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 |
|---|---|---|---|---|---|---|---|---|
| 6878-YOL082W_NumOfGenes_2 | YOL082W | ATG19 | CVT19 | Receptor protein for the cytoplasm-to-vacuole targeting (Cvt) pathway; delivers cargo proteins aminopeptidase I (Ape1p) and alpha-mannosidase (Ams1p) to the phagophore assembly site for packaging into Cvt vesicles; interaction with Atg19p during the Cvt pathway requires phosphorylation by Hrr25p | Accessory | Ancestral | NA | NA |
| 6879-YOL083W_NumOfGenes_2 | YOL083W | ATG34 | ATG19-B | Receptor protein involved in selective autophagy during starvation; specifically involved in the transport of cargo protein alpha-mannosidase (Ams1p); Atg19p paralog | Accessory | Ancestral | NA | NA |
| 6880-YOL084W | YOL084W | PHM7 | NA | Protein of unknown function; expression is regulated by phosphate levels; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery and vacuole; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 6881-YOL085C | YOL085C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YOL085C is not an essential gene; partially overlaps dubious ORF YOL085W-A | Core | NA | NA | NA |
| 6882-YOL085W-A | YOL085W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YOL085C | Accessory | Unknown | NA | NA |
| 6883-YOL086C | YOL086C | ADH1 | alcohol dehydrogenase ADH1|ADC1 | Alcohol dehydrogenase; fermentative isozyme active as homo- or heterotetramers; required for the reduction of acetaldehyde to ethanol, the last step in the glycolytic pathway; ADH1 has a paralog, ADH5, that arose from the whole genome duplication | Accessory | Introgression | S. paradoxus | NA |
| 6884-YOL086W-A | YOL086W-A | MHF1 | NA | Component of the heterotetrameric MHF histone-fold complex; in humans the MHF complex interacts with both DNA and Mph1p ortholog FANCM, a Fanconi anemia complementation group protein, to stabilize and remodel blocked replication forks and repair damaged DNA; mhf1 srs2 double mutants are MMS hypersensitive; ortholog of human centromere constitutive-associated network (CCAN) subunit CENP-S, also known as MHF1 | Core | NA | NA | NA |
| 6885-YOL087C | YOL087C | DUF1 | NA | Ubiquitin-binding protein of unknown function; contains one WD40 repeat in a beta-propeller fold; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; homolog of human WDR48/UAF1, which is involved in regulating the Fanconi anemia pathway; deletion mutant is sensitive to various chemicals including phenanthroline, sanguinarine, and nordihydroguaiaretic acid | Core | NA | NA | NA |
| 6886-YOL088C | YOL088C | MPD2 | protein disulfide isomerase MPD2 | Member of the protein disulfide isomerase (PDI) family; exhibits chaperone activity; overexpression suppresses the lethality of a pdi1 deletion but does not complement all Pdi1p functions; undergoes oxidation by Ero1p | Core | NA | NA | NA |
| 6887-YOL089C | YOL089C | HAL9 | NA | Putative transcription factor containing a zinc finger; overexpression increases salt tolerance through increased expression of the ENA1 (Na+/Li+ extrusion pump) gene while gene disruption decreases both salt tolerance and ENA1 expression; HAL9 has a paralog, TBS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6888-YOL090W | YOL090W | MSH2 | mismatch repair ATPase MSH2|PMS5 | Protein that binds to DNA mismatches; forms heterodimers with Msh3p and Msh6p that bind to DNA mismatches to initiate the mismatch repair process; contains a Walker ATP-binding motif required for repair activity and involved in interstrand cross-link repair; Msh2p-Msh6p binds to and hydrolyzes ATP | Core | NA | NA | NA |
| 6889-YOL091W | YOL091W | SPO21 | MPC70 | Component of the meiotic outer plaque of the spindle pole body; involved in modifying the meiotic outer plaque that is required prior to prospore membrane formation; SPO21 has a paralog, YSW1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6890-YOL092W | YOL092W | YPQ1 | cationic amino acid transporter | Putative vacuolar membrane transporter for cationic amino acids; likely contributes to amino acid homeostasis by exporting cationic amino acids from the vacuole; member of the PQ-loop family, with seven transmembrane domains; similar to mammalian PQLC2 vacuolar transporter; YPQ1 has a paralog, RTC2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6891-YOL093W | YOL093W | TRM10 | tRNA (guanine(9)-N(1))-methyltransferase | tRNA methyltransferase; methylates the N-1 position of guanine at position 9 in tRNAs; protein abundance increases in response to DNA replication stress; member of the SPOUT (SpoU-TrmD) methyltransferase family; human ortholog TRMT10A plays a role in the pathogenesis of microcephaly and early onset diabetes; an 18-mer originates from the TRM10 locus; genetic analysis shows the 18-mer is the translation regulator | Core | NA | NA | NA |
| 6892-YOL094C | YOL094C | RFC4 | replication factor C subunit 4 | Subunit of heteropentameric Replication factor C (RF-C); which is a DNA binding protein and ATPase that acts as a clamp loader of the proliferating cell nuclear antigen (PCNA) processivity factor for DNA polymerases delta and epsilon; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |