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 |
|---|---|---|---|---|---|---|---|---|
| 3128-YDR439W | YDR439W | LRS4 | NA | Nucleolar protein that forms a complex with Csm1p; and then Mam1p at kinetochores during meiosis I to mediate accurate homolog segregation; required for condensin recruitment to the replication fork barrier site and rDNA repeat segregation | Core | NA | NA | NA |
| 3129-YDR440W | YDR440W | DOT1 | histone methyltransferase DOT1|KMT4|PCH1 | Nucleosomal histone H3-Lys79 methylase; methylation is required for telomeric silencing, meiotic checkpoint control, and DNA damage response | Accessory | Ancestral | NA | NA |
| 3130-YDR441C | YDR441C | APT2 | adenine phosphoribosyltransferase APT2 | Potential adenine phosphoribosyltransferase; encodes a protein with similarity to adenine phosphoribosyltransferase, but artificially expressed protein exhibits no enzymatic activity; APT2 has a paralog, APT1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3131-YDR443C_NumOfGenes_2 | YDR443C | SSN2 | SSX5|MED13|RYE3|UME2|SRB9|SCA1|NUT8 | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; required for stable association of Srb10p-Srb11p kinase; essential for transcriptional regulation | Core | NA | NA | NA |
| 3132-YDR444W | YDR444W | NA | putative hydrolase | Putative hydrolase acting on ester bonds | Core | NA | NA | NA |
| 3133-YDR445C | YDR445C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Unknown | S. paradoxus | NA |
| 3134-YDR446W | YDR446W | ECM11 | NA | Meiosis-specific protein; component of the Synaptonemal Complex (SC) along with Gmc2p; required for efficient crossover formation and for the efficient loading of the SC transverse filament protein, Zip1p; is SUMOlytaed in a Gmc2p manner, and SUMOylation is required for its function in meiosis; GFP fusion protein is present in discrete clusters in the nucleus throughout mitosis; may be involved in maintaining chromatin structure | Core | NA | NA | NA |
| 3135-YDR447C | YDR447C | RPS17B | eS17|ribosomal 40S subunit protein S17B|S17e|rp51B|S17B|RPL51B|RP51B | Ribosomal protein 51 (rp51) of the small (40s) subunit; homologous to mammalian ribosomal protein S17, no bacterial homolog; RPS17B has a paralog, RPS17A, that arose from the whole genome duplication; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3136-YDR448W | YDR448W | ADA2 | chromatin-binding transcription regulator ADA2|SWI8 | Transcription coactivator; component of the ADA and SAGA transcriptional adaptor/HAT (histone acetyltransferase) complexes | Core | NA | NA | NA |
| 3137-YDR449C | YDR449C | UTP6 | snoRNA-binding rRNA-processing protein UTP6 | Nucleolar protein; component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA | Core | NA | NA | NA |
| 3138-YDR450W | YDR450W | RPS18A | uS13|ribosomal 40S subunit protein S18A|S18A|S13 | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S18 and bacterial S13; RPS18A has a paralog, RPS18B, that arose from the whole genome duplication; protein increases in abundance and relocalizes from cytoplasm to nuclear foci upon DNA replication stress | Core | NA | NA | NA |
| 3139-YDR451C | YDR451C | YHP1 | NA | Homeobox transcriptional repressor; binds Mcm1p and early cell cycle box (ECB) elements of cell cycle regulated genes, thereby restricting ECB-mediated transcription to the M/G1 interval; YHP1 has a paralog, YOX1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3140-YDR452W | YDR452W | PPN1 | endopolyphosphatase|PHM5 | Dual endo- and exopolyphosphatase with a role in phosphate metabolism; acts as both an endopolyphosphatase cleaving long chains of polyphosphate distributively to generate shorter polymer chains and as an exopolyphosphatase catalyzing the hydrolysis of terminal phosphate from polyphosphate; localizes to the vacuole, nucleus and cytosol; functions as a homodimer; relocalizes from vacuole to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 3141-YDR453C | YDR453C | TSA2 | thioredoxin peroxidase TSA2|cTPxII | Stress inducible cytoplasmic thioredoxin peroxidase; cooperates with Tsa1p in the removal of reactive oxygen, nitrogen and sulfur species using thioredoxin as hydrogen donor; deletion enhances the mutator phenotype of tsa1 mutants; protein abundance increases in response to DNA replication stress; TSA2 has a paralog, TSA1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3142-YDR454C | YDR454C | GUK1 | BRA3|guanylate kinase|PUR5 | Guanylate kinase; converts GMP to GDP; required for growth and mannose outer chain elongation of cell wall N-linked glycoproteins | Core | NA | NA | NA |