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 |
|---|---|---|---|---|---|---|---|---|
| 3803-YGL161C | YGL161C | YIP5 | NA | Protein that interacts with Rab GTPases; localized to late Golgi vesicles; computational analysis of large-scale protein-protein interaction data suggests a possible role in vesicle-mediated transport | Core | NA | NA | NA |
| 3804-YGL162W | YGL162W | SUT1 | NA | Zn(II)2Cys6 family transcription factor; positively regulates sterol uptake genes under anaerobic conditions; involved in hypoxic gene expression; represses filamentation-inducing genes during vegetative growth; positively regulates mating with SUT2 by repressing expression of genes that act as mating inhibitors; repressed by STE12; relocalizes from the nucleus to the cytoplasm upon DNA replication stress; SUT1 has a paralog, SUT2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3805-YGL163C | YGL163C | RAD54 | DNA-dependent ATPase RAD54|XRS1 | DNA-dependent ATPase that stimulates strand exchange; modifies the topology of double-stranded DNA; involved in the recombinational repair of double-strand breaks in DNA during vegetative growth and meiosis; member of the SWI/SNF family of DNA translocases; forms nuclear foci upon DNA replication stress | Core | NA | NA | NA |
| 3806-YGL164C | YGL164C | YRB30 | NA | RanGTP-binding protein; inhibits RanGAP1 (Rna1p)-mediated GTP hydrolysis of RanGTP (Gsp1p); shares similarity to proteins in other fungi but not in higher eukaryotes | Core | NA | NA | NA |
| 3807-YGL165C | YGL165C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF CUP2/YGL166W | Accessory | Unknown | NA | NA |
| 3808-YGL166W | YGL166W | CUP2 | ACE1 | Copper-binding transcription factor; activates transcription of the metallothionein genes CUP1-1 and CUP1-2 in response to elevated copper concentrations; required for regulation of copper genes in response to DNA-damaging reagents; CUP2 has a paralog, HAA1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3809-YGL167C | YGL167C | PMR1 | Ca(2+)/Mn(2+)-transporting P-type ATPase PMR1|SSC1|LDB1|BSD1 | High affinity Ca2+/Mn2+ P-type ATPase; required for Ca2+ and Mn2+ transport into Golgi; involved in Ca2+ dependent protein sorting, processing; D53A mutant (Mn2+ transporting) is rapamycin sensitive, Q783A mutant (Ca2+ transporting) is rapamycin resistant; Mn2+ transport into Golgi lumen required for rapamycin sensitivity; mutations in human homolog ATP2C1 cause acantholytic skin condition Hailey-Hailey disease; human ATP2C1 can complement yeast null mutant | Core | NA | NA | NA |
| 3810-YGL168W | YGL168W | HUR1 | NA | Protein of unknown function; reported null mutant phenotype of hydroxyurea sensitivity may be due to effects on overlapping PMR1 gene | Core | NA | NA | NA |
| 3811-YGL169W | YGL169W | SUA5 | threonylcarbamoyladenylate synthase | Protein involved in threonylcarbamoyl adenosine biosynthesis; Sua5p and Qri7p are necessary and sufficient for RNA t6A modification in vitro; null mutant lacks N6-threonylcarbamoyl adenosine (t6A) modification in the anticodon loop of ANN-decoding tRNA; member of conserved YrdC/Sua5 family; binds single-stranded telomeric DNA and null mutant has abnormal telomere length | Core | NA | NA | NA |
| 3812-YGL170C | YGL170C | SPO74 | NA | Component of the meiotic outer plaque of the spindle pole body; involved in modifying the meiotic outer plaque that is required prior to prospore membrane formation | Core | NA | NA | NA |
| 3813-YGL171W | YGL171W | ROK1 | RNA-dependent ATPase ROK1 | RNA-dependent ATPase; involved in pre-rRNA processing at sites A0, A1, and A2, and in control of cell cycle progression; contains two upstream open reading frames (uORFs) in 5' untranslated region which regulate translation | Core | NA | NA | NA |
| 3814-YGL172W | YGL172W | NUP49 | FG-nucleoporin NUP49|NSP49 | FG-nucleoporin component of central core of the nuclear pore complex; contributes directly to nucleocytoplasmic transport and maintenance of the nuclear pore complex (NPC) permeability barrier; found in stable complex with Nic96p and two other FG-nucleoproteins (Nsp1p and Nup57p) | Core | NA | NA | NA |
| 3815-YGL173C | YGL173C | XRN1 | chromatin-binding exonuclease XRN1|KEM1|SKI1|SEP1|RAR5|DST2 | Evolutionarily-conserved 5'-3' exonuclease; component of cytoplasmic processing (P) bodies involved in mRNA decay; also enters the nucleus and positively regulates transcription initiation and elongation; plays a role in microtubule-mediated processes, filamentous growth, ribosomal RNA maturation, and telomere maintenance; activated by the scavenger decapping enzyme Dcs1p | Core | NA | NA | NA |
| 3816-YGL174W | YGL174W | BUD13 | CWC26 | Subunit of the RES complex; RES complex is required for nuclear pre-mRNA retention and splicing; involved in bud-site selection; diploid mutants display a unipolar budding pattern instead of the wild-type bipolar pattern due to a specific defect in MATa1 pre-mRNA splicing which leads to haploid gene expression in diploids | Core | NA | NA | NA |
| 3817-YGL175C | YGL175C | SAE2 | ssDNA endodeoxyribonuclease SAE2|COM1 | Endonuclease required for telomere elongation; required for telomeric 5' C-rich strand resection; involved in ds-break repair and processing hairpin DNA structures with the MRX complex; function requires sumoylation and phosphorylation; exists as inactive oligomers that are transiently released into smaller active units by phosphorylation; DNA damage triggers Sae2p removal, so active Sae2p is present only transiently; sequence and functional similarity with human CtIP/RBBP8 | Core | NA | NA | NA |