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 |
|---|---|---|---|---|---|---|---|---|
| 3383-YER063W | YER063W | THO1 | NA | Conserved nuclear RNA-binding protein; specifically binds to transcribed chromatin in a THO- and RNA-dependent manner, genetically interacts with shuttling hnRNP NAB2; overproduction suppresses transcriptional defect caused by hpr1 mutation | Accessory | Ancestral | NA | NA |
| 3384-YER064C | YER064C | VHR2 | NA | Non-essential nuclear protein; null mutation has global effects on transcription; VHR2 has a paralog, VHR1, that arose from the whole genome duplication; relative distribution to the nucleus increases upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 3385-YER065C | YER065C | ICL1 | isocitrate lyase 1 | Isocitrate lyase; catalyzes the formation of succinate and glyoxylate from isocitrate, a key reaction of the glyoxylate cycle; expression of ICL1 is induced by growth on ethanol and repressed by growth on glucose | Accessory | Ancestral | NA | NA |
| 3386-YER066C-A | YER066C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps uncharacterized ORF YER067W | Accessory | Ancestral | NA | NA |
| 3387-YER066W | YER066W | RRT13 | NA | Putative protein of unknown function; non-essential gene identified in a screen for mutants with decreased levels of rDNA transcription | Accessory | Ancestral | NA | NA |
| 3388-YER067W_NumOfGenes_2 | YER067W | RGI1 | NA | Protein of unknown function; involved in energy metabolism under respiratory conditions; protein abundance is increased upon intracellular iron depletion or in response to DNA replication stress; RGI1 has a paralog, RGI2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3389-YER068C-A | YER068C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps ORF ARG5,6/YER069W | Accessory | Ancestral | NA | NA |
| 3390-YER068W | YER068W | MOT2 | CCR4-NOT core ubiquitin-protein ligase subunit MOT2|SIG1|NOT4 | Ubiquitin-protein ligase subunit of the CCR4-NOT complex; with Ubc4p, ubiquitinates nascent polypeptide-associated complex subunits and histone demethyase Jhd2p; CCR4-NOT has roles in transcription regulation, mRNA degradation, and post-transcriptional modifications; regulates levels of DNA Polymerase-{alpha} to promote efficient and accurate DNA replication | Core | NA | NA | NA |
| 3391-YER069W | YER069W | ARG5,6 | argC|argB|bifunctional acetylglutamate kinase/N-acetyl-gamma-glutamyl-phosphate reductase | Acetylglutamate kinase and N-acetyl-gamma-glutamyl-phosphate reductase; N-acetyl-L-glutamate kinase (NAGK) catalyzes the 2nd and N-acetyl-gamma-glutamyl-phosphate reductase (NAGSA), the 3rd step in arginine biosynthesis; synthesized as a precursor which is processed in the mitochondrion to yield mature NAGK and NAGSA; enzymes form a metabolon complex with Arg2p; NAGK C-terminal domain stabilizes the enzymes, slows catalysis and is involved in feed-back inhibition by arginine | Core | NA | NA | NA |
| 3392-YER070W | YER070W | RNR1 | ribonucleotide-diphosphate reductase subunit RNR1|SDS12|RIR1|CRT7 | Major isoform of large subunit of ribonucleotide-diphosphate reductase; the RNR complex catalyzes rate-limiting step in dNTP synthesis, regulated by DNA replication and DNA damage checkpoint pathways via localization of small subunits; relative distribution to the nucleus increases upon DNA replication stress; RNR1 has a paralog, RNR3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3393-YER071C | YER071C | TDA2 | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern; null mutant is sensitive to expression of the top1-T722A allele | Core | NA | NA | NA |
| 3394-YER072W | YER072W | VTC1 | PHM4|NRF1 | Regulatory subunit of the vacuolar transporter chaperone (VTC) complex; VTC complex is involved in membrane trafficking, vacuolar polyphosphate accumulation, microautophagy and non-autophagic vacuolar fusion; also has mRNA binding activity; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3395-YER073W | YER073W | ALD5 | aldehyde dehydrogenase (NAD(P)(+)) ALD5 | Mitochondrial aldehyde dehydrogenase; involved in regulation or biosynthesis of electron transport chain components and acetate formation; activated by K+; utilizes NADP+ as the preferred coenzyme; constitutively expressed | Accessory | Ancestral | NA | NA |
| 3396-YER074W | YER074W | RPS24A | eS24|ribosomal 40S subunit protein S24A|S24e|S24A|RPS24EA | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S24, no bacterial homolog; RPS24A has a paralog, RPS24B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3397-YER074W-A | YER074W-A | YOS1 | NA | Integral membrane protein required for ER to Golgi transport; localized to the Golgi, the ER, and COPII vesicles; interacts with Yip1p and Yif1p | Core | NA | NA | NA |