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 |
|---|---|---|---|---|---|---|---|---|
| 2558-YDL111C | YDL111C | RRP42 | exosome non-catalytic core subunit RRP42 | Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the nucleus and the cytoplasm; has similarity to E. coli RNase PH and to human hRrp42p (EXOSC7) | Core | NA | NA | NA |
| 2559-YDL112W | YDL112W | TRM3 | tRNA (guanosine(18)-2'-O)-methyltransferase | 2'-O-ribose methyltransferase; catalyzes the ribose methylation of the guanosine nucleotide at position 18 of tRNAs | Core | NA | NA | NA |
| 2560-YDL113C | YDL113C | ATG20 | CVT20|SNX42 | Sorting nexin family member; required for the cytoplasm-to-vacuole targeting (Cvt) pathway and for endosomal sorting; has a Phox homology domain that binds phosphatidylinositol-3-phosphate; interacts with Snx4p; potential Cdc28p substrate | Core | NA | NA | NA |
| 2561-YDL114W | YDL114W | NA | short-chain dehydrogenase/reductase | Putative short-chain dehydrogenase/reductase; YDL114W is not an essential gene | Core | NA | NA | NA |
| 2562-YDL115C_NumOfGenes_2 | YDL115C | IWR1 | NA | RNA polymerase II transport factor, conserved from yeast to humans; also has a role in transporting RNA polymerase III into the nucleus; interacts with most of the RNAP II subunits; nucleo-cytoplasmic shuttling protein; deletion causes hypersensitivity to K1 killer toxin; protein increases in abundance and relocalizes from nucleus to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 2563-YDL116W | YDL116W | NUP84 | NA | Subunit of the Nup84p subcomplex of the nuclear pore complex (NPC); contributes to nucleocytoplasmic transport and NPC biogenesis; also plays roles in several processes that may require localization of genes or chromosomes at the nuclear periphery, including double-strand break repair, transcription and chromatin silencing; homologous to human NUP107 | Core | NA | NA | NA |
| 2564-YDL117W | YDL117W | CYK3 | NA | SH3-domain protein located in the bud neck and cytokinetic actin ring; relocalizes from bud neck to nucleus upon DNA replication stress; activates the chitin synthase activity of Chs2p during cytokinesis; suppressor of growth and cytokinesis defects of chs2 phospho-mutants | Core | NA | NA | NA |
| 2565-YDL119C_NumOfGenes_2 | YDL119C | HEM25 | NA | Mitochondrial glycine transporter; required for the transport of glycine into mitochondria for initiation of heme biosynthesis, with YMC1 acting as a secondary transporter; homolog of human SLC25A38, a mitochondrial glycine transporter associated with nonsyndromic autosomal recessive congenital sideroblastic anemia; human SLC25A38 can complement the heme deficiency associated with the null mutant; GFP-fusion protein is induced in response to the DNA-damaging agent MMS | Core | NA | NA | NA |
| 2566-YDL120W | YDL120W | YFH1 | ferroxidase | Mitochondrial matrix iron chaperone; oxidizes and stores iron; interacts with Isu1p to promote Fe-S cluster assembly; mutation results in multiple Fe/S-dependent enzyme deficiencies; human frataxin homolog FXN is mutated in Friedrich's ataxia; human FTL gene can complement yeast yfh1 null mutant | Core | NA | NA | NA |
| 2567-YDL121C | YDL121C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YDL121C is not an essential protein | Core | NA | NA | NA |
| 2568-YDL122W | YDL122W | UBP1 | ubiquitin-specific protease UBP1 | Ubiquitin-specific protease; removes ubiquitin from ubiquitinated proteins; cleaves at the C terminus of ubiquitin fusions irrespective of their size; capable of cleaving polyubiquitin chains | Core | NA | NA | NA |
| 2569-YDL123W | YDL123W | SNA4 | NA | Protein of unknown function; localized to the vacuolar outer membrane; predicted to be palmitoylated | Core | NA | NA | NA |
| 2570-YDL124W | YDL124W | NA | aldo-keto reductase superfamily protein | NADPH-dependent alpha-keto amide reductase; reduces aromatic alpha-keto amides, aliphatic alpha-keto esters, and aromatic alpha-keto esters; member of the aldo-keto reductase (AKR) family; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2571-YDL125C | YDL125C | HNT1 | adenosine 5'-monophosphoramidase | Adenosine 5'-monophosphoramidase; interacts physically and genetically with Kin28p, a CDK and TFIIK subunit, and genetically with CAK1; member of histidine triad (HIT) superfamily of nucleotide-binding proteins; protein abundance increases in response to DNA replication stress; human homolog HINT1 can complement yeast hnt1 mutant | Core | NA | NA | NA |
| 2572-YDL126C | YDL126C | CDC48 | AAA family ATPase CDC48 | AAA ATPase; subunit of polyUb-selective segregase complex involved in ERAD, INM-associated degradation (INMAD), mitotic spindle disassembly, macroautophagy, PMN, ribosome-associated degradation, ribophagy, homotypic ER membrane fusion, SCF complex disassembly, cell wall integrity during heat stress, and telomerase regulation; mobilizes membrane-anchored transcription factors by regulated Ub/proteasome-dependent processing (RUP); human ortholog VCP complements a cdc48 mutant | Core | NA | NA | NA |