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 |
|---|---|---|---|---|---|---|---|---|
| 4733-YJL038C | YJL038C | LOH1 | OSW4 | Protein involved in outer spore wall assembly; likely involved directly in dityrosine layer assembly; induced during sporulation; repressed during vegetative growth by Sum1p and Hst1p; sequence similar to adjacent ORF, IRC18/YJL037W, and the irc18 loh1 double mutant exhibits reduced dityrosine fluorescence relative to the single mutants; SWAT-GFP and mCherry fusion proteins localize to the cytosol; proposed role in maintenance of genome integrity | Core | NA | NA | NA |
| 4734-YJL039C | YJL039C | NUP192 | NA | Essential subunit of inner ring of nuclear pore complex (NPC); plays a role in modulating transport through the NPC; homologous to human NUP205 | Core | NA | NA | NA |
| 4735-YJL041W | YJL041W | NSP1 | FG-nucleoporin NSP1 | FG-nucleoporin component of central core of the nuclear pore complex; also part of the nuclear pore complex (NPC) nuclear basket; contributes directly to nucleocytoplasmic transport and maintenance of the NPC permeability barrier; found in stable complex with Nup82p, Gle2p and two other FG-nucleoporins (Nup159p and Nup116p); also found in stable complex with Nic96p and two other FG-nucleoproteins (Nup49p and Nup57p) | Core | NA | NA | NA |
| 4736-YJL042W | YJL042W | MHP1 | NA | Microtubule-associated protein involved in microtubule organization; involved in assembly and stabilization of microtubules; overproduction results in cell cycle arrest at G2 phase; similar to Drosophila protein MAP and to mammalian MAP4 proteins | Core | NA | NA | NA |
| 4737-YJL043W | YJL043W | NA | NA | Putative protein of unknown function; YJL043W is a non-essential gene | Core | NA | NA | NA |
| 4738-YJL044C | YJL044C | GYP6 | NA | GTPase-activating protein (GAP) for yeast Rab family member Ypt6p; involved in vesicle mediated protein transport | Core | NA | NA | NA |
| 4739-YJL045W | YJL045W | NA | succinate dehydrogenase SDH1b|SDH1b | Minor succinate dehydrogenase isozyme; participates in oxidation of succinate and transfer of electrons to ubiquinone; induced during the diauxic shift in a Cat8p-dependent manner; YJL045W has a paralog, SDH1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4740-YJL046W | YJL046W | AIM22 | putative lipoate--protein ligase|RRG3|LIP3 | Putative lipoate-protein ligase; required along with Lip2 and Lip5 for lipoylation of Lat1p and Kgd2p; similar to E. coli LplA; null mutant displays reduced frequency of mitochondrial genome loss | Core | NA | NA | NA |
| 4741-YJL047C | YJL047C | RTT101 | cullin RTT101|CULC|CUL8 | Cullin subunit of a Roc1p-dependent E3 ubiquitin ligase complex; role in anaphase progression; required for recovery after DSB repair; implicated in Mms22-dependent DNA repair; involved with Mms1p in nonfunctional rRNA decay; modified by the ubiquitin-like protein, Rub1p | Core | NA | NA | NA |
| 4742-YJL047C-A | YJL047C-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 4743-YJL048C | YJL048C | UBX6 | CUI2 | UBX (ubiquitin regulatory X) domain-containing protein; interacts with Cdc48p, transcription is repressed when cells are grown in media containing inositol and choline; UBX6 has a paralog, UBX7, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4744-YJL049W | YJL049W | CHM7 | NA | Yeast homolog of human CHMP7, localizes to the endoplasmic reticulum presumably as part of an ESCRT-III like complex; null mutant has growth defect at 37 C in an apq12 deletion background; non-essential gene | Core | NA | NA | NA |
| 4745-YJL050W | YJL050W | MTR4 | ATP-dependent RNA helicase MTR4|DOB1 | ATP-dependent 3'-5' RNA helicase of the DExD/H family; involved in nuclear RNA processing and degradation both as a component of TRAMP complex and in TRAMP-independent processes; TRAMP unwinds RNA duplexes, with Mtr4p unwinding activity stimulated by Pap2p/Air2p but not dependent on ongoing polyadenylation; contains an arch domain, with two coiled-coil arms/stalks and a globular fist/KOW domain, which has RNA binding activity and is required for 5.8S rRNA processing | Core | NA | NA | NA |
| 4746-YJL051W | YJL051W | IRC8 | NA | Bud tip localized protein of unknown function; mRNA is targeted to the bud by a She2p dependent transport system; mRNA is cell cycle regulated via Fkh2p, peaking in G2/M phase; null mutant displays increased levels of spontaneous Rad52p foc | Core | NA | NA | NA |
| 4747-YJL052C-A | YJL052C-A | NA | NA | Putative protein of unknown function; identified based on comparison to related yeast species; mCherry fusion protein localizes to the vacuole | Core | NA | NA | NA |