NA | Putative protein of unknown function; mCherry fusion protein localizes to the cytosol and nucleus | Core | NA | NA | NA |
| 6813-YOL015W | YOL015W | IRC10 | NA | Protein of unknown function; subunit of the leading edge protein (LEP) complex (Ssp1-Ady3-Don1-Irc10) that forms a ring-like structure at the leading edge of the prospore membrane during meiosis II; null mutant displays increased levels of spontaneous Rad52p foci | Core | NA | NA | NA |
| 6814-YOL016C | YOL016C | CMK2 | calmodulin-dependent protein kinase CMK2 | Calmodulin-dependent protein kinase; may play a role in stress response, many CA++/calmodulan dependent phosphorylation substrates demonstrated in vitro, amino acid sequence similar to mammalian Cam Kinase II; CMK2 has a paralog, CMK1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6815-YOL017W | YOL017W | ESC8 | NA | Protein involved in telomeric and mating-type locus silencing; interacts with Sir2p and also interacts with Gal11p, which is a component of the RNA pol II mediator complex; ESC8 has a paralog, IOC3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6816-YOL018C | YOL018C | TLG2 | NA | Syntaxin-like t-SNARE; forms a complex with Tlg1p and Vti1p and mediates fusion of endosome-derived vesicles with the late Golgi; required along with VPS45 for an early step of the constitutive CVT pathway; interactions with Vps45 prevents Tlg2p degradation, and facilitates t-SNARE complex formation; homologous to mammalian SNARE protein syntaxin 16 (Sx16) | Core | NA | NA | NA |
| 6817-YOL019W | YOL019W | NA | TOS7 | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery and vacuole; YOL019W has a paralog, DCV1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |