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 |
|---|---|---|---|---|---|---|---|---|
| 5978-YML058W | YML058W | SML1 | ribonucleotide reductase inhibiting protein SML1 | Ribonucleotide reductase inhibitor; involved in regulating dNTP production; regulated by Mec1p and Rad53p during DNA damage and S phase; SML1 has a paralog, DIF1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5979-YML058W-A | YML058W-A | HUG1 | NA | Ribonucleotide reductase inhibitor; intrinsically disordered protein that binds to and inhibits Rnr2p; involved in the Mec1p-mediated checkpoint pathway; transcription is induced by genotoxic stress and by activation of the Rad53p pathway; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5980-YML059C | YML059C | NTE1 | lysophospholipase | Serine esterase; homolog of human neuropathy target esterase (NTE); Nte1p-mediated phosphatidylcholine turnover influences transcription factor Opi1p localization, affecting transcriptional regulation of phospholipid biosynthesis genes | Core | NA | NA | NA |
| 5981-YML060W | YML060W | OGG1 | 8-oxoguanine glycosylase OGG1 | Nuclear and mitochondrial glycosylase/lyase; specifically excises 7,8-dihydro-8-oxoguanine residues located opposite cytosine or thymine residues in DNA, repairs oxidative damage to mitochondrial DNA, contributes to UVA resistance | Core | NA | NA | NA |
| 5982-YML061C | YML061C | PIF1 | DNA helicase PIF1|TST1 | DNA helicase, potent G-quadruplex DNA binder/unwinder; possesses strand annealing activity; promotes DNA synthesis during break-induced replication; important for crossover recombination; translation from different start sites produces mitochondrial and nuclear forms; nuclear form is a catalytic inhibitor of telomerase; mitochondrial form involved in DNA repair and recombination; mutations affect Zn, Fe homeostasis; regulated by Rad53p-dependent phosphorylation in rho0 cells | Core | NA | NA | NA |
| 5983-YML062C | YML062C | MFT1 | MFT52 | Subunit of the THO complex; THO is a nuclear complex comprised of Hpr1p, Mft1p, Rlr1p, and Thp2p, that is involved in transcription elongation and mitotic recombination; involved in telomere maintenance | Core | NA | NA | NA |
| 5984-YML063W | YML063W | RPS1B | eS1|ribosomal 40S subunit protein S1B|S1e|rp10B|S1B|RP10B|PLC2 | Ribosomal protein 10 (rp10) of the small (40S) subunit; homologous to mammalian ribosomal protein S3A, no bacterial homolog; RPS1B has a paralog, RPS1A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5985-YML064C | YML064C | TEM1 | Ras family GTPase TEM1 | GTP-binding protein of the Ras superfamily; involved in termination of M-phase; controls actomyosin and septin dynamics during cytokinesis | Core | NA | NA | NA |
| 5986-YML065W | YML065W | ORC1 | origin recognition complex subunit 1 | Largest subunit of the origin recognition complex; involved in directing DNA replication by binding to replication origins; also involved in transcriptional silencing; exhibits ATPase activity; ORC1 has a paralog, SIR3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5987-YML066C | YML066C | SMA2 | NA | Meiosis-specific prospore membrane protein; required to produce bending force necessary for proper assembly of the prospore membrane during sporulation | Core | NA | NA | NA |
| 5988-YML067C | YML067C | ERV41 | NA | Protein localized to COPII-coated vesicles; forms a complex with Erv46p; involved in the membrane fusion stage of transport; has homology to human ERGIC2 (PTX1) protein | Core | NA | NA | NA |
| 5989-YML068W | YML068W | ITT1 | NA | Protein that modulates the efficiency of translation termination; interacts with translation release factors eRF1 (Sup45p) and eRF3 (Sup35p) in vitro, contains a zinc finger domain characteristic of the TRIAD class of proteins | Core | NA | NA | NA |
| 5990-YML069W | YML069W | POB3 | FACT complex subunit POB3 | Subunit of the heterodimeric FACT complex (Spt16p-Pob3p); FACT associates with chromatin via interaction with Nhp6Ap and Nhp6Bp, and reorganizes nucleosomes to facilitate access to DNA by RNA and DNA polymerases; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5991-YML070W | YML070W | DAK1 | dihydroxyacetone kinase | Dihydroxyacetone kinase; required for detoxification of dihydroxyacetone (DHA); involved in stress adaptation | Core | NA | NA | NA |
| 5992-YML071C | YML071C | COG8 | Golgi transport complex subunit COG8|DOR1 | Component of the conserved oligomeric Golgi complex; a cytosolic tethering complex (Cog1p through Cog8p) that functions in protein trafficking to mediate fusion of transport vesicles to Golgi compartments | Core | NA | NA | NA |