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 |
|---|---|---|---|---|---|---|---|---|
| 6863-YOL066C | YOL066C | RIB2 | bifunctional DRAP deaminase/tRNA pseudouridine synthase RIB2|PUS8 | Bifunctional DRAP deaminase tRNA:pseudouridine synthase; the deaminase catalyzes the third step in riboflavin biosynthesis and the synthase catalyzes formation of pseudouridine at position 32 in cytoplasmic tRNAs; RIB2 has a paralog, PUS9, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6864-YOL067C | YOL067C | RTG1 | NA | Transcription factor (bHLH) involved in interorganelle communication; contributes to communication between mitochondria, peroxisomes, and nucleus; target of Hog1p; activated in stochastic pulses of nuclear localization | Core | NA | NA | NA |
| 6865-YOL068C | YOL068C | HST1 | histone deacetylase HST1 | NAD(+)-dependent histone deacetylase; essential subunit of the Sum1p/Rfm1p/Hst1p complex required for ORC-dependent silencing and meiotic repression; non-essential subunit of the Set3C deacetylase complex; involved in telomere maintenance; HST1 has a paralog, SIR2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6866-YOL069W | YOL069W | NUF2 | kinetochore-associated Ndc80 complex subunit NUF2 | Component of the kinetochore-associated Ndc80 complex; involved in chromosome segregation, spindle checkpoint activity, and kinetochore clustering; evolutionarily conserved; other members include Ndc80p, Nuf2p, Spc24p, and Spc25p | Core | NA | NA | NA |
| 6867-YOL070C | YOL070C | NBA1 | NA | Protein of unknown function; localizes to the bud neck and cytoplasm; interacts with Nap1p; may interact with ribosomes, based on co-purification experiments; potential Cdc28p substrate | Core | NA | NA | NA |
| 6868-YOL071W | YOL071W | SDH5 | EMI5|succinate dehydrogenase assembly factor SDH5 | Protein required for flavinylation of Sdh1p; binds to Sdh1p and promotes FAD cofactor attachment, which is necessary for succinate dehydrogenase (SDH) complex assembly and activity; mutations in human ortholog PGL2 are associated with neuroendocrine tumors (paraganglioma) | Core | NA | NA | NA |
| 6869-YOL072W | YOL072W | THP1 | BUD29 | Nuclear pore-associated protein; component of TREX-2 complex (Sac3p-Thp1p-Sus1p-Cdc31p) involved in transcription elongation and mRNA export from the nucleus; involved in post-transcriptional tethering of active genes to the nuclear periphery and to non-nascent mRNP; contains a PAM domain implicated in protein-protein binding | Core | NA | NA | NA |
| 6870-YOL073C | YOL073C | DSC2 | NA | Multi-transmembrane subunit of the DSC ubiquitin ligase complex; similar in sequence to rhomboid pseudoproteases Der1p and UBAC2 that function in ERAD; ortholog of fission yeast dsc2 | Core | NA | NA | NA |
| 6871-YOL075C | YOL075C | NA | NA | Putative ABC transporter | Core | NA | NA | NA |
| 6872-YOL076W | YOL076W | MDM20 | NAA25|DEC1 | Non-catalytic subunit of the NatB N-terminal acetyltransferase; NatB catalyzes N-acetylation of proteins with specific N-terminal sequences; involved in mitochondrial inheritance and actin assembly | Core | NA | NA | NA |
| 6873-YOL077C | YOL077C | BRX1 | NA | Nucleolar protein; constituent of 66S pre-ribosomal particles; depletion leads to defects in rRNA processing and a block in the assembly of large ribosomal subunits; possesses a sigma(70)-like RNA-binding motif | Core | NA | NA | NA |
| 6874-YOL077W-A | YOL077W-A | ATP19 | F1F0 ATP synthase subunit k | Subunit k of the mitochondrial F1F0 ATP synthase; F1F0 ATP synthase is a large, evolutionarily conserved enzyme complex required for ATP synthesis; associated only with the dimeric form of ATP synthase | Core | NA | NA | NA |
| 6875-YOL078W | YOL078W | AVO1 | NA | Component of a membrane-bound complex containing the Tor2p kinase; contains Tor2p kinase and other proteins; may have a role in regulation of cell growth | Core | NA | NA | NA |
| 6876-YOL080C_NumOfGenes_2 | YOL080C | REX4 | putative 3'-5' exonuclease | Putative RNA exonuclease; possibly involved in pre-rRNA processing and ribosome assembly | Core | NA | NA | NA |
| 6877-YOL081W | YOL081W | IRA2 | Ras GTPase activating protein IRA2|GLC4|CCS1 | GTPase-activating protein; negatively regulates RAS by converting it from the GTP- to the GDP-bound inactive form, required for reducing cAMP levels under nutrient limiting conditions; IRA2 has a paralog, IRA1, that arose from the whole genome duplication; defects in human homolog NF1 are associated with neurofibromatosis | Core | NA | NA | NA |