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 |
|---|---|---|---|---|---|---|---|---|
| 2993-YDR303C | YDR303C | RSC3 | NA | Component of the RSC chromatin remodeling complex; essential gene required for maintenance of proper ploidy and regulation of ribosomal protein genes and the cell wall/stress response; RSC3 has a paralog, RSC30, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2994-YDR304C | YDR304C | CPR5 | peptidylprolyl isomerase family protein CPR5|CYP5 | Peptidyl-prolyl cis-trans isomerase (cyclophilin) of the ER; catalyzes the cis-trans isomerization of peptide bonds N-terminal to proline residues; transcriptionally induced in response to unfolded proteins in the ER; CPR5 has a paralog, CPR2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2995-YDR305C | YDR305C | HNT2 | bis(5'-adenosyl)-triphosphatase|APH1 | Dinucleoside triphosphate hydrolase; has similarity to the tumor suppressor FHIT and belongs to the histidine triad (HIT) superfamily of nucleotide-binding proteins | Core | NA | NA | NA |
| 2996-YDR306C | YDR306C | NA | NA | F-box protein of unknown function; interacts with Sgt1p via a Leucine-Rich Repeat (LRR) domain | Core | NA | NA | NA |
| 2997-YDR307W | YDR307W | PMT7 | putative dolichyl-phosphate-mannose--protein mannosyltransferase | Putative protein mannosyltransferase similar to Pmt1p; has a potential role in protein O-glycosylation | Core | NA | NA | NA |
| 2998-YDR308C | YDR308C | SRB7 | SSX1|MED21 | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation; target of the global repressor Tup1p | Core | NA | NA | NA |
| 2999-YDR309C | YDR309C | GIC2 | NA | Redundant rho-like GTPase Cdc42p effector; involved in initiation of budding and cellular polarization; interacts with Cdc42p via the Cdc42/Rac-interactive binding (CRIB) domain and with PI(4,5)P2 via a polybasic region; GIC2 has a paralog, GIC1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3000-YDR310C | YDR310C | SUM1 | NA | Transcriptional repressor that regulates middle-sporulation genes; required for mitotic repression of middle sporulation-specific genes; also acts as general replication initiation factor; involved in telomere maintenance, chromatin silencing; regulated by pachytene checkpoint | Core | NA | NA | NA |
| 3001-YDR311W | YDR311W | TFB1 | TFIIH/NER complex subunit TFB1 | Subunit of TFIIH and nucleotide excision repair factor 3 complexes; required for nucleotide excision repair, target for transcriptional activators; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 3002-YDR312W | YDR312W | SSF2 | rRNA-binding ribosome biosynthesis protein | Protein required for ribosomal large subunit maturation; functionally redundant with Ssf1p; member of the Brix family; SSF2 has a paralog, SSF1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3003-YDR313C | YDR313C | PIB1 | phosphatidylinositol-3-phosphate-binding ubiquitin-protein ligase | RING-type ubiquitin ligase of the endosomal and vacuolar membranes; binds phosphatidylinositol(3)-phosphate; contains a FYVE finger domain | Core | NA | NA | NA |
| 3004-YDR314C | YDR314C | RAD34 | NA | Protein involved in nucleotide excision repair (NER); homologous to RAD4 | Core | NA | NA | NA |
| 3005-YDR315C | YDR315C | IPK1 | inositol pentakisphosphate 2-kinase|GSL1 | Inositol 1,3,4,5,6-pentakisphosphate 2-kinase; nuclear protein required for synthesis of 1,2,3,4,5,6-hexakisphosphate (phytate), which is integral to cell function; has 2 motifs conserved in other fungi; ipk1 gle1 double mutant is inviable; human IPPK can complement ipk1 null mutant | Core | NA | NA | NA |
| 3006-YDR316W | YDR316W | OMS1 | putative RNA methyltransferase | Protein integral to the mitochondrial membrane; has a conserved methyltransferase motif and is predicted to be an RNA methyltransferase; multicopy suppressor of respiratory defects caused by OXA1 mutations | Core | NA | NA | NA |
| 3007-YDR317W | YDR317W | HIM1 | NA | Protein of unknown function involved in DNA repair | Core | NA | NA | NA |