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 |
|---|---|---|---|---|---|---|---|---|
| 4508-YIL025C | YIL025C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 4509-YIL026C | YIL026C | IRR1 | SCC3 | Subunit of the cohesin complex; which is required for sister chromatid cohesion during mitosis and meiosis and interacts with centromeres and chromosome arms; relocalizes to the cytosol in response to hypoxia; essential for viability | Core | NA | NA | NA |
| 4510-YIL027C | YIL027C | EMC5 | KRE27 | Member of conserved ER transmembrane complex; required for efficient folding of proteins in the ER; null mutant displays induction of the unfolded protein response, and also shows K1 killer toxin resistance; homologous to worm B0334.15/EMC-5, fly CG15168, human MMGT | Core | NA | NA | NA |
| 4511-YIL028W | YIL028W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Unknown | NA | NA |
| 4512-YIL029C | YIL029C | NA | NA | Putative protein of unknown function; deletion confers sensitivity to 4-(N-(S-glutathionylacetyl)amino) phenylarsenoxide (GSAO); YIL029C has a paralog, YPR071W, that arose from a single-locus duplication | Accessory | Ancestral | NA | NA |
| 4513-YIL029W-A | YIL029W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; almost completely overlaps ORF SSM4/YIL030C | Accessory | Ancestral | NA | NA |
| 4514-YIL030C | YIL030C | SSM4 | E3 ubiquitin-protein ligase SSM4|KIS3|DOA10 | Membrane-embedded ubiquitin-protein ligase; ER and inner nuclear membrane localized RING-CH domain E3 ligase involved in ER-associated protein degradation (ERAD); targets misfolded cytosolic/nucleoplasmic domains of soluble and membrane embedded proteins (ERAD-C) and a transmembrane domain containing substrate (ERAD-M), Sbh2p; C-terminal element (CTE), conserved in human ortholog MARCH10/TEB4, determines substrate selectivity | Core | NA | NA | NA |
| 4515-YIL030W-A | YIL030W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps ORF ULP2/YIL031W | Accessory | Ancestral | NA | NA |
| 4516-YIL031W | YIL031W | ULP2 | SUMO protease ULP2|SMT4 | Peptidase that deconjugates Smt3/SUMO-1 peptides from proteins; plays a role in chromosome cohesion at centromeric regions and recovery from checkpoint arrest induced by DNA damage or DNA replication defects; potential Cdc28p substrate; human homolog PML implicated in promyelocytic leukemia can partially complement yeast null mutant | Core | NA | NA | NA |
| 4517-YIL032C | YIL032C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 4518-YIL033C | YIL033C | BCY1 | cAMP-dependent protein kinase regulatory subunit BCY1|SRA1 | Regulatory subunit of the cyclic AMP-dependent protein kinase (PKA); PKA is a component of a signaling pathway that controls a variety of cellular processes, including metabolism, cell cycle, stress response, stationary phase, and sporulation | Core | NA | NA | NA |
| 4519-YIL034C | YIL034C | CAP2 | F-actin-capping protein subunit beta | Beta subunit of the capping protein heterodimer (Cap1p and Cap2p); capping protein (CP) binds to the barbed ends of actin filaments preventing further polymerization; localized predominantly to cortical actin patches; protein increases in abundance and relocalizes from bud neck to plasma membrane upon DNA replication stress | Core | NA | NA | NA |
| 4520-YIL035C | YIL035C | CKA1 | casein kinase 2 catalytic subunit CKA1 | Alpha catalytic subunit of casein kinase 2 (CK2); a Ser/Thr protein kinase with roles in cell growth and proliferation; CK2, comprised of CKA1, CKA2, CKB1 and CKB2, has many substrates including transcription factors and all RNA polymerases; regulates Fkh1p-mediated donor preference during mating-type switching | Core | NA | NA | NA |
| 4521-YIL036W | YIL036W | CST6 | SHF1|ACA2 | Basic leucine zipper (bZIP) transcription factor from ATF/CREB family involved in stress-responsive regulatory network; mediates transcriptional activation of NCE103 in response to low CO2 levels; proposed to be a regulator of oleate responsive genes; involved in utilization of non-optimal carbon sources and chromosome stability; relocalizes to the cytosol in response to hypoxia; CST6 has a paralog, ACA1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4522-YIL037C | YIL037C | PRM2 | pheromone-regulated protein PRM2 | Pheromone-regulated protein; predicted to have 4 transmembrane segments and a coiled coil domain; regulated by Ste12p; required for efficient nuclear fusion | Core | NA | NA | NA |