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 |
|---|---|---|---|---|---|---|---|---|
| 2333-YCL048W-A_NumOfGenes_2 | YCL048W-A | NA | NA | Putative protein of unknown function; SWAT-GFP and mCherry fusion proteins localize to the cell periphery and vacuole; YCL048W-A has a paralog, YDR524C-B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2334-YCL049C | YCL049C | NA | NA | Protein of unknown function; localizes to membrane fraction; YCL049C is not an essential gene | Core | NA | NA | NA |
| 2335-YCL050C | YCL050C | APA1 | bifunctional AP-4-A phosphorylase/ADP sulfurylase|DTP1 | AP4A phosphorylase; bifunctional diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase and ADP sulfurylase involved in catabolism of bis(5'-nucleosidyl) tetraphosphates; catalyzes phosphorolysis of dinucleoside oligophosphates, cleaving substrates' alpha/beta-anhydride bond and introducing Pi into the beta-position of the corresponding NDP formed; protein abundance increases under DNA replication stress; APA1 has a paralog, APA2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2336-YCL051W | YCL051W | LRE1 | NA | Protein involved in control of cell wall structure and stress response; direct inhibitor of the nuclear Dbf2 related (NDR) kinase Cbk1p-Mob2p; overproduction confers resistance to cell-wall degrading enzymes; exhibits genetic interactions with genes involved in the cell wall integrity pathway; LRE1 has a paralog, HLR1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2337-YCL052C | YCL052C | PBN1 | NA | Component of glycosylphosphatidylinositol-mannosyltransferase I; essential component; required for the autocatalytic post-translational processing of the protease B precursor Prb1p; localizes to ER in lumenal orientation; homolog of mammalian PIG-X | Core | NA | NA | NA |
| 2338-YCL054W | YCL054W | SPB1 | 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase | AdoMet-dependent methyltransferase; involved in rRNA processing and 60S ribosomal subunit maturation; methylates G2922 in the tRNA docking site of the large subunit rRNA and in the absence of snR52, U2921; suppressor of PAB1 mutants | Core | NA | NA | NA |
| 2339-YCL054W-A | YCL054W-A | RDT1 | NA | Short open reading frame, shows evidence of translation; may be new protein-coding gene that originated de novo from noncoding sequence; same allele found in at least 33 other S. cerevisiae strains; at least 3 strains have a second allele with three nucleotide substitutions leading to two amino acid differences | Core | NA | NA | NA |
| 2340-YCL055W | YCL055W | KAR4 | NA | Transcription factor required for response to pheromones; also required during meiosis; exists in two forms, a slower-migrating form more abundant during vegetative growth and a faster-migrating form induced by pheromone | Core | NA | NA | NA |
| 2341-YCL056C | YCL056C | PEX34 | NA | Protein that regulates peroxisome populations; peroxisomal integral membrane protein; interacts with Pex11p, Pex25p, and Pex27p to control both constitutive peroxisome division and peroxisome morphology and abundance during peroxisome proliferation | Core | NA | NA | NA |
| 2342-YCL057C-A | YCL057C-A | MIC10 | MOS1|MCS10|MIO10 | Conserved component of the MICOS complex; MICOS (formerly MINOS or MitOS) is a mitochondrial inner membrane complex that extends into the intermembrane space and has a role in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane; forms a subcomplex with Mic12p and Mic27p whose assembly and stability requires cardiolipin; homo-oligomers cause membrane bending; ortholog of human MINOS1 | Core | NA | NA | NA |
| 2343-YCL057W | YCL057W | PRD1 | metalloendopeptidase | Zinc metalloendopeptidase; found in the cytoplasm and intermembrane space of mitochondria; with Cym1p, involved in degradation of mitochondrial proteins and of presequence peptides cleaved from imported proteins; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2344-YCL058W-A_NumOfGenes_2 | YCL058W-A | ADF1 | NA | Transcriptional repressor encoded by the FYV5 antisense strand; negatively regulates transcription of FYV5 by binding to the promoter on the sense strand | Core | NA | NA | NA |
| 2345-YCL059C | YCL059C | KRR1 | ribosome biosynthesis protein KRR1 | Nucleolar protein required for rRNA synthesis and ribosomal assembly; required for the synthesis of 18S rRNA and for the assembly of 40S ribosomal subunit; essential gene | Core | NA | NA | NA |
| 2346-YCL061C | YCL061C | MRC1 | chromatin-modulating protein MRC1|YCL060C | S-phase checkpoint protein required for DNA replication; couples DNA helicase and polymerase; interacts with and stabilizes Pol2p at stalled replication forks during stress, where it forms a pausing complex with Tof1p and is phosphorylated by Mec1p; defines a novel S-phase checkpoint with Hog1p that coordinates DNA replication and transcription upon osmostress; protects uncapped telomeres; Dia2p-dependent degradation mediates checkpoint recovery; mammalian claspin homolog | Core | NA | NA | NA |
| 2347-YCL063W | YCL063W | VAC17 | YCL062W | Phosphoprotein involved in vacuole inheritance; degraded in late M phase of the cell cycle; acts as a vacuole-specific receptor for myosin Myo2p; involved in regulation of asymmetric inheritance of aggregated/misfolded proteins and age reset | Core | NA | NA | NA |