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 |
|---|---|---|---|---|---|---|---|---|
| 2153-YBR168W | YBR168W | PEX32 | NA | Peroxisomal integral membrane protein; involved in negative regulation of peroxisome size; partially functionally redundant with Pex31p; genetic interactions suggest action at a step downstream of steps mediated by Pex28p and Pex29p | Core | NA | NA | NA |
| 2154-YBR169C | YBR169C | SSE2 | adenyl-nucleotide exchange factor SSE2 | Member of Hsp110 subclass of the heat shock protein 70 (HSP70) family; serves as nucleotide exchange factor to load ATP onto the SSA class of cytosolic Hsp70s; may be involved in protein folding; localized to the cytoplasm; SSE2 has a paralog, SSE1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2155-YBR170C | YBR170C | NPL4 | HRD4 | Substrate-recruiting cofactor of the Cdc48p-Npl4p-Ufd1p segregase; assists Cdc48p in the dislocation of misfolded, polyubiquitinated ERAD substrates that are subsequently delivered to the proteasome for degradation; also involved in the regulated destruction of resident ER membrane proteins, such as HMG-CoA reductase (Hmg1/2p) and cytoplasmic proteins (Fbp1p); role in mobilizing membrane bound transcription factors by regulated ubiquitin/proteasome-dependent processing (RUP) | Core | NA | NA | NA |
| 2156-YBR171W | YBR171W | SEC66 | KAR7|Sec63 complex subunit SEC66|SEC71|HSS1 | Non-essential subunit of Sec63 complex; with Sec61 complex, Kar2p/BiP and Lhs1p forms a channel competent for SRP-dependent and post-translational SRP-independent protein targeting and import into the ER; other members are Sec63p, Sec62p, and Sec72p | Core | NA | NA | NA |
| 2157-YBR172C | YBR172C | SMY2 | NA | GYF domain protein; involved in COPII vesicle formation; interacts with the Sec23p/Sec24p subcomplex; overexpression suppresses the temperature sensitivity of a myo2 mutant; similar to S. pombe Mpd2; SMY2 has a paralog, SYH1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2158-YBR173C | YBR173C | UMP1 | RNS2 | Chaperone required for correct maturation of the 20S proteasome; short-lived chaperone; may inhibit premature dimerization of proteasome half-mers; degraded by proteasome upon completion of its assembly | Core | NA | NA | NA |
| 2159-YBR175W_NumOfGenes_2 | YBR175W | SWD3 | SAF35|CPS30 | Essential subunit of the COMPASS (Set1C) complex; COMPASS methylates histone H3 on lysine 4 and is required in transcriptional silencing near telomeres; WD40 beta propeller superfamily member and ortholog of mammalian WDR5 | Core | NA | NA | NA |
| 2160-YBR176W | YBR176W | ECM31 | 3-methyl-2-oxobutanoate hydroxymethyltransferase | Ketopantoate hydroxymethyltransferase; required for pantothenic acid biosynthesis, converts 2-oxoisovalerate into 2-dehydropantoate | Core | NA | NA | NA |
| 2161-YBR177C | YBR177C | EHT1 | medium-chain fatty acid ethyl ester synthase/esterase | Acyl-coenzymeA:ethanol O-acyltransferase; plays a minor role in medium-chain fatty acid ethyl ester biosynthesis; possesses short-chain esterase activity; localizes to lipid particles and the mitochondrial outer membrane; EHT1 has a paralog, EEB1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2162-YBR178W | YBR178W | 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 YBR177C | Core | NA | NA | NA |
| 2163-YBR179C | YBR179C | FZO1 | mitofusin | Mitofusin; integral membrane protein involved in mitochondrial outer membrane tethering and fusion; role in mitochondrial genome maintenance; efficient tethering and degradation of Fzo1p requires an intact N-terminal GTPase domain; targeted for destruction by the ubiquitin ligase SCF-Mdm30p and the cytosolic ubiquitin-proteasome system | Core | NA | NA | NA |
| 2164-YBR180W | YBR180W | DTR1 | NA | Putative dityrosine transporter of the major facilitator superfamily; member of the 12-spanner drug:H(+) antiporter DHA1 family; required for spore wall synthesis; sequence similarity to QDR1 and QDR3, and the triple mutant dtr1 qdr1 qdr3 exhibits reduced dityrosine fluorescence relative to the single mutants; expressed during sporulation | Accessory | Ancestral | NA | NA |
| 2165-YBR181C | YBR181C | RPS6B | eS6|ribosomal 40S subunit protein S6B|S6e|RPS102|RPS101|LPG18 | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S6, no bacterial homolog; phosphorylated on S233 by Ypk3p in a TORC1-dependent manner, and on S232 in a TORC1/2-dependent manner by Ypk1/2/3p; RPS6B has a paralog, RPS6A, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2166-YBR182C | YBR182C | SMP1 | NA | MADS-box transcription factor involved in osmotic stress response; SMP1 has a paralog, RLM1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2167-YBR182C-A | YBR182C-A | NA | NA | Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching | Core | NA | NA | NA |