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 |
|---|---|---|---|---|---|---|---|---|
| 7598-YPL250C | YPL250C | ATG41 | ICY2 | Protein of unknown function; required for selective and nonselective autophagy, and mitophagy; regulates the rate of autophagosome formation; interacts with Atg9p, and has a similar peri-mitochondrial localization; elevated Gcn4p-dependent expression under autophagy-inducing conditions; mobilized into polysomes upon a shift from a fermentable to nonfermentable carbon source; potential Cdc28p substrate; ATG41 has a paralog, ICY1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7599-YPL252C_NumOfGenes_2 | YPL252C | YAH1 | adrenodoxin | Ferredoxin of the mitochondrial matrix; required for formation of cellular iron-sulfur proteins; involved in heme A biosynthesis; human homolog FDX1L can complement yeast by allowing growth during down-regulation of yeast YAH1 | Core | NA | NA | NA |
| 7600-YPL253C | YPL253C | VIK1 | NA | Protein that forms a kinesin-14 heterodimeric motor with Kar3p; localizes Kar3p at mitotic spindle poles; has a structure similar to a kinesin motor domain but lacks an ATP-binding site and is catalytically inactive; binds microtubules; required for sister chromatid cohesion; VIK1 has a paralog, CIK1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7601-YPL254W | YPL254W | HFI1 | GAN1|SRM12|SUP110|ADA1 | Adaptor protein required for structural integrity of the SAGA complex; a histone acetyltransferase-coactivator complex that is involved in global regulation of gene expression through acetylation and transcription functions | Core | NA | NA | NA |
| 7602-YPL255W | YPL255W | BBP1 | NA | Protein required for the spindle pole body (SPB) duplication; localizes at the cytoplasmic side of the central plaque periphery of the SPB; forms a complex with a nuclear envelope protein Mps2p and SPB components Spc29p and Kar1p; required for mitotic functions of Cdc5p | Core | NA | NA | NA |
| 7603-YPL256C | YPL256C | CLN2 | cyclin CLN2 | G1 cyclin involved in regulation of the cell cycle; activates Cdc28p kinase to promote the G1 to S phase transition; late G1 specific expression depends on transcription factor complexes, MBF (Swi6p-Mbp1p) and SBF (Swi6p-Swi4p); CLN2 has a paralog, CLN1, that arose from the whole genome duplication; cell cycle arrest phenotype of the cln1 cln2 cln3 triple null mutant is complemented by any of human cyclins CCNA2, CCNB1, CCNC, CCND1, or CCNE1 | Core | NA | NA | NA |
| 7604-YPL257W | YPL257W | NA | NA | Putative protein of unknown function; homozygous diploid deletion strain exhibits low budding index; physically interacts with Hsp82p; YPL257W is not an essential gene | Accessory | Unknown | NA | NA |
| 7605-YPL258C | YPL258C | THI21 | bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase | Hydroxymethylpyrimidine (HMP) and HMP-phosphate kinase; involved in thiamine biosynthesis; member of a gene family with THI20 and THI22; functionally redundant with Thi20p | Core | NA | NA | NA |
| 7606-YPL259C | YPL259C | APM1 | YAP54 | Mu1-like medium subunit of the AP-1 complex; binds clathrin; involved in clathrin-dependent Golgi protein sorting; the AP-1 complex is the clathrin-associated protein complex | Core | NA | NA | NA |
| 7607-YPL260W | YPL260W | CUB1 | NA | Conserved fungal gene linked to DNA repair and proteasome function; putative substrate of cAMP-dependent protein kinase (PKA); green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YPL260W is not an essential gene; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 7608-YPL261C | YPL261C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YPL261C is not an essential gene; partially overlaps verified ORF YPL260W | Core | NA | NA | NA |
| 7609-YPL262W | YPL262W | FUM1 | fumarase FUM1 | Fumarase; converts fumaric acid to L-malic acid in the TCA cycle; cytosolic and mitochondrial distribution determined by the N-terminal targeting sequence, protein conformation, and status of glyoxylate shunt; phosphorylated in mitochondria | Core | NA | NA | NA |
| 7610-YPL263C | YPL263C | KEL3 | NA | Cytoplasmic protein of unknown function | Core | NA | NA | NA |
| 7611-YPL264C | YPL264C | NA | NA | Putative membrane protein of unknown function; physically interacts with Hsp82p; YPL264C is not an essential gene | Core | NA | NA | NA |
| 7612-YPL265W | YPL265W | DIP5 | NA | Dicarboxylic amino acid permease; mediates high-affinity and high-capacity transport of L-glutamate and L-aspartate; also a transporter for Gln, Asn, Ser, Ala, and Gly; relocalizes from plasma membrane to vacuole upon DNA replication stress | Core | NA | NA | NA |