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 |
|---|---|---|---|---|---|---|---|---|
| 6713-YNL329C | YNL329C | PEX6 | AAA family ATPase peroxin 6|PAS8 | AAA-peroxin; heterodimerizes with AAA-peroxin Pex1p and participates in the recycling of peroxisomal signal receptor Pex5p from the peroxisomal membrane to the cystosol; mutations in human PEX6 can lead to severe peroxisomal disorders and early death | Core | NA | NA | NA |
| 6714-YNL330C | YNL330C | RPD3 | histone deacetylase RPD3|MOF6|SDS6|SDI2|REC3 | Histone deacetylase, component of both the Rpd3S and Rpd3L complexes; regulates transcription, silencing, autophagy and other processes by influencing chromatin remodeling; forms at least two different complexes which have distinct functions and members; Rpd3(L) recruitment to the subtelomeric region is regulated by interaction with the arginine methyltransferase, Hmt1p | Core | NA | NA | NA |
| 6715-YNL331C_NumOfGenes_2 | YNL331C | AAD14 | putative aryl-alcohol dehydrogenase | Putative aryl-alcohol dehydrogenase; similar to P. chrysosporium aryl-alcohol dehydrogenase; mutational analysis has not yet revealed a physiological role; members of the AAD gene family comprise three pairs (AAD3 + AAD15, AAD6/AAD16 + AAD4, AAD10 + AAD14) whose two genes are more related to one another than to other members of the family | Accessory | Introgression | S. paradoxus | NA |
| 6716-YNL334C_NumOfGenes_2 | YNL334C | SNO2 | putative pyridoxal 5'-phosphate synthase | Protein of unknown function; nearly identical to Sno3p; expression is induced before the diauxic shift and also in the absence of thiamin | Accessory | Ancestral | NA | NA |
| 6717-YNL336W_NumOfGenes_11 | YNL336W | COS1 | NA | Endosomal protein involved in turnover of plasma membrane proteins; member of the DUP380 subfamily of conserved, often subtelomeric COS genes; required for the multivesicular vesicle body sorting pathway that internalizes plasma membrane proteins for degradation; Cos proteins provide ubiquitin in trans for nonubiquitinated cargo proteins | Accessory | Ancestral | NA | NA |
| 6718-YNL338W | YNL338W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; completely overlaps TEL14L-XC, which is a telomeric X element core sequence on the left arm of chromosome XIV | Accessory | Unknown | S. paradoxus | NA |
| 6719-YNR001C | YNR001C | CIT1 | citrate (Si)-synthase CIT1|LYS6|CS1 | Citrate synthase; catalyzes the condensation of acetyl coenzyme A and oxaloacetate to form citrate; the rate-limiting enzyme of the TCA cycle; nuclear encoded mitochondrial protein; CIT1 has a paralog, CIT2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6720-YNR001W-A | YNR001W-A | NA | NA | Dubious open reading frame unlikely to encode a functional protein; identified by homology | Core | NA | NA | NA |
| 6721-YNR002C | YNR002C | ATO2 | putative ammonium permease ATO2|FUN34 | Putative transmembrane protein involved in export of ammonia; ammonia is a starvation signal that promotes cell death in aging colonies; phosphorylated in mitochondria; member of the TC 9.B.33 YaaH family; homolog of Y. lipolytica Gpr1p; ATO2 has a paralog, ADY2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6722-YNR003C_NumOfGenes_2 | YNR003C | RPC34 | DNA-directed RNA polymerase III subunit C34|C34 | RNA polymerase III subunit C34; interacts with TFIIIB70 and is a key determinant in pol III recruitment by the preinitiation complex | Core | NA | NA | NA |
| 6723-YNR004W | YNR004W | SWM2 | NA | Protein with a role in snRNA and snoRNA cap trimethylation; interacts with Tgs1p and shows similar phenotypes; required for trimethylation of the caps of spliceosomal snRNAs and the U3 snoRNA, and for efficient 3' end processing of U3 snoRNA; may act as a specificity factor for Tgs1p | Core | NA | NA | NA |
| 6724-YNR006W_NumOfGenes_2 | YNR006W | VPS27 | ESCRT-0 subunit protein VPS27|DID7|VPT27|VPL23|SSV17|GRD11 | Endosomal protein that forms a complex with Hse1p; required for recycling Golgi proteins, forming lumenal membranes and sorting ubiquitinated proteins destined for degradation; has Ubiquitin Interaction Motifs which bind ubiquitin (Ubi4p) | Core | NA | NA | NA |
| 6725-YNR007C | YNR007C | ATG3 | AUT1|APG3 | E2-like enzyme; involved in autophagy and cytoplasm-to-vacuole targeting (Cvt) pathway; plays a role in formation of Atg8p-phosphatidylethanolamine conjugates, which are involved in membrane dynamics during autophagy and Cvt; interaction with Atg8p regulated by acetylation by NuA4 histone acetyltransferase Esa1p while attenuation of Atg3 acetylation is mediated by histone deacetylase Rpd3p; Atg12p-Atg5p conjugate enhances E2 activity of Atg3p by rearranging its catalytic site | Core | NA | NA | NA |
| 6726-YNR008W | YNR008W | LRO1 | phospholipid:diacylglycerol acyltransferase | Acyltransferase that catalyzes diacylglycerol esterification; one of several acyltransferases that contribute to triglyceride synthesis; Lro1p and Dga1p can O-acylate ceramides; putative homolog of human lecithin cholesterol acyltransferase | Core | NA | NA | NA |
| 6727-YNR009W | YNR009W | NRM1 | NA | Transcriptional co-repressor of MBF-regulated gene expression; Nrm1p associates stably with promoters via MCB binding factor (MBF) to repress transcription upon exit from G1 phase | Core | NA | NA | NA |