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 |
|---|---|---|---|---|---|---|---|---|
| 5573-YLR113W | YLR113W | HOG1 | mitogen-activated protein kinase HOG1|SSK3 | Mitogen-activated protein kinase involved in osmoregulation; controls global reallocation of RNAPII during osmotic shock; mediates recruitment/activation of RNAPII at Hot1p-dependent promoters; binds calmodulin; stimulates antisense transcription to activate CDC28; defines novel S-phase checkpoint with Mrc1p that prevent replication/transcription conflicts; nuclear form represses pseudohyphal growth; autophosphorylates; protein abundance increases under DNA replication stress | Core | NA | NA | NA |
| 5574-YLR114C | YLR114C | AVL9 | NA | Conserved protein involved in exocytic transport from the Golgi; mutation is synthetically lethal with apl2 vps1 double mutation; member of a protein superfamily with orthologs in diverse organisms; relocalizes from bud neck to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 5575-YLR115W | YLR115W | CFT2 | cleavage polyadenylation factor subunit CFT2|YDH1 | Subunit of the mRNA cleavage and polyadenlylation factor (CPF); required for pre-mRNA cleavage, polyadenylation and poly(A) site recognition, 43% similarity with the mammalian CPSF-100 protein. | Core | NA | NA | NA |
| 5576-YLR116W | YLR116W | MSL5 | mRNA splicing protein MSL5|BBP | Component of commitment complex; which defines first step in splicing pathway; essential protein that interacts with Mud2p and Prp40p, forming a bridge between the intron ends; also involved in nuclear retention of pre-mRNA; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 5577-YLR117C | YLR117C | CLF1 | NTC77|SYF3 | Member of the NineTeen Complex (NTC); this complex contains Prp19p and stabilizes U6 snRNA in catalytic forms of the spliceosome containing U2, U5, and U6 snRNAs; homolog of Drosophila crooked neck protein; interacts with U1 snRNP proteins | Core | NA | NA | NA |
| 5578-YLR118C | YLR118C | NA | palmitoyl-(protein) hydrolase|APT1 | Acyl-protein thioesterase responsible for depalmitoylation of Gpa1p; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and nucleus and is induced in response to the DNA-damaging agent MMS | Accessory | Ancestral | NA | NA |
| 5579-YLR119W | YLR119W | SRN2 | ESCRT-I subunit protein SRN2|VPL16|VPS37|SRN10 | Component of the ESCRT-I complex; ESCRT-I is involved in ubiquitin-dependent sorting of proteins into the endosome; suppressor of rna1-1 mutation; may be involved in RNA export from nucleus | Accessory | Ancestral | NA | NA |
| 5580-YLR120C | YLR120C | YPS1 | aspartyl protease|YAP3 | Aspartic protease; hyperglycosylated member of the yapsin family of proteases, attached to the plasma membrane via a glycosylphosphatidylinositol (GPI) anchor; involved in nutrient limitation-induced cleavage of the extracellular inhibitory domain of signaling mucin Msb2p, resulting in activation of the filamentous growth MAPK pathway; involved with other yapsins in the cell wall integrity response; role in KEX2-independent processing of the alpha factor precursor | Core | NA | NA | NA |
| 5581-YLR120W-A | YLR120W-A | 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 YLR121C | Accessory | Unknown | NA | NA |
| 5582-YLR121C | YLR121C | YPS3 | aspartyl protease|YPS4 | Aspartic protease; member of the yapsin family of proteases involved in cell wall growth and maintenance; attached to the plasma membrane via a glycosylphosphatidylinositol (GPI) anchor | Accessory | Ancestral | NA | NA |
| 5583-YLR122C_NumOfGenes_2 | YLR122C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; partially overlaps dubious ORF YLR123C | Accessory | Unknown | NA | NA |
| 5584-YLR124W_NumOfGenes_2 | YLR124W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Unknown | NA | NA |
| 5585-YLR125W_NumOfGenes_2 | YLR125W | NA | NA | Putative protein of unknown function; mutant has decreased Ty3 transposition; YLR125W is not an essential gene | Accessory | Unknown | NA | NA |
| 5586-YLR126C | YLR126C | NA | putative amidotransferase | Putative glutamine amidotransferase; has Aft1p-binding motif in the promoter; may be involved in copper and iron homeostasis; YLR126C is not an essential protein; relocalizes from nucleus to cytoplasmic foci upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 5587-YLR127C | YLR127C | APC2 | anaphase promoting complex subunit 2|TID2|RSI1 | Subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C); which is a ubiquitin-protein ligase required for degradation of anaphase inhibitors, including mitotic cyclins, during the metaphase/anaphase transition; component of the catalytic core of the APC/C; has similarity to cullin Cdc53p | Accessory | Ancestral | NA | NA |