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 |
|---|---|---|---|---|---|---|---|---|
| 1973-YBL102W | YBL102W | SFT2 | NA | Tetra-spanning membrane protein found mostly in the late Golgi; non-essential; can suppress some sed5 alleles; may be part of the transport machinery, but precise function is unknown; similar to mammalian syntaxin 5 | Core | NA | NA | NA |
| 1974-YBL103C | YBL103C | RTG3 | NA | bHLH/Zip transcription factor for retrograde (RTG) and TOR pathways; forms a complex with another bHLH/Zip protein, Rtg1p, to activate the pathways; target of Hog1p | Core | NA | NA | NA |
| 1975-YBL104C | YBL104C | SEA4 | YBL103C-A | Subunit of SEACAT, a subcomplex of the SEA complex; Sea4p, along with Rtc1p and Mtc5p, redundantly inhibit the TORC1 inhibitory role of the Iml1p/SEACIT (Iml1p-Npr2p-Npr3p) subcomplex, a GAP for GTPase Gtr1p (EGOC subunit) in response to amino acid limitation, thereby resulting in activation of TORC1 signaling; SEA is a coatomer-related complex that associates dynamically with the vacuole; contains an N-terminal beta-propeller fold and a C-terminal RING motif | Core | NA | NA | NA |
| 1976-YBL105C | YBL105C | PKC1 | protein kinase C|CLY7|CLY5|STT1|HPO2|CLY15 | Protein serine/threonine kinase; essential for cell wall remodeling during growth; localized to sites of polarized growth and the mother-daughter bud neck; homolog of the alpha, beta, and gamma isoforms of mammalian protein kinase C (PKC) | Core | NA | NA | NA |
| 1977-YBL106C | YBL106C | SRO77 | putative Rab GTPase-binding protein SRO77|SNI2|SOP2 | Protein with roles in exocytosis and cation homeostasis; functions in docking and fusion of post-Golgi vesicles with plasma membrane; regulates cell proliferation and colony development via the Rho1-Tor1 pathway; interacts with SNARE protein Sec9p; homolog of Drosophila lethal giant larvae tumor suppressor; SRO77 has a paralog, SRO7, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1978-YBL107C | YBL107C | MIX23 | MIC23 | Mitochondrial intermembrane space protein of unknown function; imported via the MIA import machinery; contains an unusual twin cysteine motif (CX13C CX14C) | Core | NA | NA | NA |
| 1979-YBL108C-A_NumOfGenes_18 | YBL108C-A | PAU9 | seripauperin PAU9 | Protein of unknown function; member of the seripauperin multigene family encoded mainly in subtelomeric regions; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum and vacuole respectively | Core | NA | NA | NA |
| 1980-YBL108W | YBL108W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Unknown | S. mikatae | NA |
| 1981-YBL109W | YBL109W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Unknown | S. paradoxus | NA |
| 1982-YBR001C | YBR001C | NTH2 | alpha,alpha-trehalase NTH2 | Putative neutral trehalase, required for thermotolerance; may mediate resistance to other cellular stresses; NTH2 has a paralog, NTH1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1983-YBR002C | YBR002C | RER2 | ditrans,polycis-polyprenyl diphosphate synthase | Forms the dehydrodolichyl diphosphate syntase (DDS) complex with NUS1; major enzyme of polyprenol synthesis in both the endoplasmic reticulum (ER) and in lipid droplets; participates in ER protein sorting; human ortholog DHDDS functionally complements the heat sensitive growth defect of a ts allele, and is associated with retinitis pigmentosa | Core | NA | NA | NA |
| 1984-YBR003W | YBR003W | COQ1 | trans-hexaprenyltranstransferase | Hexaprenyl pyrophosphate synthetase; catalyzes the first step in ubiquinone (coenzyme Q) biosynthesis | Core | NA | NA | NA |
| 1985-YBR004C | YBR004C | GPI18 | GPI-anchor transamidase GPI18|FMP44 | Functional ortholog of human PIG-V; PIG-V is a mannosyltransferase that transfers the second mannose in glycosylphosphatidylinositol biosynthesis; the authentic, non-tagged protein was localized to mitochondria | Core | NA | NA | NA |
| 1986-YBR005W | YBR005W | RCR1 | SSH6 | Protein of the ER membrane involved in cell wall chitin deposition; may function in the endosomal-vacuolar trafficking pathway, helping determine whether plasma membrane proteins are degraded or routed to the plasma membrane; RCR1 has a paralog, RCR2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1987-YBR006W | YBR006W | UGA2 | succinate-semialdehyde dehydrogenase (NAD(P)(+))|UGA5 | Succinate semialdehyde dehydrogenase; involved in the utilization of gamma-aminobutyrate (GABA) as a nitrogen source; part of the 4-aminobutyrate and glutamate degradation pathways; localized to the cytoplasm | Core | NA | NA | NA |