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 |
|---|---|---|---|---|---|---|---|---|
| 6683-YNL297C_NumOfGenes_2 | YNL297C | MON2 | YSL2 | Protein with a role in endocytosis and vacuole integrity; peripheral membrane protein; interacts with and negatively regulates Arl1p; localizes to the endosome; member of the Sec7p family of proteins | Core | NA | NA | NA |
| 6684-YNL298W | YNL298W | CLA4 | serine/threonine protein kinase CLA4|ERC10 | Cdc42p-activated signal transducing kinase; member of the PAK (p21-activated kinase) family, along with Ste20p and Skm1p; involved in septin ring assembly, vacuole inheritance, cytokinesis, sterol uptake regulation; phosphorylates Cdc3p and Cdc10p; CLA4 has a paralog, SKM1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6685-YNL299W | YNL299W | TRF5 | non-canonical poly(A) polymerase TRF5 | Non-canonical poly(A) polymerase; involved in nuclear RNA degradation as a component of the TRAMP complex; catalyzes polyadenylation of hypomodified tRNAs, and snoRNA and rRNA precursors; overlapping but non-redundant functions with Pap2p | Core | NA | NA | NA |
| 6686-YNL300W | YNL300W | TOS6 | NA | Glycosylphosphatidylinositol-dependent cell wall protein; expression is periodic and decreases in respone to ergosterol perturbation or upon entry into stationary phase; depletion increases resistance to lactic acid | Core | NA | NA | NA |
| 6687-YNL301C | YNL301C | RPL18B | eL18|ribosomal 60S subunit protein L18B|L18e|rp28B|L18B|RP28B | Ribosomal 60S subunit protein L18B; homologous to mammalian ribosomal protein L18, no bacterial homolog; RPL18B has a paralog, RPL18A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6688-YNL302C | YNL302C | RPS19B | eS19|ribosomal 40S subunit protein S19B|S19e|rp55B|YS16B|S19B|S16aB|RP55B | Protein component of the small (40S) ribosomal subunit; required for assembly and maturation of pre-40 S particles; homologous to mammalian ribosomal protein S19, no bacterial homolog; mutations in human RPS19 are associated with Diamond Blackfan anemia; RPS19B has a paralog, RPS19A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6689-YNL303W | YNL303W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 6690-YNL304W | YNL304W | YPT11 | Rab family GTPase YPT11 | Rab GTPase; Myo2p-binding protein implicated in mother-to-bud transport of cortical endoplasmic reticulum (ER), late Golgi, and mitochondria during cell division; function is regulated at multiple levels; abundance of active Ypt11p forms is controlled by phosphorylation status and degradation; normally a low-abundance protein whose ER localization is only detected when protein is highly over expressed | Core | NA | NA | NA |
| 6691-YNL305C | YNL305C | BXI1 | YBH3 | Protein involved in apoptosis; variously described as containing a BCL-2 homology (BH3) domain or as a member of the BAX inhibitor family; reported to promote apoptosis under some conditions and to inhibit it in others; localizes to ER and vacuole; may link the unfolded protein response to apoptosis via regulation of calcium-mediated signaling; translocates to mitochondria under apoptosis-inducing conditions in a process involving Mir1p and Cor1p | Core | NA | NA | NA |
| 6692-YNL306W | YNL306W | MRPS18 | mitochondrial 37S ribosomal protein YmS18|YmS18 | Mitochondrial ribosomal protein of the small subunit; essential for viability, unlike most other mitoribosomal proteins | Core | NA | NA | NA |
| 6693-YNL307C | YNL307C | MCK1 | serine/threonine/tyrosine protein kinase MCK1|CMS1|YPK1 | Dual-specificity ser/thr and tyrosine protein kinase; roles in chromosome segregation, meiotic entry, genome stability, phosphorylation-dependent protein degradation (Rcn1p and Cdc6p), inhibition of protein kinase A, transcriptional regulation, inhibition of RNA pol III, calcium stress and inhibition of Clb2p-Cdc28p after nuclear division; MCK1 has a paralog, YGK3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6694-YNL308C | YNL308C | KRI1 | NA | Essential nucleolar protein required for 40S ribosome biogenesis; associate with snR30; physically and functionally interacts with Krr1p | Core | NA | NA | NA |
| 6695-YNL309W | YNL309W | STB1 | NA | Protein with role in regulation of MBF-specific transcription at Start; phosphorylated by Cln-Cdc28p kinases in vitro; unphosphorylated form binds Swi6p, which is required for Stb1p function; expression is cell-cycle regulated; STB1 has a paralog, YOL131W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6696-YNL310C | YNL310C | ZIM17 | HEP1|TIM15|FMP28 | Protein co-chaperone with a zinc finger motif; essential for protein import into mitochondria; may act with Pam18p to facilitate recognition and folding of imported proteins by Ssc1p (mtHSP70) in the mitochondrial matrix; required for the maintenance of Ssc1p solubility and assists in the functional interaction of Ssc1p with substrate proteins | Core | NA | NA | NA |
| 6697-YNL311C | YNL311C | SKP2 | putative SCF ubiquitin ligase complex subunit SKP2 | F-box protein of unknown function; predicted to be part of an SCF ubiquitin protease complex; involved in regulating protein levels of sulfur metabolism enzymes; may interact with ribosomes, based on co-purification experiments | Core | NA | NA | NA |