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 |
|---|---|---|---|---|---|---|---|---|
| 3143-YDR455C | YDR455C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YDR456W | Accessory | Ancestral | NA | NA |
| 3144-YDR456W | YDR456W | NHX1 | bifunctional K:H/Na:H antiporter NHX1|VPL27|NHA2|VPS44 | Na+/H+ and K+/H+ exchanger; required for intracellular sequestration of Na+ and K+; located in the vacuole and late endosome compartments; required for osmotolerance to acute hypertonic shock and for vacuolar fusion; ortholog of human NHE9, which is linked to autism | Core | NA | NA | NA |
| 3145-YDR457W | YDR457W | TOM1 | E3 ubiquitin-protein ligase TOM1 | E3 ubiquitin ligase of the hect-domain class; has a role in mRNA export from the nucleus and may regulate transcriptional coactivators; involved in degradation of excess histones; interacts with Dia2p and is required for Dia2p degradation; required to target Cdc6p for ubiquitin-mediated destruction during G1 phase | Core | NA | NA | NA |
| 3146-YDR458C | YDR458C | HEH2 | NA | Inner nuclear membrane (INM) protein; contains helix-extension-helix (HEH) motif, nuclear localization signal sequence; targeting to the INM requires the Srp1p-Kap95p karyopherins and the Ran cycle; HEH2 has a paralog, SRC1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3147-YDR459C | YDR459C | PFA5 | palmitoyltransferase PFA5 | Palmitoyltransferase with autoacylation activity; likely functions in pathway(s) outside Ras; member of a family of putative palmitoyltransferases containing an Asp-His-His-Cys-cysteine rich (DHHC-CRD) domain | Core | NA | NA | NA |
| 3148-YDR460W | YDR460W | TFB3 | TFIIH/NER complex subunit TFB3|RIG2 | Subunit of TFIIH and nucleotide excision repair factor 3 complexes; involved in transcription initiation, required for nucleotide excision repair; ring finger protein similar to mammalian CAK and TFIIH subunit | Core | NA | NA | NA |
| 3149-YDR461C-A | YDR461C-A | NA | NA | Putative protein of unknown function | Accessory | Ancestral | NA | NA |
| 3150-YDR461W | YDR461W | MFA1 | mating pheromone a | Mating pheromone a-factor; made by a cells; interacts with alpha cells to induce cell cycle arrest and other responses leading to mating; biogenesis involves C-terminal modification, N-terminal proteolysis, and export; also encoded by MFA2 | Core | NA | NA | NA |
| 3151-YDR462W | YDR462W | MRPL28 | mitochondrial 54S ribosomal protein YmL28|YmL28 | Mitochondrial ribosomal protein of the large subunit; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3152-YDR463W | YDR463W | STP1 | SSY2|BAP1 | Transcription factor; contains a N-terminal regulatory motif (RI) that acts as a cytoplasmic retention determinant and as an Asi dependent degron in the nucleus; undergoes proteolytic processing by SPS (Ssy1p-Ptr3p-Ssy5p)-sensor component Ssy5p in response to extracellular amino acids; activates transcription of amino acid permease genes and may have a role in tRNA processing; STP1 has a paralog, STP2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3153-YDR464W_NumOfGenes_2 | YDR464W | SPP41 | NA | Protein of unknown function; involved in negative regulation of expression of spliceosome components PRP4 and PRP3; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 3154-YDR465C | YDR465C | RMT2 | protein-arginine N5-methyltransferase | Arginine N5 methyltransferase; methylates ribosomal protein Rpl12 (L12) on Arg67; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 3155-YDR466W | YDR466W | PKH3 | protein kinase PKH3 | Protein kinase with similarity to mammalian PDK1 and yeast Pkh1p/Phk2p; yeast Pkh1p and Pkh2p are two redundant upstream activators of Pkc1p; identified as a multicopy suppressor of a pkh1 pkh2 double mutant | Core | NA | NA | NA |
| 3156-YDR467C | YDR467C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 3157-YDR468C | YDR468C | TLG1 | NA | Essential t-SNARE that mediates fusion of vesicles with the late Golgi; forms a complex with Tlg2p and Vti1p; mediates fusion of endosome-derived vesicles with the late Golgi; binds the docking complex VFT (Vps fifty-three) through interaction with Vps51p | Core | NA | NA | NA |