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 |
|---|---|---|---|---|---|---|---|---|
| 7178-YOR219C | YOR219C | STE13 | YCI1 | Dipeptidyl aminopeptidase; Golgi integral membrane protein that cleaves on the carboxyl side of repeating -X-Ala- sequences, required for maturation of alpha factor, transcription is induced by a-factor | Core | NA | NA | NA |
| 7179-YOR220W | YOR220W | RCN2 | WSP1 | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; phosphorylated in response to alpha factor; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 7180-YOR221C | YOR221C | MCT1 | [acyl-carrier-protein] S-malonyltransferase | Predicted malonyl-CoA:ACP transferase; putative component of a type-II mitochondrial fatty acid synthase that produces intermediates for phospholipid remodeling | Core | NA | NA | NA |
| 7181-YOR222W | YOR222W | ODC2 | mitochondrial 2-oxodicarboxylate carrier | Mitochondrial inner membrane transporter; 2-oxodicarboxylate transporter, exports 2-oxoadipate and 2-oxoglutarate from the mitochondrial matrix to the cytosol for use in lysine and glutamate biosynthesis and in lysine catabolism; ODC2 has a paralog, ODC1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7182-YOR223W | YOR223W | DSC3 | NA | Subunit of the DSC ubiquitin ligase complex; protein of unknown function that localizes to the ER and vacuole lumen; overexpression affects endocytic protein trafficking; ortholog of fission yeast dsc3 | Core | NA | NA | NA |
| 7183-YOR224C | YOR224C | RPB8 | DNA-directed RNA polymerase core subunit RPB8|ABC14.5 | RNA polymerase subunit ABC14.5; common to RNA polymerases I, II, and III | Core | NA | NA | NA |
| 7184-YOR225W | YOR225W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Unknown | S. paradoxus | NA |
| 7185-YOR226C | YOR226C | ISU2 | putative iron-binding protein ISU2|NUA2 | Mitochondrial protein required for iron-sulfur protein synthesis; performs scaffolding function during Fe/S cluster assembly; involved in Fe-S cluster assembly for both mitochondrial and cytosolic proteins; protein abundance increases under DNA replication stress; ISU2 has a paralog, ISU1, that arose from the whole genome duplication; isu1 isu2 double mutant is inviable; human homolog ISCU implicated in mitochondrial myopathy, can complement isu1 isu2 double mutant | Core | NA | NA | NA |
| 7186-YOR227W | YOR227W | HER1 | NA | Protein of unknown function; required for proliferation or remodeling of the ER that is caused by overexpression of Hmg2p; may interact with ribosomes, based on co-purification experiments; HER1 has a paralog, GIP3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7187-YOR228C | YOR228C | MCP1 | NA | Mitochondrial protein of unknown function involved in lipid homeostasis; integral membrane protein that localizes to the mitochondrial outer membrane; involved in mitochondrial morphology; interacts genetically with MDM10, and other members of the ERMES complex; contains five predicted transmembrane domains | Core | NA | NA | NA |
| 7188-YOR229W | YOR229W | WTM2 | transcriptional modulator | Transcriptional modulator; involved in regulation of meiosis, silencing, and expression of RNR genes; involved in response to replication stress; contains WD repeats; relocalizes to the cytosol in response to hypoxia; WTM2 has a paralog, UME1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7189-YOR230W | YOR230W | WTM1 | transcriptional modulator | Transcriptional modulator; involved in regulation of meiosis, silencing, and expression of RNR genes; required for nuclear localization of the ribonucleotide reductase small subunit Rnr2p and Rnr4p; contains WD repeats | Core | NA | NA | NA |
| 7190-YOR231W_NumOfGenes_2 | YOR231W | MKK1 | mitogen-activated protein kinase kinase MKK1|SSP32 | MAPKK involved in the protein kinase C signaling pathway; involved in control of cell integrity; upon activation by Bck1p phosphorylates downstream target, Slt2p; functionally redundant with Mkk2p; MKK1 has a paralog, MKK2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7191-YOR232W | YOR232W | MGE1 | GRPE|YGE1 | Mitochondrial matrix cochaperone; nucleotide release factor for Ssc1p in protein translocation and folding; also acts as cochaperone for Ssq1p in folding of Fe-S cluster proteins; acts as oxidative sensor to regulate mitochondrial Ssc1p; in presence of oxidative stress, dimeric Mge1p becomes a monomer and unable to regulate Ssc1p function; homolog of E. coli GrpE and human Mge1 (GRPEL1), which also responds to oxidative stress | Core | NA | NA | NA |
| 7192-YOR233W | YOR233W | KIN4 | putative serine/threonine protein kinase KIN4|KIN3|KIN31 | Serine/threonine protein kinase; inhibits the mitotic exit network (MEN) when the spindle position checkpoint is activated; localized asymmetrically to mother cell cortex, spindle pole body and bud neck; KIN4 has a paralog, FRK1, that arose from the whole genome duplication | Core | NA | NA | NA |