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 |
|---|---|---|---|---|---|---|---|---|
| 1898-YBL028C_NumOfGenes_2 | YBL028C | NA | NA | Protein of unknown function that may interact with ribosomes; green fluorescent protein (GFP)-fusion protein localizes to the nucleolus; predicted to be involved in ribosome biogenesis | Core | NA | NA | NA |
| 1899-YBL029C-A_NumOfGenes_2 | YBL029C-A | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery; protein abundance increases in response to DNA replication stress; has potential orthologs in Saccharomyces species and in Yarrowia lipolytica | Core | NA | NA | NA |
| 1900-YBL029W_NumOfGenes_2 | YBL029W | NA | NA | Non-essential protein of unknown function | Core | NA | NA | NA |
| 1901-YBL030C_NumOfGenes_2 | YBL030C | PET9 | ADP/ATP carrier protein PET9|OP1|ANC2|AAC2 | Major ADP/ATP carrier of the mitochondrial inner membrane; exchanges cytosolic ADP for mitochondrially synthesized ATP; also imports heme and ATP; required for viability in many lab strains that carry a sal1 mutation; PET9 has a paralog, AAC3, that arose from the whole genome duplication; human homolog SLC25A4 implicated in progressive external ophthalmoplegia can complement yeast null mutant | Core | NA | NA | NA |
| 1902-YBL031W_NumOfGenes_2 | YBL031W | SHE1 | NA | Mitotic spindle protein; interacts with components of the Dam1 (DASH) complex, its effector Sli15p, and microtubule-associated protein Bim1p; also localizes to nuclear microtubules and to the bud neck in a ring-shaped structure; inhibits dynein function | Core | NA | NA | NA |
| 1903-YBL032W_NumOfGenes_2 | YBL032W | HEK2 | KHD1 | RNA binding protein involved in asymmetric localization of ASH1 mRNA; represses translation of ASH1 mRNA, an effect reversed by Yck1p-dependent phosphoryation; regulates telomere position effect and length; similarity to hnRNP-K | Accessory | Ancestral | NA | NA |
| 1904-YBL033C_NumOfGenes_2 | YBL033C | RIB1 | GTP cyclohydrolase II | GTP cyclohydrolase II; catalyzes the first step of the riboflavin biosynthesis pathway | Core | NA | NA | NA |
| 1905-YBL034C_NumOfGenes_2 | YBL034C | STU1 | NA | Component of the mitotic spindle; binds to interpolar microtubules via its association with beta-tubulin (Tub2p); required for interpolar microtubules to provide an outward force on the spindle poles | Core | NA | NA | NA |
| 1906-YBL035C_NumOfGenes_2 | YBL035C | POL12 | DNA-directed DNA polymerase alpha subunit POL12 | B subunit of DNA polymerase alpha-primase complex; required for initiation of DNA replication during mitotic and premeiotic DNA synthesis; also functions in telomere capping and length regulation | Core | NA | NA | NA |
| 1907-YBL036C_NumOfGenes_2 | YBL036C | NA | NA | Putative non-specific single-domain racemase; based on structural similarity; binds pyridoxal 5'-phosphate; expression of GFP-fusion protein induced in response to the DNA-damaging agent MMS | Core | NA | NA | NA |
| 1908-YBL037W_NumOfGenes_2 | YBL037W | APL3 | NA | Alpha-adaptin; large subunit of the clathrin associated protein complex (AP-2); involved in vesicle mediated transport | Core | NA | NA | NA |
| 1909-YBL038W_NumOfGenes_2 | YBL038W | MRPL16 | RML16|mitochondrial 54S ribosomal protein YmL47|YmL47 | Mitochondrial ribosomal protein of the large subunit; homologous to bacterial L16 ribosomal protein; synthetic lethality with hac1 mutation suggests a possible role in synthesis of precursors for protein glycosylation | Core | NA | NA | NA |
| 1910-YBL039C_NumOfGenes_3 | YBL039C | URA7 | CTP synthase URA7 | Major CTP synthase isozyme (see also URA8); catalyzes the ATP-dependent transfer of the amide nitrogen from glutamine to UTP, forming CTP, the final step in de novo biosynthesis of pyrimidines; involved in phospholipid biosynthesis; capable of forming cytoplasmic filaments termed cytoophidium, especially during conditions of glucose depletion; URA7 has a paralog, URA8, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1911-YBL039W-B | YBL039W-B | NA | YBL039W-A | Putative protein of unknown function; mCherry fusion protein localizes to the vacuole | Core | NA | NA | NA |
| 1912-YBL040C_NumOfGenes_2 | YBL040C | ERD2 | NA | HDEL receptor; an integral membrane protein that binds to the HDEL motif in proteins destined for retention in the endoplasmic reticulum; has a role in maintenance of normal levels of ER-resident proteins | Core | NA | NA | NA |