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 |
|---|---|---|---|---|---|---|---|---|
| 7748-YPR129W_NumOfGenes_2 | YPR129W | SCD6 | LSM13 | Repressor of translation initiation; binds eIF4G through its RGG domain and inhibits recruitment of the preinitiation complex; also contains an Lsm domain; may have a role in RNA processing; overproduction suppresses null mutation in clathrin heavy chain gene CHC1; forms cytoplasmic foci upon DNA replication stress | Core | NA | NA | NA |
| 7749-YPR131C | YPR131C | NAT3 | peptide alpha-N-acetyltransferase complex B subunit NAT3|RAD56|NAA20 | Catalytic subunit of the NatB N-terminal acetyltransferase; NatB catalyzes acetylation of the amino-terminal methionine residues of all proteins beginning with Met-Asp or Met-Glu and of some proteins beginning with Met-Asn or Met-Met | Core | NA | NA | NA |
| 7750-YPR132W | YPR132W | RPS23B | uS12|ribosomal 40S subunit protein S23B|rp37|YS14|S28B|S23B|S12 | Ribosomal protein 28 (rp28) of the small (40S) ribosomal subunit; required for translational accuracy; homologous to mammalian ribosomal protein S23 and bacterial S12; RPS23B has a paralog, RPS23A, that arose from the whole genome duplication; deletion of both RPS23A and RPS23B is lethal | Core | NA | NA | NA |
| 7751-YPR133C | YPR133C | SPN1 | IWS1 | Protein involved in RNA polymerase II transcription; is constitutively recruited to the CYC1 promoter and is required for recruitment of chromatin remodeling factors for the expression of CYC1 gene; interacts genetically or physically with RNAP II, TBP, TFIIS, and chromatin remodelling factors; central domain highly conserved throughout eukaryotes; mutations confer an Spt- phenotype | Core | NA | NA | NA |
| 7752-YPR133W-A | YPR133W-A | TOM5 | MOM8A | Component of the TOM (translocase of outer membrane) complex; responsible for recognition and initial import of all mitochondrially directed proteins; involved in transfer of precursors from the Tom70p and Tom20p receptors to the Tom40p pore | Core | NA | NA | NA |
| 7753-YPR134W | YPR134W | MSS18 | NA | Nuclear encoded protein needed for splicing of mitochondrial intron; required for efficient splicing of mitochondrial COX1 aI5beta intron; mss18 mutations block cleavage of 5' exon - intron junction; phenotype of intronless strain suggests additional functions | Core | NA | NA | NA |
| 7754-YPR135W | YPR135W | CTF4 | chromatin-binding protein CTF4|POB1|CHL15 | Chromatin-associated protein; required for sister chromatid cohesion; interacts with DNA polymerase alpha (Pol1p) and may link DNA synthesis to sister chromatid cohesion | Core | NA | NA | NA |
| 7755-YPR137W_NumOfGenes_2 | YPR137W | RRP9 | NA | Protein involved in pre-rRNA processing; associated with U3 snRNP; component of small ribosomal subunit (SSU) processosome; ortholog of the human U3-55k protein | Core | NA | NA | NA |
| 7756-YPR138C_NumOfGenes_2 | YPR138C | MEP3 | ammonium permease MEP3 | Ammonium permease of high capacity and low affinity; belongs to a ubiquitous family of cytoplasmic membrane proteins that transport only ammonium (NH4+); expression is under the nitrogen catabolite repression regulation ammonia permease; MEP3 has a paralog, MEP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7757-YPR139C_NumOfGenes_2 | YPR139C | LOA1 | lysophosphatidic acid acyltransferase LOA1|VPS66 | Lysophosphatidic acid acyltransferase; involved in triacelglyceride homeostasis and lipid droplet formation; localized to lipid droplets and the ER; specificity for oleoyl-CoA | Core | NA | NA | NA |
| 7758-YPR140W_NumOfGenes_2 | YPR140W | TAZ1 | lysophosphatidylcholine acyltransferase | Lyso-phosphatidylcholine acyltransferase; required for normal phospholipid content of mitochondrial membranes; major determinant of the final acyl chain composition of the mitochondrial-specific phospholipid cardiolipin; mutations in human ortholog tafazzin (TAZ) cause Barth syndrome, a rare X-linked disease characterized by skeletal and cardiomyopathy and bouts of cyclic neutropenia; a specific splice variant of human TAZ can complement yeast null mutant | Core | NA | NA | NA |
| 7759-YPR141C_NumOfGenes_2 | YPR141C | KAR3 | OSR11 | Minus-end-directed microtubule motor; functions in mitosis and meiosis, localizes to the spindle pole body and localization is dependent on functional Cik1p, required for nuclear fusion during mating; potential Cdc28p substrate | Core | NA | NA | NA |
| 7760-YPR142C | YPR142C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF RRP15, which is required for ribosomal RNA processing | Accessory | Unknown | S. paradoxus | NA |
| 7761-YPR143W | YPR143W | RRP15 | NA | Nucleolar protein; constituent of pre-60S ribosomal particles; required for proper processing of the 27S pre-rRNA at the A3 and B1 sites to yield mature 5.8S and 25S rRNAs | Accessory | Unknown | S. paradoxus | NA |
| 7762-YPR144C | YPR144C | NOC4 | ribosome biosynthesis protein NOC4|UTP19 | Nucleolar protein; forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits; relocalizes to the cytosol in response to hypoxia | Accessory | Ancestral | NA | NA |