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 |
|---|---|---|---|---|---|---|---|---|
| 1838-YAL064W-B | YAL064W-B | NA | NA | Fungal-specific protein of unknown function | Accessory | Ancestral | NA | NA |
| 1839-YAL065C_NumOfGenes_2 | YAL065C | NA | NA | Putative protein of unknown function; shows sequence similarity to FLO1 and other flocculins | Accessory | Ancestral | NA | NA |
| 1840-YAL066W | YAL066W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Unknown | NA | NA |
| 1841-YAL067C | YAL067C | SEO1 | putative permease SEO1 | Putative permease; member of the allantoate transporter subfamily of the major facilitator superfamily; mutation confers resistance to ethionine sulfoxide | Accessory | Ancestral | NA | NA |
| 1842-YAL068W-A | YAL068W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching | Accessory | Ancestral | NA | NA |
| 1843-YAL069W | YAL069W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 1844-YAR002C-A | YAR002C-A | ERP1 | NA | Member of the p24 family involved in ER to Golgi transport; role in misfolded protein quality control; forms heterotrimeric complex with Erp2p, Emp24p, and Erv25p; localized to COPII-coated vesicles; ERP1 has a paralog, ERP6, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1845-YAR002W | YAR002W | NUP60 | FG-nucleoporin NUP60 | 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 and is involved in gene tethering at the nuclear periphery; relocalizes to the cytosol in response to hypoxia; both NUP1 and NUP60 are homologous to human NUP153 | Core | NA | NA | NA |
| 1846-YAR003W | YAR003W | SWD1 | COMPASS subunit protein SWD1|SAF49|CPS50|FUN16 | Subunit of the COMPASS (Set1C) complex; COMPASS methylates histone H3 on lysine 4 and is required in transcriptional silencing near telomeres; WD40 beta propeller superfamily member with similarity to mammalian Rbbp7 | Core | NA | NA | NA |
| 1847-YAR007C | YAR007C | RFA1 | replication factor A subunit protein RFA1|RPA70|RPA1|FUN3|BUF2 | Subunit of heterotrimeric Replication Protein A (RPA); RPA is a highly conserved single-stranded DNA binding protein involved in DNA replication, repair, and recombination; RPA protects against inappropriate telomere recombination, and upon telomere uncapping, prevents cell proliferation by a checkpoint-independent pathway; role in DNA catenation/decatenation pathway of chromosome disentangling; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 1848-YAR008W | YAR008W | SEN34 | tRNA splicing endonuclease subunit SEN34|FUN4 | Subunit of the tRNA splicing endonuclease; tRNA splicing endonuclease (Sen complex) is composed of Sen2p, Sen15p, Sen34p, and Sen54p; Sen complex also cleaves the CBP1 mRNA at the mitochondrial surface; Sen34p contains the active site for tRNA 3' splice site cleavage and has similarity to Sen2p and to Archaeal tRNA splicing endonuclease | Core | NA | NA | NA |
| 1849-YAR014C | YAR014C | BUD14 | protein phosphatase regulator BUD14 | Protein involved in bud-site selection; Bud14p-Glc7p complex is a cortical regulator of dynein; forms a complex with Kel1p and Kel2p that regulates Bnr1p (formin) to affect actin cable assembly, cytokinesis, and polarized growth; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 1850-YAR015W | YAR015W | ADE1 | phosphoribosylaminoimidazolesuccinocarboxamide synthase | N-succinyl-5-aminoimidazole-4-carboxamide ribotide synthetase; required for 'de novo' purine nucleotide biosynthesis; red pigment accumulates in mutant cells deprived of adenine; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 1851-YAR018C | YAR018C | KIN3 | serine/threonine protein kinase KIN3|NPK1|FUN52 | Nonessential serine/threonine protein kinase; possible role in DNA damage response; influences tolerance to high levels of ethanol | Core | NA | NA | NA |
| 1852-YAR019C | YAR019C | CDC15 | serine/threonine protein kinase CDC15|LYT1 | Protein kinase of the Mitotic Exit Network; localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p; required for spindle disassembly after meiosis II; relocalizes to the cytoplasm upon DNA replication stress | Core | NA | NA | NA |