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 |
|---|---|---|---|---|---|---|---|---|
| 4808-YJL115W | YJL115W | ASF1 | nucleosome assembly factor ASF1|CIA1 | Nucleosome assembly factor; involved in chromatin assembly, disassembly; required for recovery after DSB repair; role in H3K56 acetylation required for expression homeostasis, buffering mRNA synthesis rate against gene dosage changes in S phase; anti-silencing protein, derepresses silent loci when overexpressed; role in regulating Ty1 transposition; relocalizes to cytosol under hypoxia; growth defect of asf1 null is functionally complemented by either human ASF1A or ASF1B | Core | NA | NA | NA |
| 4809-YJL116C | YJL116C | NCA3 | SUN family protein NCA3 | Protein involved in mitochondrion organization; functions with Nca2p to regulate mitochondrial expression of subunits 6 (Atp6p) and 8 (Atp8p) of the Fo-F1 ATP synthase; SWAT-GFP, seamless-GFP and mCherry fusion proteins localize to the vacuole; member of the SUN family; expression induced in cells treated with the mycotoxin patulin; NCA3 has a paralog, UTH1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4810-YJL117W | YJL117W | PHO86 | NA | Endoplasmic reticulum (ER) resident protein; required for ER exit of the high-affinity phosphate transporter Pho84p, specifically required for packaging of Pho84p into COPII vesicles; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4811-YJL118W_NumOfGenes_2 | YJL118W | NA | NA | Protein of unknown function; may interact with ribosomes, based on co-purification experiments; YJL118W is a non-essential gene; deletion enhances the toxicity of heterologously expressed human alpha-synuclein | Core | NA | NA | NA |
| 4812-YJL120W | YJL120W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YJL121C/RPE1; deletion confers sensitivity to GSAO | Core | NA | NA | NA |
| 4813-YJL121C | YJL121C | RPE1 | ribulose-phosphate 3-epimerase RPE1|POS18|EPI1 | D-ribulose-5-phosphate 3-epimerase; catalyzes a reaction in the non-oxidative part of the pentose-phosphate pathway; mutants are sensitive to oxidative stress | Core | NA | NA | NA |
| 4814-YJL122W | YJL122W | ALB1 | NA | Shuttling pre-60S factor; involved in the biogenesis of ribosomal large subunit; interacts directly with Arx1p; responsible for Tif6p recycling defects in absence of Rei1p | Core | NA | NA | NA |
| 4815-YJL123C | YJL123C | MTC1 | NA | Protein of unknown function that may interact with ribosomes; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and to COPI-coated vesicles (early Golgi); mtc1 is synthetically lethal with cdc13-1 | Core | NA | NA | NA |
| 4816-YJL124C | YJL124C | LSM1 | SPB8 | Lsm (Like Sm) protein; forms heteroheptameric complex (with Lsm2p, Lsm3p, Lsm4p, Lsm5p, Lsm6p, and Lsm7p) involved in degradation of cytoplasmic mRNAs; also enters the nucleus and positively regulates transcription initiation; unlike most Sm-like proteins, Lsm1p requires both its SM-domain and C-terminal domain for RNA-binding; binds to mRNAs under glucose starvation, most often in the 3' UTR; forms cytoplasmic foci upon DNA replication stress | Core | NA | NA | NA |
| 4817-YJL125C | YJL125C | GCD14 | tRNA 1-methyladenosine methyltransferase subunit GCD14|TRM61 | Subunit of tRNA (1-methyladenosine) methyltransferase; required, along with Gcd10p, for the modification of the adenine at position 58 in tRNAs, especially tRNAi-Met; first identified as a negative regulator of GCN4 expression | Core | NA | NA | NA |
| 4818-YJL126W | YJL126W | NIT2 | putative hydrolase | Nit protein; one of two proteins in S. cerevisiae with similarity to the Nit domain of NitFhit from fly and worm and to the mouse and human Nit protein which interacts with the Fhit tumor suppressor; nitrilase superfamily member | Core | NA | NA | NA |
| 4819-YJL127C | YJL127C | SPT10 | SUD1|CRE1 | Histone H3 acetylase with a role in transcriptional regulation; sequence-specific activator of histone genes, binds specifically and cooperatively to pairs of UAS elements in core histone promoters, functions at or near TATA box; involved in S phase-specific acetylation of H3K56 at histone promoters, which is required for recruitment of SWI/SNF nucleosome remodeling complex and subsequent transcription | Core | NA | NA | NA |
| 4820-YJL127C-B | YJL127C-B | NA | YJL127C-A | Putative protein of unknown function; identified based on homology to the filamentous fungus, <i>Ashbya gossypii</i>; SWAT-GFP and seamless-GFP fusion proteins localize to the mitochondria | Core | NA | NA | NA |
| 4821-YJL127W-A | YJL127W-A | NA | YJL127W-B | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 4822-YJL128C | YJL128C | PBS2 | mitogen-activated protein kinase kinase PBS2|SSK4|SFS4|HOG4 | MAP kinase kinase of the HOG signaling pathway; activated under severe osmotic stress; mitophagy-specific regulator; plays a role in regulating Ty1 transposition | Core | NA | NA | NA |