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 |
|---|---|---|---|---|---|---|---|---|
| 4313-YHR062C | YHR062C | RPP1 | RNA-binding RNA processing protein RPP1 | Subunit of both RNase MRP and nuclear RNase P; RNase MRP cleaves pre-rRNA, while nuclear RNase P cleaves tRNA precursors to generate mature 5' ends and facilitates turnover of nuclear RNAs; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 4314-YHR063C | YHR063C | PAN5 | 2-dehydropantoate 2-reductase PAN5 | 2-dehydropantoate 2-reductase; part of the pantothenic acid pathway, structurally homologous to E. coli panE | Core | NA | NA | NA |
| 4315-YHR064C_NumOfGenes_2 | YHR064C | SSZ1 | PDR13 | Hsp70 protein that interacts with Zuo1p (a DnaJ homolog); interacts with Zuo1p to form a ribosome-associated complex that binds the ribosome via the Zuo1p subunit; also involved in pleiotropic drug resistance via sequential activation of PDR1 and PDR5; binds ATP | Core | NA | NA | NA |
| 4316-YHR065C | YHR065C | RRP3 | RNA-dependent ATPase RRP3 | Protein involved in rRNA processing; required for maturation of the 35S primary transcript of pre-rRNA and for cleavage leading to mature 18S rRNA; homologous to eIF-4a, which is a DEAD box RNA-dependent ATPase with helicase activity | Core | NA | NA | NA |
| 4317-YHR066W | YHR066W | SSF1 | rRNA-binding ribosome biosynthesis protein | Constituent of 66S pre-ribosomal particles; required for ribosomal large subunit maturation; functionally redundant with Ssf2p; member of the Brix family; SSF1 has a paralog, SSF2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4318-YHR067W | YHR067W | HTD2 | hydroxyacyl-thioester dehydratase HTD2|RMD12 | Mitochondrial 3-hydroxyacyl-thioester dehydratase; involved in fatty acid biosynthesis, required for respiratory growth and for normal mitochondrial morphology | Core | NA | NA | NA |
| 4319-YHR068W | YHR068W | DYS1 | deoxyhypusine synthase | Deoxyhypusine synthase; catalyzes formation of deoxyhypusine, the first step in hypusine biosynthesis; triggers posttranslational hypusination of translation elongation factor eIF-5A and regulates its intracellular levels; tetrameric; human homolog DHPS allows growth of yeast haploid dys1 null mutant after sporulation of heterozygous diploid | Core | NA | NA | NA |
| 4320-YHR069C | YHR069C | RRP4 | exosome non-catalytic core subunit RRP4 | Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the nucleus and the cytoplasm; predicted to contain RNA binding domains; has similarity to human hRrp4p (EXOSC2) | Core | NA | NA | NA |
| 4321-YHR070C-A | YHR070C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps the verified gene TRM5/YHR070W | Accessory | Unknown | NA | NA |
| 4322-YHR070W_NumOfGenes_2 | YHR070W | TRM5 | tRNA (guanine) methyltransferase | tRNA(m(1)G37)methyltransferase; methylates a tRNA base adjacent to the anticodon that has a role in prevention of frameshifting; localized to both cytoplasm and mitochondria, and modifies both cytoplasmic and mitochondrial tRNAs; mutations in human ortholog TRMT5 are associated with skeletal muscle respiratory chain deficiencies, and trm5 mutations analogous to disease mutations decrease respiration | Core | NA | NA | NA |
| 4323-YHR071C-A | YHR071C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF ERG7/YHR072W | Accessory | Ancestral | NA | NA |
| 4324-YHR071W | YHR071W | PCL5 | NA | Cyclin; interacts with and phosphorylated by Pho85p cyclin-dependent kinase (Cdk), induced by Gcn4p at level of transcription, specifically required for Gcn4p degradation, may be sensor of cellular protein biosynthetic capacity | Core | NA | NA | NA |
| 4325-YHR072W | YHR072W | ERG7 | lanosterol synthase ERG7 | Lanosterol synthase; an essential enzyme that catalyzes the cyclization of squalene 2,3-epoxide, a step in ergosterol biosynthesis; human LSS functionally complements the lethality of the erg7 null mutation | Core | NA | NA | NA |
| 4326-YHR072W-A | YHR072W-A | NOP10 | snoRNP complex protein NOP10 | Subunit of box H/ACA snoRNP complex; required for pseudouridylation and processing of pre-18S rRNA | Core | NA | NA | NA |
| 4327-YHR073W_NumOfGenes_3 | YHR073W | OSH3 | oxysterol-binding protein related protein OSH3 | Member of an oxysterol-binding protein family; this family has seven members in S. cerevisiae; family members have overlapping, redundant functions in sterol metabolism and collectively perform a function essential for viability; contains FFAT motif; interacts with ER anchor Scs2p at patches at the plasma membrane; regulated by sterol binding | Core | NA | NA | NA |