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 |
|---|---|---|---|---|---|---|---|---|
| 5378-YKR086W | YKR086W | PRP16 | DEAH-box RNA helicase PRP16|PRP23|RNA16 | DEAH-box RNA helicase involved in second catalytic step of splicing and in exon ligation; exhibits ATP-dependent RNA unwinding activity; mediates the release of Yju2p and Cwc25p in the second step; in the absence of ATP, stabilizes the binding of Cwc25p to the spliceosome in the first catalytic step; missense mutation in human ortholog DHX38 associated with early-onset retinitis pigmentosa | Core | NA | NA | NA |
| 5379-YKR087C | YKR087C | OMA1 | metalloendopeptidase | Metalloendopeptidase of the mitochondrial inner membrane; important for adaptive responses to various homeostatic insults, preservation of normal mitochondrial function under damage-eliciting conditions, and stability of respiratory supercomplexes; involved in turnover of membrane-embedded proteins; mediates degradation of Cox1p in coa2 mutant cells; zebrafish ortholog has a role in organ development and mouse ortholog is also required for respiratory supercomplex stability | Core | NA | NA | NA |
| 5380-YKR088C | YKR088C | TVP38 | NA | Integral membrane protein; localized to late Golgi vesicles along with the v-SNARE Tlg2p; required for asymmetric localization of Kar9p during mitosis; GFP-fusion protein localizes to the cytoplasm in a punctate pattern | Core | NA | NA | NA |
| 5381-YKR089C | YKR089C | TGL4 | STC1 | Multifunctional lipase/hydrolase/phospholipase; triacylglycerol lipase, steryl ester hydrolase, and Ca2+-independent phospholipase A2; catalyzes acyl-CoA dependent acylation of LPA to PA; required with Tgl3p for timely bud formation; phosphorylated and activated by Cdc28p; TGL4 has a paralog, TGL5, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5382-YKR090W | YKR090W | PXL1 | NA | Protein that localizes to sites of polarized growth; required for selection and/or maintenance of polarized growth sites, may modulate signaling by the GTPases Cdc42p and Rho1p; contains LIM domains and has similarity to metazoan paxillin; relocalizes from bud neck to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 5383-YKR091W | YKR091W | SRL3 | DNA-binding protein SRL3|WHI7 | GTB motif (G1/S transcription factor binding) containing protein; binds SBF-regulated promoters in hydroxyurea-treated cells; when overexpressed, suppresses the lethality of a rad53 null mutation; potential Cdc28p substrate; SRL3 has a paralog, WHI5, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5384-YKR092C | YKR092C | SRP40 | NA | Nucleolar serine-rich protein; role in preribosome assembly or transport; may function as a chaperone of small nucleolar ribonucleoprotein particles (snoRNPs); immunologically and structurally to rat Nopp140 | Core | NA | NA | NA |
| 5385-YKR093W | YKR093W | PTR2 | NA | Integral membrane peptide transporter; mediates transport of di- and tri-peptides; conserved protein that contains 12 transmembrane domains; PTR2 expression is regulated by the N-end rule pathway via repression by Cup9p | Core | NA | NA | NA |
| 5386-YKR094C | YKR094C | RPL40B | eL40|ubiquitin-ribosomal 60S subunit protein L40B fusion protein|L40e|L40B|UB12|CEP52B|UBI2 | Ubiquitin-ribosomal 60S subunit protein L40B fusion protein; cleaved to yield ubiquitin and ribosomal protein L40B; ubiquitin may facilitate assembly of the ribosomal protein into ribosomes; homologous to mammalian ribosomal protein L40, no bacterial homolog; RPL40B has a paralog, RPL40A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5387-YKR095W | YKR095W | MLP1 | MPL1 | Myosin-like protein associated with the nuclear envelope; nuclear basket protein that connects the nuclear pore complex with the nuclear interior; involved with Tel1p in telomere length control; involved with Pml1p and Pml39p in nuclear retention of unspliced mRNAs; MLP1 has a paralog, MLP2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5388-YKR095W-A | YKR095W-A | PCC1 | chromatin DNA-binding EKC/KEOPS complex subunit PCC1 | Component of the EKC/KEOPS protein complex; EKC/KEOPS complex is required for t6A tRNA modification and telomeric TG1-3 recombination; may have role in transcription; other complex members are Kae1p, Gon7p, Bud32p, and Cgi121p | Core | NA | NA | NA |
| 5389-YKR096W | YKR096W | ESL2 | NA | hEST1A/B (SMG5/6)-like protein; contributes to environment-sensing adaptive gene expression responses; Esl2p and Esl1p contain a 14-3-3-like domain and a putative PilT N-terminus ribonuclease domain; interacts with Pex14p; may interact with ribosomes, based on co-purification experiments; green fluorescent protein (GFP)-fusion protein localizes to the nucleus and cytoplasm; ESL2 has a paralog, ESL1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5390-YKR097W | YKR097W | PCK1 | phosphoenolpyruvate carboxykinase PCK1|PPC1|JPM2 | Phosphoenolpyruvate carboxykinase; key enzyme in gluconeogenesis, catalyzes early reaction in carbohydrate biosynthesis, glucose represses transcription and accelerates mRNA degradation, regulated by Mcm1p and Cat8p, located in the cytosol | Core | NA | NA | NA |
| 5391-YKR098C | YKR098C | UBP11 | ubiquitin-specific protease UBP11 | Ubiquitin-specific protease; cleaves ubiquitin from ubiquitinated proteins; UBP11 has a paralog, UBP7, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5392-YKR099W | YKR099W | BAS1 | NA | Myb-related transcription factor; involved in regulating basal and induced expression of genes of the purine and histidine biosynthesis pathways; also involved in regulation of meiotic recombination at specific genes | Core | NA | NA | NA |