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 |
|---|---|---|---|---|---|---|---|---|
| 7118-YOR157C | YOR157C | PUP1 | proteasome core particle subunit beta 2 | Beta 2 subunit of the 20S proteasome; endopeptidase with trypsin-like activity that cleaves after basic residues; synthesized as a proprotein before being proteolytically processed for assembly into 20S particle; human homolog is subunit Z | Core | NA | NA | NA |
| 7119-YOR158W | YOR158W | PET123 | mitochondrial 37S ribosomal protein PET123 | Mitochondrial ribosomal protein of the small subunit; PET123 exhibits genetic interactions with PET122, which encodes a COX3 mRNA-specific translational activator | Core | NA | NA | NA |
| 7120-YOR159C | YOR159C | SME1 | mRNA splicing protein SME1|Sm E|SmE | Core Sm protein Sm E; part of heteroheptameric complex (with Smb1p, Smd1p, Smd2p, Smd3p, Smx3p, and Smx2p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; homolog of human Sm E | Core | NA | NA | NA |
| 7121-YOR160W | YOR160W | MTR10 | KAP111 | Nuclear import receptor; mediates the nuclear localization of proteins involved in mRNA-nucleus export; promotes dissociation of mRNAs from the nucleus-cytoplasm mRNA shuttling protein Npl3p; required for retrograde import of mature tRNAs; relocalizes from cytoplasm to the nuclear periphery upon DNA replication stress | Core | NA | NA | NA |
| 7122-YOR161C_NumOfGenes_3 | YOR161C | PNS1 | NA | Protein of unknown function; has similarity to Torpedo californica tCTL1p, which is postulated to be a choline transporter, neither null mutation nor overexpression affects choline transport | Accessory | Ancestral | NA | NA |
| 7123-YOR161C-C | YOR161C-C | NA | NA | Protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching | Accessory | Unknown | NA | NA |
| 7124-YOR162C | YOR162C | YRR1 | PDR2 | Zn2-Cys6 zinc-finger transcription factor; activates genes involved in multidrug resistance; paralog of Yrm1p, acting on an overlapping set of target genes; YRR1 has a paralog, PDR8, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 7125-YOR163W | YOR163W | DDP1 | polyphosphatase DDP1 | Polyphosphate phosphatase; hydrolyzes diphosphorylated inositol polyphosphates and diadenosine polyphosphates; high specificity for diadenosine hexa- and pentaphosphates; contains endopolyphosphatase activity with a high affinity for polyphosphates, an activity also observed for its human DIPP homologs; possesses mRNA decapping activity; nudix hydrolase family member; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 7126-YOR164C | YOR164C | GET4 | ENV8 | Protein involved in inserting tail-anchored proteins into ER membranes; forms a complex with Mdy2p; highly conserved across species and homologous to human gene C7orf20 | Accessory | Ancestral | NA | NA |
| 7127-YOR165W | YOR165W | SEY1 | dynamin-like GTPase SEY1 | Dynamin-like GTPase that mediates homotypic ER fusion; has a role in ER morphology; interacts physically and genetically with Yop1p and Rtn1p; functional ortholog of the human atlastin ATL1, defects in which cause a form of the human disease hereditary spastic paraplegia; homolog of Arabidopsis RHD3 | Core | NA | NA | NA |
| 7128-YOR166C | YOR166C | SWT1 | mRNA-processing endoribonuclease | RNA endoribonuclease involved in perinuclear mRNP quality control; involved in perinuclear mRNP quality control via the turnover of aberrant, unprocessed pre-mRNAs; interacts with subunits of THO/TREX, TREX-2, and RNA polymerase II; contains a PIN (PilT N terminus) domain | Core | NA | NA | NA |
| 7129-YOR167C | YOR167C | RPS28A | eS28|ribosomal 40S subunit protein S28A|S28e|YS27|S33A|S28A|RPS33A | Protein component of the small (40S) ribosomal subunit; has an extraribosomal function in regulation of RPS28B, in which Rps28Ap binds to a decapping complex via Edc3p, which then binds to RPS28B mRNA leading to its decapping and degradation; homologous to mammalian ribosomal protein S28, no bacterial homolog; RPS28A has a paralog, RPS28B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7130-YOR168W_NumOfGenes_2 | YOR168W | GLN4 | glutamine--tRNA ligase | Glutamine tRNA synthetase; monomeric class I tRNA synthetase that catalyzes the specific glutaminylation of tRNA(Gln); N-terminal domain proposed to be involved in enzyme-tRNA interactions | Core | NA | NA | NA |
| 7131-YOR170W | YOR170W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene LCB4 | Accessory | Ancestral | NA | NA |
| 7132-YOR171C | YOR171C | LCB4 | sphinganine kinase LCB4 | Sphingoid long-chain base kinase; responsible for synthesis of long-chain base phosphates, which function as signaling molecules, regulates synthesis of ceramide from exogenous long-chain bases, localizes to the Golgi and late endosomes; LCB4 has a paralog, LCB5, that arose from the whole genome duplication | Core | NA | NA | NA |