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 |
|---|---|---|---|---|---|---|---|---|
| 3338-YER025W | YER025W | GCD11 | translation initiation factor eIF2 subunit gamma|SUI4 | Gamma subunit of the translation initiation factor eIF2; involved in the identification of the start codon; binds GTP when forming the ternary complex with GTP and tRNAi-Met; mutations in human ortholog cause X-linked intellectual disability (XLID) | Core | NA | NA | NA |
| 3339-YER026C | YER026C | CHO1 | CDP-diacylglycerol-serine O-phosphatidyltransferase|PSS1 | Phosphatidylserine synthase; functions in phospholipid biosynthesis; catalyzes the reaction CDP-diaclyglycerol + L-serine = CMP + L-1-phosphatidylserine, transcriptionally repressed by myo-inositol and choline | Core | NA | NA | NA |
| 3340-YER027C | YER027C | GAL83 | SPM1 | One of three possible beta-subunits of the Snf1 kinase complex; allows nuclear localization of the Snf1 kinase complex in the presence of a nonfermentable carbon source; necessary and sufficient for phosphorylation of the Mig2p transcription factor in response to alkaline stress; functionally redundant with SIP1 and SIP2 for the phosphorylation of Mig1p in response to glucose deprivation; contains a glycogen-binding domain | Core | NA | NA | NA |
| 3341-YER028C | YER028C | MIG3 | NA | Transcriptional regulator; partially nonfunctional in S288C strains but has a major role in catabolite repression and ethanol response in some other strains; involved in response to toxic agents; phosphorylation by Snf1p or the Mec1p pathway inactivates Mig3p, allowing induction of damage response genesenvironment | Core | NA | NA | NA |
| 3342-YER029C | YER029C | SMB1 | mRNA splicing protein SMB1|Sm B|SmB | Core Sm protein Sm B; part of heteroheptameric complex (with Smd1p, Smd2p, Smd3p, Sme1p, Smx3p, and Smx2p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; homolog of human Sm B and Sm B' | Core | NA | NA | NA |
| 3343-YER030W | YER030W | CHZ1 | NA | Histone chaperone for Htz1p/H2A-H2B dimer; required for the stabilization of the Chz1p-Htz1-H2B complex; has overlapping function with Nap1p; null mutant displays weak sensitivity to MMS and benomyl; contains a highly conserved CHZ motif; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3344-YER031C | YER031C | YPT31 | Rab family GTPase YPT31|YPT8 | Rab family GTPase; involved in the exocytic pathway; mediates intra-Golgi traffic or the budding of post-Golgi vesicles from the trans-Golgi; YPT31 has a paralog, YPT32, that arose from the whole genome duplication; localizes to the transitional and late Golgi | Core | NA | NA | NA |
| 3345-YER032W | YER032W | FIR1 | PIP1 | Protein involved in 3' mRNA processing; interacts with Ref2p; APCC(Cdh1) substrate; potential Cdc28p substrate | Core | NA | NA | NA |
| 3346-YER033C | YER033C | ZRG8 | NA | Protein of unknown function; authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; GFP-fusion protein is localized to the cytoplasm; transcription induced under conditions of zinc deficiency | Core | NA | NA | NA |
| 3347-YER034W | YER034W | NA | NA | Protein of unknown function; non-essential gene; expression induced upon calcium shortage; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3348-YER035W | YER035W | EDC2 | NA | RNA-binding protein that directly activates mRNA decapping; binds mRNA substrate and enhances activity of decapping proteins Dcp1p and Dcp2p; has a role in translation during heat stress; protein increases in abundance and relocalizes to nucleolus and to nuclear foci upon DNA replication stress; EDC2 has a paralog, EDC1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3349-YER036C | YER036C | ARB1 | ATP-binding cassette family ATPase ARB1 | ATPase of the ATP-binding cassette (ABC) family; involved in 40S and 60S ribosome biogenesis, has similarity to Gcn20p; shuttles from nucleus to cytoplasm, physically interacts with Tif6p, Lsg1p; human homolog ABCF2 can complement yeast ARB1 mutant | Core | NA | NA | NA |
| 3350-YER037W | YER037W | PHM8 | bifunctional nucleotidase/lysophosphatidic acid phosphatase | Lysophosphatidic acid (LPA) phosphatase, nucleotidase; principle and physiological nucleotidase working on GMP, UMP and CMP; involved in LPA hydrolysis in response to phosphate starvation and ribose salvage pathway; phosphatase activity is soluble and Mg2+ dependent; expression is induced by low phosphate levels and by inactivation of Pho85p; repressed by Gcn4p under normal conditions; PHM8 has a paralog, SDT1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3351-YER038C | YER038C | KRE29 | Smc5-Smc6 complex subunit KRE29|NSE6 | Subunit of the SMC5-SMC6 complex; this complex is involved in removal of X-shaped DNA structures that arise between sister chromatids during DNA replication and repair; heterozygous mutant shows haploinsufficiency in K1 killer toxin resistance | Core | NA | NA | NA |
| 3352-YER038W-A_NumOfGenes_2 | YER038W-A | FMP49 | NA | Mitochondrial protein of unknown function; almost completely overlaps ORF HVG1/YER039C | Core | NA | NA | NA |