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 |
|---|---|---|---|---|---|---|---|---|
| 2633-YDL188C | YDL188C | PPH22 | phosphoprotein phosphatase 2A catalytic subunit PPH22|PPH2 | Catalytic subunit of protein phosphatase 2A (PP2A); functionally redundant with Pph21p; methylated at C terminus; forms alternate complexes with several regulatory subunits; involved in signal transduction and regulation of mitosis; protein abundance increases in response to DNA replication stress; dephosphorylates Tel1p/Mec1p-phosphorylated Cdc13p to promote telomerase release from telomeres at G2/M; PPH22 has a paralog, PPH21, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2634-YDL189W | YDL189W | RBS1 | NA | Protein involved in assembly of the RNA polymerase III (Pol III) complex; high copy suppressor of Pol III assembly mutation and psk1 psk2 mutations that confer temperature-sensitivity for galactose utilization; physically interacts with Pol III; proposed to bind single-stranded nucleic acids via its R3H domain | Core | NA | NA | NA |
| 2635-YDL190C | YDL190C | UFD2 | ubiquitin-ubiquitin ligase UFD2 | Ubiquitin chain assembly factor (E4); cooperates with a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin protein ligase (E3) to conjugate ubiquitin to substrates; also functions as an E3 | Core | NA | NA | NA |
| 2636-YDL191W | YDL191W | RPL35A | uL29|ribosomal 60S subunit protein L35A|L35A|L29|SOS1 | Ribosomal 60S subunit protein L35A; homologous to mammalian ribosomal protein L35 and bacterial L29; RPL35A has a paralog, RPL35B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2637-YDL192W | YDL192W | ARF1 | Arf family GTPase ARF1 | ADP-ribosylation factor; GTPase of the Ras superfamily involved in regulation of coated vesicle formation in intracellular trafficking within the Golgi; ARF1 has a paralog, ARF2, that arose from the whole genome duplication; arf1 arf2 double null mutation is complemented by human ARF1, ARF4, ARF5, or ARF6 | Core | NA | NA | NA |
| 2638-YDL193W | YDL193W | NUS1 | ditrans,polycis-polyprenyl diphosphate synthase | Forms dehydrodolichyl diphosphate syntase complex with RER2 or SRT1; tet-repressible mutant shows accumulation of hypoglycosylated forms of CPY, suggesting that Nus1p may be involved in protein trafficking; mutations in human homolog NUS1 have been implicated in congenital scoliosis, neurological impairment, refractory epilepsy, hearing deficit, and visual impairment; human cis-prenyltransferase complex complements yeast null mutant | Core | NA | NA | NA |
| 2639-YDL194W | YDL194W | SNF3 | glucose sensor | Plasma membrane low glucose sensor, regulates glucose transport; high affinity sensor that contains 12 predicted transmembrane segments and a long C-terminal tail required for induction of hexose transporters; also senses fructose and mannose; SNF3 has a paralog, RGT2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2640-YDL195W | YDL195W | SEC31 | WEB1 | Component of the Sec13p-Sec31p complex of the COPII vesicle coat; COPII coat is required for vesicle formation in ER to Golgi transport; mutant has increased aneuploidy tolerance | Core | NA | NA | NA |
| 2641-YDL196W | YDL196W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; open reading frame is located in promoter region of essential gene SEC31 | Core | NA | NA | NA |
| 2642-YDL197C | YDL197C | ASF2 | NA | Anti-silencing protein; causes derepression of silent loci when overexpressed | Core | NA | NA | NA |
| 2643-YDL198C | YDL198C | GGC1 | SHM1|YHM1 | Mitochondrial GTP/GDP transporter; essential for mitochondrial genome maintenance; has a role in mitochondrial iron transport; member of the mitochondrial carrier family | Core | NA | NA | NA |
| 2644-YDL199C | YDL199C | NA | NA | Putative transporter; member of the sugar porter family | Core | NA | NA | NA |
| 2645-YDL200C | YDL200C | MGT1 | methylated-DNA--protein-cysteine methyltransferase|MGMT | DNA repair methyltransferase (6-O-methylguanine-DNA methylase); involved in protection against DNA alkylation damage | Core | NA | NA | NA |
| 2646-YDL201W | YDL201W | TRM8 | tRNA (guanine46-N7)-methyltransferase | Noncatalytic subunit of a tRNA methyltransferase complex; Trm8p and Trm82p comprise an enzyme that catalyzes a methyl-transfer from S-adenosyl-l-methionine to the N(7) atom of guanine at position 46 in tRNA; Trm8 lacks catalytic activity if not bound to Trm82p | Core | NA | NA | NA |
| 2647-YDL202W | YDL202W | MRPL11 | mitochondrial 54S ribosomal protein YmL11|YmL11 | Mitochondrial ribosomal protein of the large subunit; localizes to vacuole in response to H2O2 | Core | NA | NA | NA |