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 |
|---|---|---|---|---|---|---|---|---|
| 6923-YOL125W | YOL125W | TRM13 | tRNA:m4X modification enzyme | 2'-O-methyltransferase; responsible for modification of tRNA at position 4; C-terminal domain has similarity to Rossmann-fold (RFM) superfamily of RNA methyltransferases | Core | NA | NA | NA |
| 6924-YOL126C | YOL126C | MDH2 | malate dehydrogenase MDH2 | Cytoplasmic malate dehydrogenase; one of three isozymes that catalyze interconversion of malate and oxaloacetate; involved in the glyoxylate cycle and gluconeogenesis during growth on two-carbon compounds; interacts with Pck1p and Fbp1 | Core | NA | NA | NA |
| 6925-YOL127W | YOL127W | RPL25 | uL23|ribosomal 60S subunit protein L25|L23|rpl6L|YL25|L25 | Ribosomal 60S subunit protein L25; primary rRNA-binding ribosomal protein component of large ribosomal subunit; binds to 25S rRNA via a conserved C-terminal motif; homologous to mammalian ribosomal protein L23A and bacterial L23 | Core | NA | NA | NA |
| 6926-YOL128C | YOL128C | YGK3 | serine/threonine protein kinase YGK3 | Protein kinase related to mammalian GSK-3 glycogen synthase kinases; GSK-3 homologs (Mck1p, Rim11p, Mrk1p, Ygk3p) are involved in control of Msn2p-dependent transcription of stress responsive genes and in protein degradation; YGK3 has a paralog, MCK1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6927-YOL129W | YOL129W | VPS68 | NA | Vacuolar membrane protein of unknown function; involved in vacuolar protein sorting; also detected in the mitochondria | Accessory | Ancestral | NA | NA |
| 6928-YOL130W | YOL130W | ALR1 | Mg(2+) transporter ALR1|SWC3 | Plasma membrane Mg(2+) transporter; expression and turnover are regulated by Mg(2+) concentration; overexpression confers increased tolerance to Al(3+) and Ga(3+) ions; magnesium transport defect of the null mutant is functionally complemented by either of the human genes MAGT1 and TUSC3 that are not orthologous to ALR1 | Core | NA | NA | NA |
| 6929-YOL131W | YOL131W | NA | NA | Putative protein of unknown function; YOL131W has a paralog, STB1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6930-YOL132W_NumOfGenes_2 | YOL132W | GAS4 | 1,3-beta-glucanosyltransferase | 1,3-beta-glucanosyltransferase; involved with Gas2p in spore wall assembly; has similarity to Gas1p; localizes to the cell wall | Core | NA | NA | NA |
| 6931-YOL133W_NumOfGenes_2 | YOL133W | HRT1 | SCF ubiquitin ligase complex subunit HRT1|HRT2|ROC1|RBX1 | RING-H2 domain core subunit of multiple ubiquitin ligase complexes; subunit of Skp1-Cullin-F-box (SCF) that tethers the Cdc34p (E2) and Cdc53p (cullin) SCF subunits, and is required for degradation of Gic2p, Far1p, Sic1p and Cln2p; subunit of the Rtt101p-Mms1p-Mms22p ubiquitin ligase that stabilizes replication forks after DNA lesions; subunit of the Cul3p-Elc1p-Ela1p ubiquitin ligase involved in Rpb1p degradation as part of transcription-coupled repair | Accessory | Ancestral | NA | NA |
| 6932-YOL134C | YOL134C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps HRT1, a verified gene that encodes an SCF ubiquitin ligase subunit | Accessory | Ancestral | NA | NA |
| 6933-YOL135C_NumOfGenes_2 | YOL135C | MED7 | mediator complex subunit MED7 | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation | Core | NA | NA | NA |
| 6934-YOL136C | YOL136C | PFK27 | 6-phosphofructo-2-kinase|PFK-2 | 6-phosphofructo-2-kinase; catalyzes synthesis of fructose-2,6-bisphosphate; inhibited by phosphoenolpyruvate and sn-glycerol 3-phosphate, expression induced by glucose and sucrose, transcriptional regulation involves protein kinase A | Accessory | Ancestral | NA | NA |
| 6935-YOL137W | YOL137W | BSC6 | NA | Protein of unknown function with 8 putative transmembrane segments; ORF exhibits genomic organization compatible with a translational readthrough-dependent mode of expression | Core | NA | NA | NA |
| 6936-YOL138C | YOL138C | RTC1 | SEA2 | Subunit of SEACAT, a subcomplex of the SEA complex; Rtc1p, along with Mtc5p and Sea4p, 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; has N-terminal WD-40 repeats and a C-terminal RING motif; null suppresses cdc13-1 | Core | NA | NA | NA |
| 6937-YOL139C_NumOfGenes_2 | YOL139C | CDC33 | translation initiation factor eIF4E|eIF4E|TIF45 | mRNA cap binding protein and translation initiation factor eIF4E; the eIF4E-cap complex is responsible for mediating cap-dependent mRNA translation via interactions with translation initiation factor eIF4G (Tif4631p or Tif4632p); protein abundance increases in response to DNA replication stress; mutants are defective for adhesion and pseudohyphal growth; human homolog EIF4E can complement yeast cdc33 null mutant | Core | NA | NA | NA |