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 |
|---|---|---|---|---|---|---|---|---|
| 3368-YER051W | YER051W | JHD1 | [Histone H3]-lysine-36 demethylase|KDM2|JHDM1 | JmjC domain family histone demethylase specific for H3-K36; similar to proteins found in human, mouse, drosophila, X. laevis, C. elegans, and S. pombe | Core | NA | NA | NA |
| 3369-YER052C | YER052C | HOM3 | aspartate kinase|THR3|SIL4|BOR1 | Aspartate kinase (L-aspartate 4-P-transferase); cytoplasmic enzyme that catalyzes the first step in the common pathway for methionine and threonine biosynthesis; expression regulated by Gcn4p and the general control of amino acid synthesis | Core | NA | NA | NA |
| 3370-YER053C | YER053C | PIC2 | Cu/Pi carrier | Mitochondrial copper and phosphate carrier; imports copper and inorganic phosphate into mitochondria; functionally redundant with Mir1p but less abundant than Mir1p under normal conditions; expression is induced at high temperature | Core | NA | NA | NA |
| 3371-YER053C-A | YER053C-A | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3372-YER054C | YER054C | GIP2 | NA | Putative regulatory subunit of protein phosphatase Glc7p; involved in glycogen metabolism; contains a conserved motif (GVNK motif) that is also found in Gac1p, Pig1p, and Pig2p; GIP2 has a paralog, PIG2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3373-YER055C | YER055C | HIS1 | ATP phosphoribosyltransferase | ATP phosphoribosyltransferase; a hexameric enzyme, catalyzes the first step in histidine biosynthesis; mutations cause histidine auxotrophy and sensitivity to Cu, Co, and Ni salts; transcription is regulated by general amino acid control | Core | NA | NA | NA |
| 3374-YER056C | YER056C | FCY2 | purine-cytosine permease|BRA7 | Purine-cytosine permease; mediates purine (adenine, guanine, and hypoxanthine) and cytosine accumulation; relative distribution to the vacuole increases upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 3375-YER056C-A | YER056C-A | RPL34A | eL34|ribosomal 60S subunit protein L34A|L34e|L34A | Ribosomal 60S subunit protein L34A; homologous to mammalian ribosomal protein L34, no bacterial homolog; RPL34A has a paralog, RPL34B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3376-YER057C | YER057C | HMF1 | putative isoleucine biosynthesis protein HMF1|HIG1 | Member of the p14.5 protein family; functionally complements Mmf1p function when targeted to mitochondria; heat shock inducible; high-dosage growth inhibitor; forms a homotrimer in vitro; HMF1 has a paralog, MMF1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3377-YER058W | YER058W | PET117 | NA | Protein required for assembly of cytochrome c oxidase | Core | NA | NA | NA |
| 3378-YER059W | YER059W | PCL6 | NA | Pho85p cyclin of the Pho80p subfamily; forms the major Glc8p kinase together with Pcl7p and Pho85p; involved in the control of glycogen storage by Pho85p; stabilized by Elongin C binding; PCL6 has a paralog, PCL7, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3379-YER060W | YER060W | FCY21 | purine-cytosine permease | Putative purine-cytosine permease; very similar to Fcy2p but cannot substitute for its function | Core | NA | NA | NA |
| 3380-YER060W-A | YER060W-A | FCY22 | purine-cytosine permease | Putative purine-cytosine permease; very similar to Fcy2p but cannot substitute for its function | Accessory | Ancestral | NA | NA |
| 3381-YER061C_NumOfGenes_2 | YER061C | CEM1 | fatty acid synthase CEM1 | Mitochondrial beta-keto-acyl synthase; possible role in fatty acid synthesis; required for mitochondrial respiration; human homolog OXSM can complement yeast cem1 null mutant | Accessory | Ancestral | NA | NA |
| 3382-YER062C_NumOfGenes_2 | YER062C | GPP2 | HOR2|glycerol-1-phosphatase HOR2 | DL-glycerol-3-phosphate phosphatase involved in glycerol biosynthesis; also known as glycerol-1-phosphatase; induced in response to hyperosmotic or oxidative stress, and during diauxic shift; GPP2 has a paralog, GPP1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |