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 |
|---|---|---|---|---|---|---|---|---|
| 4373-YHR117W | YHR117W | TOM71 | protein channel TOM71|TOM72 | Mitochondrial outer membrane protein; probable minor component of the TOM (translocase of outer membrane) complex responsible for recognition and import of mitochondrially directed proteins; TOM71 has a paralog, TOM70, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4374-YHR118C | YHR118C | ORC6 | origin recognition complex subunit 6 | Subunit of the origin recognition complex (ORC); ORC directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; phosphorylated by Cdc28p; mutation in the human Orc6p is linked to Meier-Gorlin syndrome | Core | NA | NA | NA |
| 4375-YHR119W | YHR119W | SET1 | histone methyltransferase SET1|KMT2|YTX1 | Histone methyltransferase, subunit of the COMPASS (Set1C) complex; COMPASS methylates histone H3K4; Set1p-dependent H3K4 trimethylation recruits Nrd1p, allowing efficient termination of snoRNAs and cryptic unstable transcripts (CUTs) by Nrd1p-Nab3p-Sen1p pathway; modulates histone acetylation levels in promoter proximal regions to ensure efficient Nrd1p-dependent termination; required in transcriptional silencing near telomeres and at silent mating type loci; has a SET domain | Core | NA | NA | NA |
| 4376-YHR120W | YHR120W | MSH1 | mismatch repair ATPase MSH1 | DNA-binding protein of the mitochondria; involved in repair of mitochondrial DNA; has ATPase activity and binds to DNA mismatches; has homology to E. coli MutS; transcription is induced during meiosis | Core | NA | NA | NA |
| 4377-YHR121W | YHR121W | LSM12 | NA | Protein of unknown function that may function in RNA processing; interacts with Pbp1p and Pbp4p and associates with ribosomes; contains an RNA-binding LSM domain and an AD domain; GFP-fusion protein is induced by the DNA-damaging agent MMS; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 4378-YHR122W | YHR122W | CIA2 | iron-sulfur cluster assembly protein CIA2 | Component of cytosolic iron-sulfur protein assembly (CIA) machinery; acts at a late step of Fe-S cluster assembly; forms the CIA targeting complex with Cia1p and Met18p that directs Fe-S cluster incorporation into a subset of proteins involved in methionine biosynthesis, DNA replication and repair, transcription, and telomere maintenance; ortholog of human FAM96B | Core | NA | NA | NA |
| 4379-YHR123W | YHR123W | EPT1 | bifunctional diacylglycerol cholinephosphotransferase/ethanolaminephosphotransferase | sn-1,2-diacylglycerol ethanolamine- and cholinephosphotranferase; not essential for viability; EPT1 has a paralog, CPT1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4380-YHR124W | YHR124W | NDT80 | transcription factor NDT80 | Meiosis-specific transcription factor; required for exit from pachytene and for full meiotic recombination; activates middle sporulation genes; competes with Sum1p for binding to promoters containing middle sporulation elements (MSE) | Core | NA | NA | NA |
| 4381-YHR125W | YHR125W | NA | NA | Putative protein of unknown function; conserved across S. cerevisiae strains | Accessory | Unknown | NA | NA |
| 4382-YHR126C | YHR126C | ANS1 | NA | Putative GPI protein; SWAT-GFP and mCherry fusion proteins localize to the vacuole; transcription dependent upon Azf1p | Core | NA | NA | NA |
| 4383-YHR127W | YHR127W | NA | HSN1 | Protein of unknown function; localizes to the nucleus; required for asymmetric localization of Kar9p during mitosis | Core | NA | NA | NA |
| 4384-YHR128W | YHR128W | FUR1 | uracil phosphoribosyltransferase | Uracil phosphoribosyltransferase; synthesizes UMP from uracil; involved in the pyrimidine salvage pathway | Core | NA | NA | NA |
| 4385-YHR129C | YHR129C | ARP1 | actin-related protein 1|ACT5 | Actin-related protein of the dynactin complex; required for spindle orientation and nuclear migration; forms actin-like short filament composed of 9 or 10 Arp1p monomers; putative ortholog of mammalian centractin | Accessory | Ancestral | NA | NA |
| 4386-YHR130C | YHR130C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YHR130C is not an essential gene | Accessory | Unknown | NA | NA |
| 4387-YHR131C | YHR131C | NA | NA | Putative protein of unknown function; GFP-fusion protein localizes to the cytoplasm; overexpression causes cell cycle delay or arrest; contains a PH domain and binds phosphatidylinositols and other lipids in a large-scale study; YHR131C has a paralog, YNL144C, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |