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 |
|---|---|---|---|---|---|---|---|---|
| 6398-YNL002C | YNL002C | RLP7 | RPL7 | Nucleolar protein similar to large ribosomal subunit L7 proteins; constituent of 66S pre-ribosomal particles; plays an essential role in processing of precursors to the large ribosomal subunit RNAs; binds junction of ITS2 and ITS2-proximal stem between the 3' end of 5.8S rRNA and the 5' end of 25S rRNA | Core | NA | NA | NA |
| 6399-YNL003C | YNL003C | PET8 | SAM5 | S-adenosylmethionine transporter of the mitochondrial inner membrane; member of the mitochondrial carrier family; required for biotin biosynthesis and respiratory growth | Core | NA | NA | NA |
| 6400-YNL004W | YNL004W | HRB1 | mRNA-binding protein|TOM34 | Poly(A+) RNA-binding protein; key surveillance factor for the selective export of spliced mRNAs from the nucleus to the cytoplasm; preference for intron-containing genes; similar to Npl3p; HRB1 has a paralog, GBP2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6401-YNL005C | YNL005C | MRP7 | mitochondrial 54S ribosomal protein YmL2|YmL2|MRPL2 | Mitochondrial ribosomal protein of the large subunit | Core | NA | NA | NA |
| 6402-YNL006W | YNL006W | LST8 | TOR complex subunit LST8 | Protein required for the transport of Gap1p; required for the transport of amino acid permease Gap1p from the Golgi to the cell surface; component of the TOR signaling pathway; associates with both Tor1p and Tor2p; contains a WD-repeat | Core | NA | NA | NA |
| 6403-YNL007C | YNL007C | SIS1 | type II HSP40 co-chaperone SIS1 | Type II HSP40 co-chaperone that interacts with the HSP70 protein Ssa1p; shuttles between cytosol and nucleus; mediates delivery of misfolded proteins into the nucleus for degradation; involved in proteasomal degradation of misfolded cytosolic proteins; protein abundance increases in response to DNA replication stress; polyQ aggregates sequester Sis1p and interfere with clearance of misfolded proteins; similar to bacterial DnaJ proteins and mammalian DnaJB1 | Core | NA | NA | NA |
| 6404-YNL008C | YNL008C | ASI3 | putative ubiquitin-protein ligase ASI3 | Subunit of the inner nuclear membrane Asi ubiquitin ligase complex; Asi complex targets both misfolded proteins of the inner nuclear membrane-associated degradation (INMAD) pathway and regulators of sterol biosynthesis for ubiquitin-mediated degradation; acts with Asi1p and Asi2p to ensure the fidelity of SPS-sensor signaling by targeting latent unprocessed forms of Stp1p and Stp2p, maintaining the repressed state of gene expression in the absence of inducing amino acids | Core | NA | NA | NA |
| 6405-YNL009W | YNL009W | IDP3 | isocitrate dehydrogenase (NADP(+)) IDP3 | Peroxisomal NADP-dependent isocitrate dehydrogenase; catalyzes oxidation of isocitrate to alpha-ketoglutarate with the formation of NADP(H+), required for growth on unsaturated fatty acids; IDP3 has a paralog, IDP2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6406-YNL010W | YNL010W | NA | putative phosphoric monoester hydrolase | Putative protein of unknown function; similar to phosphoserine phosphatases; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; homozygous diploid mutant shows an increase in glycogen accumulation | Core | NA | NA | NA |
| 6407-YNL011C | YNL011C | NA | NA | Putative protein of unknown function; YNL011C is not an essential gene | Core | NA | NA | NA |
| 6408-YNL012W | YNL012W | SPO1 | putative carboxylic ester hydrolase | Meiosis-specific prospore protein; required for meiotic spindle pole body duplication and separation; required to produce bending force necessary for proper prospore membrane assembly during sporulation; has similarity to phospholipase B | Core | NA | NA | NA |
| 6409-YNL014W_NumOfGenes_2 | YNL014W | HEF3 | translation elongation factor EF-3|ZRG7 | Translational elongation factor EF-3; member of the ABC superfamily; stimulates EF-1 alpha-dependent binding of aminoacyl-tRNA by the ribosome; normally expressed in zinc deficient cells; HEF3 has a paralog, YEF3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6410-YNL015W | YNL015W | PBI2 | IB2|I2B|LMA1 | Cytosolic inhibitor of vacuolar proteinase B (PRB1); required for efficient vacuole inheritance; with thioredoxin forms protein complex LMA1, which assists in priming SNARE molecules and promotes vacuole fusion; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6411-YNL016W | YNL016W | PUB1 | RNP1 | Poly (A)+ RNA-binding protein; abundant mRNP-component protein that binds mRNA and is required for stability of many mRNAs; component of glucose deprivation induced stress granules, involved in P-body-dependent granule assembly; implicated in regulation of translation; carries Q/N-rich domain at C- terminus, identified as candidate prion; human homolog Tia1 is critical for normal synaptic plasticity; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6412-YNL017C | YNL017C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; completely overlaps the tRNA ORF tI(AAU)N2 | Core | NA | NA | NA |