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 |
|---|---|---|---|---|---|---|---|---|
| 3683-YGL036W | YGL036W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YGL036W is not an essential gene | Accessory | Ancestral | NA | NA |
| 3684-YGL037C | YGL037C | PNC1 | nicotinamidase | Nicotinamidase that converts nicotinamide to nicotinic acid; part of the NAD(+) salvage pathway; required for life span extension by calorie restriction; lacks a peroxisomal targeting signal but is imported into peroxisomes via binding to Gpd1p; PNC1 expression responds to all known stimuli that extend replicative life span; protein increases in abundance and relative distribution to cytoplasmic foci decreases upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 3685-YGL038C | YGL038C | OCH1 | LDB12|NGD29 | Mannosyltransferase of the cis-Golgi apparatus; initiates the polymannose outer chain elongation of N-linked oligosaccharides of glycoproteins | Accessory | Ancestral | NA | NA |
| 3686-YGL039W | YGL039W | NA | carbonyl reductase (NADPH-dependent) | Aldehyde reductase; reduces aliphatic aldehyde substrates using NADH as cofactor; shown to reduce carbonyl compounds to chiral alcohols | Accessory | Ancestral | NA | NA |
| 3687-YGL040C | YGL040C | HEM2 | porphobilinogen synthase HEM2|OLE4|SLU1 | Aminolevulinate dehydratase; a homo-octameric enzyme, catalyzes the conversion of 5-aminolevulinate to porphobilinogen, the second step in heme biosynthesis; enzymatic activity is zinc-dependent; localizes to the cytoplasm and nucleus; human homolog ALAD can complement yeast hem2 mutant | Accessory | Ancestral | NA | NA |
| 3688-YGL041C-B | YGL041C-B | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum | Accessory | Ancestral | NA | NA |
| 3689-YGL041W-A_NumOfGenes_2 | YGL041W-A | NA | NA | Putative protein of unknown function; conserved in fungi; identified by expression profiling and mass spectrometry | Accessory | Ancestral | NA | NA |
| 3690-YGL042C | YGL042C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; not conserved in closely related Saccharomyces species; deletion mutation blocks replication of Brome mosaic virus in S. cerevisiae, but this is likely due to effects on the overlapping gene DST1 | Accessory | Ancestral | NA | NA |
| 3691-YGL043W | YGL043W | DST1 | SII|S-II|TFIIS|P37|PPR2 | General transcription elongation factor TFIIS; enables RNA polymerase II to read through blocks to elongation by stimulating cleavage of nascent transcripts stalled at transcription arrest sites; maintains RNAPII elongation activity on ribosomal protein genes during conditions of transcriptional stress | Accessory | Ancestral | NA | NA |
| 3692-YGL044C_NumOfGenes_2 | YGL044C | RNA15 | NA | Component of the cleavage and polyadenylation factor I (CF I); CF 1, composed of the CF 1A complex (Rna14p, Rna15p, Clp1p, Pcf11p) and Hrp1, is involved in cleavage and polyadenylation of mRNA 3' ends; interacts with the A-rich polyadenylation signal in complex with Rna14p and Hrp1p; mutant displays reduced transcription elongation in the G-less-based run-on (GLRO) assay; required for gene looping and maintenance of genome stability | Core | NA | NA | NA |
| 3693-YGL045W_NumOfGenes_2 | YGL045W | RIM8 | ART9|YGL046W|PAL3 | Protein involved in proteolytic activation of Rim101p; part of response to alkaline pH; interacts with ESCRT-1 subunits Stp22p and Vps28p; essential for anaerobic growth; member of the arrestin-related trafficking adaptor family | Core | NA | NA | NA |
| 3694-YGL047W_NumOfGenes_2 | YGL047W | ALG13 | N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase catalytic subunit ALG13 | Catalytic component of UDP-GlcNAc transferase; required for the second step of dolichyl-linked oligosaccharide synthesis; anchored to the ER membrane via interaction with Alg14p; similar to bacterial and human glycosyltransferases; protein abundance increases in response to DNA replication stress; both human homologs ALG13 and ALG14 are required to complement yeast alg13 mutant | Core | NA | NA | NA |
| 3695-YGL048C_NumOfGenes_2 | YGL048C | RPT6 | proteasome regulatory particle base subunit RPT6|SUG1|SCB68|CRL3|CIM3 | ATPase of the 19S regulatory particle of the 26S proteasome; one of six ATPases of the regulatory particle; involved in the degradation of ubiquitinated substrates; bound by ubiquitin-protein ligases Ubr1p and Ufd4p; localized mainly to the nucleus throughout the cell cycle; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3696-YGL049C | YGL049C | TIF4632 | translation initiation factor eIF4G|eIF4G2 | Translation initiation factor eIF4G; subunit of the mRNA cap-binding protein complex (eIF4F) that also contains eIF4E (Cdc33p); associates with the poly(A)-binding protein Pab1p, also interacts with eIF4A (Tif1p); TIF4632 has a paralog, TIF4631, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3697-YGL050W | YGL050W | TYW3 | tRNA methyltransferase TYW3 | tRNA methyltransferase required for synthesis of wybutosine; a modified guanosine found at the 3'-position adjacent to the anticodon of phenylalanine tRNA which supports reading frame maintenance by stabilizing codon-anticodon interactions | Accessory | Ancestral | NA | NA |