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 |
|---|---|---|---|---|---|---|---|---|
| 3488-YER159C_NumOfGenes_2 | YER159C | BUR6 | negative cofactor 2 transcription regulator complex subunit BUR6|NCB1 | Subunit of a heterodimeric NC2 transcription regulator complex; complex binds to TBP and can repress transcription by preventing preinitiation complex assembly or stimulate activated transcription; homologous to human NC2alpha; complex also includes Ncb2p; bur6 ncb2 double mutation is functionally complemented by coexpression of human DRAP1 and DR1, although the single bur6 mutation is not complemented by its ortholog DRAP1 | Core | NA | NA | NA |
| 3489-YER161C_NumOfGenes_2 | YER161C | SPT2 | EXA1|SIN1 | Protein involved in negative regulation of transcription; required for RNA polyadenylation; exhibits regulated interactions with both histones and SWI-SNF components; relocalizes to the cytosol in response to hypoxia; similar to mammalian HMG1 proteins | Accessory | Ancestral | NA | NA |
| 3490-YER162C | YER162C | RAD4 | NA | Protein that recognizes and binds damaged DNA (with Rad23p) during NER; subunit of Nuclear Excision Repair Factor 2 (NEF2); also involved, with Rad23p, in turnover of ubiquitylated proteins; Rad4p-Rad23p heterodimer binds to promoters of DNA damage response genes to repress their transcription in the absence of DNA damage; NER stands for nucleotide excision repair | Accessory | Ancestral | NA | NA |
| 3491-YER163C | YER163C | GCG1 | gamma-glutamylcyclotransferase | Gamma-glutamyl cyclotransferase; cleaves the gamma-glutamyl bond of glutathione to yield 5-oxoproline and a Cys-Gly dipeptide; similar to mammalian pro-apoptotic protein ChaC1; expression of mouse ChaC1 in yeast increases apoptosis; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; periodically expressed during the metabolic cycle | Accessory | Ancestral | NA | NA |
| 3492-YER164W | YER164W | CHD1 | chromatin-remodeling ATPase CHD1 | Chromatin remodeler that regulates various aspects of transcription; acts in in conjunction with Isw1b to regulate chromatin structure and maintain chromatin integrity during transcription elongation by RNAP II by preventing trans-histone exchange over coding regions; contains a chromo domain, a helicase domain and a DNA-binding domain; component of both the SAGA and SLIK complexes | Accessory | Ancestral | NA | NA |
| 3493-YER165C-A | YER165C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps the verified gene DNF1/YER166W | Accessory | Ancestral | NA | NA |
| 3494-YER165W | YER165W | PAB1 | polyadenylate-binding protein | Poly(A) binding protein; part of the 3'-end RNA-processing complex, mediates interactions between the 5' cap structure and the 3' mRNA poly(A) tail, involved in control of poly(A) tail length, interacts with translation factor eIF-4G; stimulates, but is not required for the deadenylation activity of the Pan2p-Pan3p poly(A)-ribonuclease complex | Core | NA | NA | NA |
| 3495-YER166W | YER166W | DNF1 | aminophospholipid-translocating P4-type ATPase DNF1 | Aminophospholipid translocase (flippase); type 4 P-type ATPase; involved in phospholipid translocation, contributing to endocytosis, protein transport, and cellular polarization; localizes primarily to the plasma membrane; localizes to the shmoo tip where it has a redundant role in the cellular response to mating pheromone; DNF1 has a paralog, DNF2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3496-YER167W | YER167W | BCK2 | CTR7 | Serine/threonine-rich protein involved in PKC1 signaling pathway; protein kinase C (PKC1) signaling pathway controls cell integrity; overproduction suppresses pkc1 mutations | Core | NA | NA | NA |
| 3497-YER168C | YER168C | CCA1 | tRNA adenylyltransferase|TNT1 | ATP (CTP):tRNA-specific tRNA nucleotidyltransferase; different forms targeted to the nucleus, cytosol, and mitochondrion are generated via the use of multiple transcriptional and translational start sites; human homolog TRNT1 complements yeast null mutant | Accessory | Ancestral | NA | NA |
| 3498-YER169W | YER169W | RPH1 | KDM4 | JmjC domain-containing histone demethylase; targets tri- and dimethylated H3K36; associates with actively transcribed regions and promotes elongation; repressor of autophagy-related genes in nutrient-replete conditions; damage-responsive repressor of PHR1; phosphorylated by the Rad53p-dependent DNA damage checkpoint pathway and by a Rim1p-mediated event during starvation; target of stress-induced hormesis; RPH1 has a paralog, GIS1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3499-YER170W_NumOfGenes_2 | YER170W | ADK2 | adenylate kinase ADK2|PAK3|AKY3 | Mitochondrial adenylate kinase; catalyzes the reversible synthesis of GTP and AMP from GDP and ADP; may serve as a back-up for synthesizing GTP or ADP depending on metabolic conditions; 3' sequence of ADK2 varies with strain background | Core | NA | NA | NA |
| 3500-YER171W | YER171W | RAD3 | TFIIH/NER complex ATP-dependent 5'-3' DNA helicase subunit RAD3|REM1 | 5' to 3' DNA helicase; involved in nucleotide excision repair and transcription; subunit of RNA polII initiation factor TFIIH and of Nucleotide Excision Repair Factor 3 (NEF3); homolog of human XPD protein; mutant has aneuploidy tolerance; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 3501-YER172C | YER172C | BRR2 | ATP-dependent RNA helicase BRR2|PRP44|SNU246|SLT22|RSS1 | RNA-dependent ATPase RNA helicase (DEIH box); required for disruption of U4/U6 base-pairing in native snRNPs to activate the spliceosome for catalysis; homologous to human U5-200kD | Accessory | Ancestral | NA | NA |
| 3502-YER173W_NumOfGenes_2 | YER173W | RAD24 | RS1 | Checkpoint protein; involved in the activation of the DNA damage and meiotic pachytene checkpoints; subunit of a clamp loader that loads Rad17p-Mec3p-Ddc1p onto DNA; homolog of human and S. pombe Rad17 protein | Core | NA | NA | NA |