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 |
|---|---|---|---|---|---|---|---|---|
| 6563-YNL170W | YNL170W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 6564-YNL171C | YNL171C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 6565-YNL172W | YNL172W | APC1 | anaphase promoting complex subunit 1 | Largest subunit of the Anaphase-Promoting Complex/Cyclosome; APC/C is a ubiquitin-protein ligase required for degradation of anaphase inhibitors, including mitotic cyclins, during the metaphase/anaphase transition; component of the platform domain of the APC/C, based on structural analysis; localizes to nuclear foci that become diffuse upon DNA replication stress | Core | NA | NA | NA |
| 6566-YNL173C | YNL173C | MDG1 | NA | Plasma membrane protein; involved in G-protein mediated pheromone signaling pathway; overproduction suppresses bem1 mutations; MDG1 has a paralog, CRP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6567-YNL175C_NumOfGenes_2 | YNL175C | NOP13 | NA | Nucleolar protein found in preribosomal complexes; contains an RNA recognition motif (RRM); relative distribution to the nucleolus increases upon DNA replication stress | Core | NA | NA | NA |
| 6568-YNL176C_NumOfGenes_2 | YNL176C | TDA7 | NA | Cell cycle-regulated gene of unknown function; promoter bound by Fkh2p; null mutant is sensitive to expression of the top1-T722A allele; TDA7 has a paralog, YDL211C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6569-YNL177C_NumOfGenes_2 | YNL177C | MRPL22 | mitochondrial 54S ribosomal protein YmL22|YmL22 | Mitochondrial ribosomal protein of the large subunit | Core | NA | NA | NA |
| 6570-YNL178W_NumOfGenes_2 | YNL178W | RPS3 | uS3|ribosomal 40S subunit protein S3|rp13|YS3|S3|SUF14 | Protein component of the small (40S) ribosomal subunit; has apurinic/apyrimidinic (AP) endonuclease activity; essential for viability; nascent Rps3p is bound by specific chaperone Yar1p during translation; homologous to mammalian ribosomal protein S3 and bacterial S3 | Core | NA | NA | NA |
| 6571-YNL179C | YNL179C | NA | SRF6 | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; not conserved in closely related Saccharomyces species; deletion in cyr1 mutant results in loss of stress resistance | Accessory | Ancestral | NA | NA |
| 6572-YNL180C_NumOfGenes_2 | YNL180C | RHO5 | Rho family GTPase RHO5|YNS0 | Non-essential small GTPase of the Rho/Rac family of Ras-like proteins; RAC1 ortholog; regulated by phosphorylation and ubiquitination; likely involved in protein kinase C (Pkc1p)-dependent signal transduction pathway that controls cell integrity | Core | NA | NA | NA |
| 6573-YNL181W | YNL181W | PBR1 | putative oxidoreductase | Putative oxidoreductase; required for cell viability | Core | NA | NA | NA |
| 6574-YNL182C | YNL182C | IPI3 | chromatin-binding/pre-rRNA-processing protein IPI3 | Component of the Rix1 complex and pre-replicative complexes (pre-RCs); required for processing of ITS2 sequences from 35S pre-rRNA; component of the pre-60S ribosomal particle with the dynein-related AAA-type ATPase Mdn1p; required for pre-RC formation and maintenance during DNA replication licensing; highly conserved protein which contains several WD40 motifs; IPI3 is an essential gene; other members include Rix1p, Ipi1p, and Ipi3p | Core | NA | NA | NA |
| 6575-YNL183C | YNL183C | NPR1 | serine/threonine protein kinase NPR1 | Protein kinase; stabilizes several plasma membrane amino acid transporters by antagonizing their ubiquitin-mediated degradation; phosphorylates Aly2p; negatively regulates Ldb19p-mediated endocytosis through phosphorylation of Ldb19p, which prevents its association with the plasma membrane; Npr1p activity is negatively regulated via phosphorylation by the TOR complex; NPR1 has a paralog, PRR2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6576-YNL184C | YNL184C | NA | NA | Protein of unknown function; expressed at both mRNA and protein levels | Core | NA | NA | NA |
| 6577-YNL185C | YNL185C | MRPL19 | mitochondrial 54S ribosomal protein YmL19|YmL19 | Mitochondrial ribosomal protein of the large subunit | Core | NA | NA | NA |