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 |
|---|---|---|---|---|---|---|---|---|
| 3518-YER187W | YER187W | NA | NA | Putative protein of unknown function; induced in respiratory-deficient cells | Accessory | Introgression | S. paradoxus | NA |
| 3519-YER188C-A_NumOfGenes_9 | YER188C-A | NA | NA | Putative protein of unknown function | Accessory | Ancestral | NA | NA |
| 3520-YER188W_NumOfGenes_2 | YER188W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; large-scale analyses show mRNA expression increases under anaerobic conditions and two-hybrid interactions with Sst2p | Accessory | Ancestral | NA | NA |
| 3521-YFL001W_NumOfGenes_2 | YFL001W | DEG1 | pseudouridine synthase DEG1|HRM3|PUS3 | tRNA:pseudouridine synthase; introduces pseudouridines at position 38 or 39 in tRNA; also responsible for pseudouracil modification of some mRNAs; important for maintenance of translation efficiency and normal cell growth, localizes to both the nucleus and cytoplasm; non-essential for viability | Core | NA | NA | NA |
| 3522-YFL002C | YFL002C | SPB4 | putative ATP-dependent RNA helicase SPB4 | Putative ATP-dependent RNA helicase; nucleolar protein required for synthesis of 60S ribosomal subunits at a late step in the pathway; sediments with 66S pre-ribosomes in sucrose gradients | Core | NA | NA | NA |
| 3523-YFL003C | YFL003C | MSH4 | MutS family protein MSH4 | Protein involved in meiotic recombination; required for normal levels of crossing over, colocalizes with Zip2p to discrete foci on meiotic chromosomes, has homology to bacterial MutS protein | Core | NA | NA | NA |
| 3524-YFL004W | YFL004W | VTC2 | vacuolar transporter chaperone|PHM1 | Regulatory subunit of the vacuolar transporter chaperone (VTC) complex; involved in membrane trafficking, vacuolar polyphosphate accumulation, microautophagy and non-autophagic vacuolar fusion; VTC2 has a paralog, VTC3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3525-YFL005W | YFL005W | SEC4 | Rab family GTPase SEC4|SRO6 | Rab family GTPase; essential for vesicle-mediated exocytic secretion and autophagy; associates with the exocyst component Sec15p and may regulate polarized delivery of transport vesicles to the exocyst at the plasma membrane | Core | NA | NA | NA |
| 3526-YFL007W | YFL007W | BLM10 | YFL006W | Proteasome activator; binds the core proteasome (CP) and stimulates proteasome-mediated protein degradation by inducing gate opening; required for sequestering CP into proteasome storage granule (PSG) during quiescent phase and for nuclear import of CP in proliferating cells; required for resistance to bleomycin, may be involved in protecting against oxidative damage; similar to mammalian PA200 | Core | NA | NA | NA |
| 3527-YFL008W | YFL008W | SMC1 | cohesin subunit SMC1|CHL10 | Subunit of the multiprotein cohesin complex; essential protein involved in chromosome segregation and in double-strand DNA break repair; SMC chromosomal ATPase family member, binds DNA with a preference for DNA with secondary structure | Accessory | Ancestral | NA | NA |
| 3528-YFL009W | YFL009W | CDC4 | SCF ubiquitin ligase complex subunit CDC4 | F-box protein required for both the G1/S and G2/M phase transitions; modular substrate specificity factor which associates with core SCF (Cdc53p, Skp1p and Hrt1p/Rbx1p) to form the SCFCdc4 complex; SCFCdc4 acts as a ubiquitin-protein ligase directing ubiquitination of cyclin-dependent kinase (CDK) phosphorylated substrates, such as: Sic1p, Far1p, Cdc6p, Clb6p, and Cln3p | Accessory | Ancestral | NA | NA |
| 3529-YFL010C | YFL010C | WWM1 | NA | WW domain containing protein of unknown function; binds to Mca1p, a caspase-related protease that regulates H2O2-induced apoptosis; overexpression causes G1 phase growth arrest and clonal death that is suppressed by overexpression of MCA1 | Accessory | Ancestral | NA | NA |
| 3530-YFL010W-A | YFL010W-A | AUA1 | YFL011W-A | Protein required for the negative regulation by ammonia of Gap1p; Gap1p is a general amino acid permease | Accessory | Ancestral | NA | NA |
| 3531-YFL011W_NumOfGenes_2 | YFL011W | HXT10 | hexose transporter HXT10 | Putative hexose transporter; expressed at low levels and expression is repressed by glucose | Accessory | Ancestral | NA | NA |
| 3532-YFL012W | YFL012W | NA | NA | Putative protein of unknown function; transcribed during sporulation; null mutant exhibits increased resistance to rapamycin | Accessory | Unknown | NA | NA |