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 |
|---|---|---|---|---|---|---|---|---|
| 2948-YDR256C | YDR256C | CTA1 | catalase A | Catalase A; breaks down hydrogen peroxide in the peroxisomal matrix formed by acyl-CoA oxidase (Pox1p) during fatty acid beta-oxidation | Core | NA | NA | NA |
| 2949-YDR257C | YDR257C | RKM4 | ribosomal lysine N-methyltransferase|SET7|RMS1 | Ribosomal lysine methyltransferase; specific for monomethylation of Rpl42ap and Rpl42bp (lysine 55); nuclear SET-domain containing protein | Accessory | Ancestral | NA | NA |
| 2950-YDR258C | YDR258C | HSP78 | chaperone ATPase HSP78 | Oligomeric mitochondrial matrix chaperone; cooperates with Ssc1p in mitochondrial thermotolerance after heat shock; able to prevent the aggregation of misfolded proteins as well as resolubilize protein aggregates | Accessory | Ancestral | NA | NA |
| 2951-YDR259C | YDR259C | YAP6 | HAL7 | Basic leucine zipper (bZIP) transcription factor; physically interacts with the Tup1-Cyc8 complex and recruits Tup1p to its targets; overexpression increases sodium and lithium tolerance; computational analysis suggests a role in regulation of expression of genes involved in carbohydrate metabolism; YAP6 has a paralog, CIN5, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2952-YDR260C | YDR260C | SWM1 | APC13 | Subunit of the anaphase-promoting complex (APC); APC is an E3 ubiquitin ligase that regulates the metaphase-anaphase transition and exit from mitosis; required for activation of the daughter-specific gene expression and spore wall maturation | Accessory | Ancestral | NA | NA |
| 2953-YDR261C | YDR261C | EXG2 | glucan exo-1,3-beta-glucosidase | Exo-1,3-beta-glucanase; involved in cell wall beta-glucan assembly; may be anchored to the plasma membrane via a glycosylphosphatidylinositol (GPI) anchor | Accessory | Ancestral | NA | NA |
| 2954-YDR262W | YDR262W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole and is induced in response to the DNA-damaging agent MMS; gene expression increases in response to Zymoliase treatment | Accessory | Ancestral | NA | NA |
| 2955-YDR263C | YDR263C | DIN7 | exodeoxyribonuclease DIN7|DIN3 | Mitochondrial nuclease functioning in DNA repair and replication; modulates the stability of the mitochondrial genome, induced by exposure to mutagens, also induced during meiosis at a time nearly coincident with commitment to recombination; DIN7 has a paralog, EXO1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2956-YDR264C | YDR264C | AKR1 | palmitoyltransferase AKR1 | Palmitoyl transferase involved in protein palmitoylation; acts as a negative regulator of pheromone response pathway; required for endocytosis of pheromone receptors; involved in cell shape control; contains ankyrin repeats; AKR1 has a paralog, AKR2, that arose from the whole genome duplication; any of several human homologs encoding DHHC-type zinc fingers (ZDHHC) can complement temperature sensitivity of yeast akr1 null mutant | Core | NA | NA | NA |
| 2957-YDR265W | YDR265W | PEX10 | ubiquitin-protein ligase peroxin 10|PAS4 | Peroxisomal membrane E3 ubiquitin ligase; required for for Ubc4p-dependent Pex5p ubiquitination and peroxisomal matrix protein import; contains zinc-binding RING domain; mutations in human homolog cause various peroxisomal disorders | Core | NA | NA | NA |
| 2958-YDR266C | YDR266C | HEL2 | E3 ubiquitin-protein ligase HEL2 | RING finger ubiquitin ligase (E3); involved in ubiquitination and degradation of excess histones; interacts with Ubc4p and Rad53p; null mutant sensitive to hydroxyurea (HU); green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; computational analysis suggests a role as a transcription factor | Core | NA | NA | NA |
| 2959-YDR267C | YDR267C | CIA1 | iron-sulfur cluster assembly protein CIA1 | Component of cytosolic iron-sulfur protein assembly (CIA) machinery; acts at late step of Fe-S cluster assembly; forms CIA targeting complex with Cia2p and Met18p that directs Fe-S cluster incorporation into subset of proteins involved in methionine biosynthesis, DNA replication and repair, transcription, telomere maintenance; contains WD40 repeats; human homolog CIAO1 can complement yeast cia1 null mutant | Core | NA | NA | NA |
| 2960-YDR268W | YDR268W | MSW1 | tryptophan--tRNA ligase MSW1 | Mitochondrial tryptophanyl-tRNA synthetase | Core | NA | NA | NA |
| 2961-YDR270W_NumOfGenes_3 | YDR270W | CCC2 | Cu(2+)-transporting P-type ATPase CCC2 | Cu(+2)-transporting P-type ATPase; required for export of copper from the cytosol into an extracytosolic compartment; similar to human proteins involved in Menkes and Wilsons diseases; protein abundance increases in response to DNA replication stress; affects TBSV model (+)RNA virus replication by regulating copper metabolism; human homologs ATP7A and ATP7B both complement yeast null mutant | Core | NA | NA | NA |
| 2962-YDR272W | YDR272W | GLO2 | hydroxyacylglutathione hydrolase GLO2 | Cytoplasmic glyoxalase II; catalyzes the hydrolysis of S-D-lactoylglutathione into glutathione and D-lactate; GLO2 has a paralog, GLO4, that arose from the whole genome duplication | Core | NA | NA | NA |