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 |
|---|---|---|---|---|---|---|---|---|
| 2093-YBR110W | YBR110W | ALG1 | chitobiosyldiphosphodolichol beta-1,4 mannosyltransferase | Mannosyltransferase; involved in asparagine-linked glycosylation in the endoplasmic reticulum (ER); essential for viability; human homolog ALG1 complements yeast null mutant | Core | NA | NA | NA |
| 2094-YBR111C | YBR111C | YSA1 | ADP-ribose diphosphatase|RMA2 | Nudix hydrolase family member with ADP-ribose pyrophosphatase activity; shown to metabolize O-acetyl-ADP-ribose to AMP and acetylated ribose 5'-phosphate | Core | NA | NA | NA |
| 2095-YBR111W-A | YBR111W-A | SUS1 | NA | Component of both the SAGA histone acetylase and TREX-2 complexes; interacts with RNA polymerase II; involved in mRNA export coupled transcription activation and elongation; involved in post-transcriptional tethering of active genes to the nuclear periphery and to non-nascent mRNP | Core | NA | NA | NA |
| 2096-YBR112C | YBR112C | CYC8 | transcription regulator CYC8|[OCT]|[OCT1+]|SSN6|CRT8 | General transcriptional co-repressor; acts together with Tup1p; also acts as part of a transcriptional co-activator complex that recruits the SWI/SNF and SAGA complexes to promoters; can form the prion [OCT+] | Core | NA | NA | NA |
| 2097-YBR113W | YBR113W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene CYC8 | Accessory | Ancestral | NA | NA |
| 2098-YBR114W | YBR114W | RAD16 | DNA repair protein RAD16|PSO5 | Nucleotide excision repair (NER) protein; binds damaged DNA during NER; binds DNA in an ATP-dependent manner (with Rad7p) during NER; required for NER of non-transcribed chromatin; subunit of Nucleotide Excision Repair Factor 4 (NEF4) and the Elongin-Cullin-Socs (ECS) ligase complex | Core | NA | NA | NA |
| 2099-YBR115C | YBR115C | LYS2 | L-aminoadipate-semialdehyde dehydrogenase | Alpha aminoadipate reductase; catalyzes the reduction of alpha-aminoadipate to alpha-aminoadipate 6-semialdehyde, which is the fifth step in biosynthesis of lysine; activation requires posttranslational phosphopantetheinylation by Lys5p | Core | NA | NA | NA |
| 2100-YBR116C | YBR116C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene TKL2 | Accessory | Ancestral | NA | NA |
| 2101-YBR117C | YBR117C | TKL2 | transketolase TKL2 | Transketolase; catalyzes conversion of xylulose-5-phosphate and ribose-5-phosphate to sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate in the pentose phosphate pathway; needed for synthesis of aromatic amino acids; TKL2 has a paralog, TKL1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2102-YBR119W | YBR119W | MUD1 | U1A|U1-A | U1 snRNP A protein; homolog of human U1-A; involved in nuclear mRNA splicing | Core | NA | NA | NA |
| 2103-YBR120C | YBR120C | CBP6 | NA | Mitochondrial protein required for translation of the COB mRNA; forms a complex with Cbp3p that binds to mt ribosomes near the polypeptide tunnel exit and promotes efficient translation of the COB mRNA; Cbp3p-Cbp6p complex also interacts with newly synthesized cytochrome b (Cobp) and Cbp4p to promote assembly of Cobp into the cytochrome bc1 complex; Cbp3p-Cbp6p complex is sequestered if assembly of Complex III is blocked, downregulating COB mRNA translation | Core | NA | NA | NA |
| 2104-YBR121C_NumOfGenes_2 | YBR121C | GRS1 | glycine--tRNA ligase | Cytoplasmic and mitochondrial glycyl-tRNA synthase; ligates glycine to the cognate anticodon-bearing tRNA; transcription termination factor that may interact with the 3'-end of pre-mRNA to promote 3'-end formation; GRS1 has a paralog, GRS2, that arose from the whole genome duplication; human homolog GARS implicated in Charcot-Marie-Tooth disease, can complement yeast null mutant | Core | NA | NA | NA |
| 2105-YBR122C | YBR122C | MRPL36 | mitochondrial 54S ribosomal protein YmL36|YmL36 | Mitochondrial ribosomal protein of the large subunit; overproduction suppresses mutations in the COX2 leader peptide-encoding region | Core | NA | NA | NA |
| 2106-YBR123C | YBR123C | TFC1 | transcription factor TFIIIC subunit TFC1|tau 95 | Subunit of RNA polymerase III transcription initiation factor complex; one of six subunits of the RNA polymerase III transcription initiation factor complex (TFIIIC); part of the TauA globular domain of TFIIIC that binds DNA at the BoxA promoter sites of tRNA and similar genes; human homolog is TFIIIC-63 | Core | NA | NA | NA |
| 2107-YBR124W | YBR124W | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |