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 |
|---|---|---|---|---|---|---|---|---|
| 6353-YMR283C | YMR283C | RIT1 | tRNA A64-2'-O-ribosylphosphate transferase | Initiator methionine 2'-O-ribosyl phosphate transferase; modifies the initiator methionine tRNA at position 64 to distinguish it from elongator methionine tRNA | Core | NA | NA | NA |
| 6354-YMR284W | YMR284W | YKU70 | ATP-dependent DNA helicase YKU70|KU70|NES24|HDF1 | Subunit of the telomeric Ku complex (Yku70p-Yku80p); involved in telomere length maintenance, structure and telomere position effect; required for localization of telomerase ribonucleoprotein to nucleus via interaction with the TLC1 guide RNA; relocates to sites of double-strand cleavage to promote nonhomologous end joining during DSB repair | Core | NA | NA | NA |
| 6355-YMR285C | YMR285C | NGL2 | RNA exonuclease | Protein involved in 5.8S rRNA processing; Ccr4p-like RNase required for correct 3'-end formation of 5.8S rRNA at site E; similar to Ngl1p; NGL2 has a paralog, NGL3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6356-YMR286W | YMR286W | MRPL33 | mitochondrial 54S ribosomal protein YmL33|YmL33 | Mitochondrial ribosomal protein of the large subunit | Core | NA | NA | NA |
| 6357-YMR287C | YMR287C | DSS1 | MSU1 | 3'-5' exoribonuclease; component of the mitochondrial degradosome along with the ATP-dependent RNA helicase Suv3p; the degradosome associates with the ribosome and mediates turnover of aberrant or unprocessed RNAs | Core | NA | NA | NA |
| 6358-YMR288W | YMR288W | HSH155 | U2 snRNP complex subunit HSH155 | U2-snRNP associated splicing factor; forms extensive associations with the branch site-3' splice site-3' exon region upon prespliceosome formation; similarity to the mammalian U2 snRNP-associated splicing factor SAP155 | Core | NA | NA | NA |
| 6359-YMR289W | YMR289W | ABZ2 | aminodeoxychorismate lyase ABZ2 | Aminodeoxychorismate lyase (4-amino-4-deoxychorismate lyase); catalyzes the third step in para-aminobenzoic acid biosynthesis; involved in folic acid biosynthesis | Core | NA | NA | NA |
| 6360-YMR290C | YMR290C | HAS1 | ATP-dependent RNA helicase HAS1 | ATP-dependent RNA helicase; involved in the biogenesis of 40S and 60S ribosome subunits; localizes to both the nuclear periphery and nucleolus; highly enriched in nuclear pore complex fractions; constituent of 66S pre-ribosomal particles | Core | NA | NA | NA |
| 6361-YMR290W-A | YMR290W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps 5' end of essential HAS1/YMR290C gene which encodes an ATP-dependent RNA helicase | Accessory | Ancestral | NA | NA |
| 6362-YMR291W | YMR291W | TDA1 | protein kinase TDA1 | Protein kinase of unknown cellular role; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; null mutant is sensitive to expression of the top1-T722A allele; not an essential gene; relocalizes from nucleus to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 6363-YMR292W | YMR292W | GOT1 | NA | Homodimeric protein that is packaged into COPII vesicles; cycles between the ER and Golgi; involved in secretory transport but not directly required for aspects of transport assayed in vitro; may influence membrane composition | Core | NA | NA | NA |
| 6364-YMR293C | YMR293C | HER2 | QRS1|glutamyl-tRNA(Gln) amidotransferase subunit HER2|RRG6|GEP6|LRC6 | Subunit of the trimeric GatFAB AmidoTransferase(AdT) complex; involved in the formation of Q-tRNAQ; required for remodeling of ER caused by Hmg2p overexpression; similar to bacterial GatA glutamyl-tRNA amidotransferase | Core | NA | NA | NA |
| 6365-YMR294W | YMR294W | JNM1 | PAC3|INS1 | Component of the yeast dynactin complex; consisting of Nip100p, Jnm1p, and Arp1p; required for proper nuclear migration and spindle partitioning during mitotic anaphase B | Core | NA | NA | NA |
| 6366-YMR295C_NumOfGenes_2 | YMR295C | NA | IBI2 | Protein of unknown function that associates with ribosomes; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery and bud; not an essential gene; protein abundance increases in response to DNA replication stress; YMR295C has a paralog, YGR273C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6367-YMR296C | YMR296C | LCB1 | serine C-palmitoyltransferase LCB1|TSC2|END8 | Component of serine palmitoyltransferase; responsible along with Lcb2p for the first committed step in sphingolipid synthesis, which is the condensation of serine with palmitoyl-CoA to form 3-ketosphinganine | Core | NA | NA | NA |