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 |
|---|---|---|---|---|---|---|---|---|
| 5723-YLR265C | YLR265C | NEJ1 | LIF2 | Protein involved in regulation of nonhomologous end joining; interacts with DNA ligase IV components Dnl4p and Lif1p; repressed by MAT heterozygosity; regulates cellular distribution of Lif1p | Core | NA | NA | NA |
| 5724-YLR266C | YLR266C | PDR8 | NA | Transcription factor; targets include ATP-binding cassette (ABC) transporters, major facilitator superfamily transporters, and other genes involved in the pleiotropic drug resistance (PDR) phenomenon; PDR8 has a paralog, YRR1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5725-YLR267W | YLR267W | BOP2 | NA | Protein of unknown function | Core | NA | NA | NA |
| 5726-YLR268W | YLR268W | SEC22 | SNAP receptor SEC22|TS26|TSL26|SLY2 | R-SNARE protein; assembles into SNARE complex with Bet1p, Bos1p and Sed5p; cycles between the ER and Golgi complex; involved in anterograde and retrograde transport between the ER and Golgi; synaptobrevin homolog | Core | NA | NA | NA |
| 5727-YLR269C | YLR269C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 5728-YLR270W | YLR270W | DCS1 | 5'-(N(7)-methyl 5'-triphosphoguanosine)-(mRNA) diphosphatase|DcpS | Non-essential hydrolase involved in mRNA decapping; activates Xrn1p; may function in a feedback mechanism to regulate deadenylation, contains pyrophosphatase activity and a HIT (histidine triad) motif; acts as inhibitor of neutral trehalase Nth1p; required for growth on glycerol medium; protein abundance increases in response to DNA replication stress; DCS1 has a paralog, DCS2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5729-YLR271W | YLR271W | CMG1 | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and the nucleus and is induced in response to the DNA-damaging agent MMS | Core | NA | NA | NA |
| 5730-YLR272C | YLR272C | YCS4 | condensin subunit YCS4|LOC7 | Subunit of the condensin complex; required for establishment and maintenance of chromosome condensation, chromosome segregation, chromatin binding of condensin, tRNA gene clustering at the nucleolus, and silencing at the mating type locus; required for replication slow zone (RSZ) breakage following Mec1p inactivation | Core | NA | NA | NA |
| 5731-YLR273C_NumOfGenes_2 | YLR273C | PIG1 | protein phosphatase regulator PIG1 | Putative targeting subunit for type-1 protein phosphatase Glc7p; tethers Glc7p to Gsy2p glycogen synthase; PIG1 has a paralog, GAC1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5732-YLR274W_NumOfGenes_2 | YLR274W | MCM5 | MCM DNA helicase complex subunit MCM5|CDC46|BOB1 | Component of the Mcm2-7 hexameric helicase complex; MCM complex is important for priming origins of DNA replication in G1 and becomes an active ATP-dependent helicase that promotes DNA melting and elongation when activated by Cdc7p-Dbf4p in S-phase | Core | NA | NA | NA |
| 5733-YLR275W_NumOfGenes_2 | YLR275W | SMD2 | mRNA splicing protein SMD2|Sm D2 | Core Sm protein Sm D2; part of heteroheptameric complex (with Smb1p, Smd1p, Smd3p, Sme1p, Smx3p, and Smx2p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; homolog of human Sm D2 | Core | NA | NA | NA |
| 5734-YLR276C_NumOfGenes_2 | YLR276C | DBP9 | ATP-dependent DNA/RNA helicase | DEAD-box protein required for 27S rRNA processing; exhibits DNA, RNA and DNA/RNA helicase activities; ATPase activity shows preference for DNA over RNA; DNA helicase activity abolished by mutation in RNA-binding domain | Core | NA | NA | NA |
| 5735-YLR277C | YLR277C | YSH1 | cleavage polyadenylation factor subunit YSH1|BRR5 | Endoribonuclease; subunit of the mRNA cleavage and polyadenylation specificity complex; required for 3' processing, splicing, and transcriptional termination of mRNAs and snoRNAs; protein abundance increases in response to DNA replication stress; YSH1 has a paralog, SYC1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5736-YLR278C | YLR278C | NA | NA | Zinc-cluster protein; GFP-fusion protein localizes to the nucleus; mutant shows moderate growth defect on caffeine; has a prion-domain like fragment that increases frequency of [URE3]; YLR278C is not an essential gene | Core | NA | NA | NA |
| 5737-YLR279W | YLR279W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |