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 |
|---|---|---|---|---|---|---|---|---|
| 6503-YNL111C | YNL111C | CYB5 | NA | Cytochrome b5; involved in the sterol and lipid biosynthesis pathways; acts as an electron donor to support sterol C5-6 desaturation | Core | NA | NA | NA |
| 6504-YNL112W | YNL112W | DBP2 | DEAD-box ATP-dependent RNA helicase DBP2 | ATP-dependent RNA helicase of the DEAD-box protein family; has strong preference for dsRNA; interacts with YRA1; required for assembly of Yra1p, Nab2p and Mex67p onto mRNA and formation of nuclear mRNP; involved in mRNA decay and rRNA processing; may be involved in suppression of transcription from cryptic initiation sites | Core | NA | NA | NA |
| 6505-YNL113W_NumOfGenes_2 | YNL113W | RPC19 | DNA-directed RNA polymerase core subunit RPC19|AC19 | RNA polymerase subunit AC19; common to RNA polymerases I and III | Core | NA | NA | NA |
| 6506-YNL115C | YNL115C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to mitochondria; YNL115C is not an essential gene | Core | NA | NA | NA |
| 6507-YNL116W | YNL116W | DMA2 | ubiquitin-conjugating protein DMA2|CHF2 | Ubiquitin-protein ligase (E3); controls septin dynamics and spindle position checkpoint (SPOC) with ligase Dma1p by regulating recruitment of Elm1p to bud neck; regulates levels of eIF2 subunit Gcd11p, as well as abundance, localization, and ubiquitination of Cdk inhibitory kinase Swe1p; ortholog of human RNF8, similar to human Chfr; contains FHA and RING finger domains; DMA2 has a paralog, DMA1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6508-YNL117W | YNL117W | MLS1 | malate synthase MLS1 | Malate synthase, enzyme of the glyoxylate cycle; involved in utilization of non-fermentable carbon sources; expression is subject to carbon catabolite repression; localizes in peroxisomes during growth on oleic acid, otherwise cytosolic; can accept butyryl-CoA as acyl-CoA donor in addition to traditional substrate acetyl-CoA | Core | NA | NA | NA |
| 6509-YNL118C | YNL118C | DCP2 | decapping enzyme complex catalytic subunit|PSU1 | Catalytic subunit of Dcp1p-Dcp2p decapping enzyme complex; removes 5' cap structure from mRNAs prior to their degradation; also enters nucleus and positively regulates transcription initiation; nudix hydrolase family member; forms cytoplasmic foci upon DNA replication stress; human homolog DCP2 complements yeast dcp2 thermosensitive mutant | Core | NA | NA | NA |
| 6510-YNL119W_NumOfGenes_2 | YNL119W | NCS2 | TUC2 | Protein required for uridine thiolation of Lys(UUU) and Glu(UUC) tRNAs; required for the thiolation of uridine at the wobble position of Lys(UUU) and Glu(UUC) tRNAs; has a role in urmylation and in invasive and pseudohyphal growth; inhibits replication of Brome mosaic virus in S. cerevisiae | Core | NA | NA | NA |
| 6511-YNL121C | YNL121C | TOM70 | protein channel TOM70|OMP1|MOM72|MAS70 | Component of the TOM (translocase of outer membrane) complex; involved in the recognition and initial import steps for all mitochondrially directed proteins; acts as a receptor for incoming precursor proteins; TOM70 has a paralog, TOM71, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6512-YNL122C | YNL122C | NA | NA | Mitochondrial ribosomal protein of the large subunit; homologous to bacterial L35 and human MRPL35 ribosomal proteins | Core | NA | NA | NA |
| 6513-YNL123W | YNL123W | NMA111 | YNM3 | Serine protease and general molecular chaperone; involved in response to heat stress and promotion of apoptosis; may contribute to lipid homeostasis; sequence similarity to the mammalian Omi/HtrA2 family of serine proteases | Core | NA | NA | NA |
| 6514-YNL124W | YNL124W | NAF1 | RNA-binding snoRNP assembly protein | RNA-binding protein required for the assembly of box H/ACA snoRNPs; thus required for pre-rRNA processing; forms a complex with Shq1p and interacts with H/ACA snoRNP components Nhp2p and Cbf5p; similar to Gar1p | Core | NA | NA | NA |
| 6515-YNL125C | YNL125C | ESBP6 | MCH3 | Protein with similarity to monocarboxylate permeases; appears not to be involved in transport of monocarboxylates such as lactate, pyruvate or acetate across the plasma membrane | Core | NA | NA | NA |
| 6516-YNL126W | YNL126W | SPC98 | NA | Component of the microtubule-nucleating Tub4p (gamma-tubulin) complex; interacts with Spc110p at the spindle pole body (SPB) inner plaque and with Spc72p at the SPB outer plaque | Core | NA | NA | NA |
| 6517-YNL127W | YNL127W | FAR11 | NA | Protein involved in recovery from cell cycle arrest; acts in response to pheromone; also involved in regulation of intra-S DNA damage checkpoint and autophagy; is essential for dephosphorylation of Atg13p; interacts with Far3p, Far7p, Far8p, Far9p, Far10p and with the phosphatases Pph21p, Pph22p and Pph3p; has similarity to the N- and C-termini of N. crassa HAM-2; similar to human Fam40A and Fam40B | Core | NA | NA | NA |