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 |
|---|---|---|---|---|---|---|---|---|
| 5318-YKR025W_NumOfGenes_2 | YKR025W | RPC37 | DNA-directed RNA polymerase III subunit C37|C37 | RNA polymerase III subunit C37 | Core | NA | NA | NA |
| 5319-YKR026C_NumOfGenes_2 | YKR026C | GCN3 | translation initiation factor eIF2B subunit alpha|AAS2 | Alpha subunit of translation initiation factor eIF2B; guanine-nucleotide exchange factor for eIF2; activity subsequently regulated by phosphorylated eIF2; positive regulator of GCN4 expression; assembles into filaments with Gcd2p, Gcd6p, Gcd7p, and Sui2p as cells approach stationary phase and under cytosolic acidification and starvation conditions; human homolog EIF2B1 can complement yeast null mutant | Core | NA | NA | NA |
| 5320-YKR027W_NumOfGenes_2 | YKR027W | BCH2 | FMP50 | Member of the ChAPs (Chs5p-Arf1p-binding proteins) family; part of the exomer complex with Chs5p to mediate export of specific cargo proteins, including Chs3p, from the Golgi to the plasma membrane; BCH2 has a paralog, CHS6, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5321-YKR028W_NumOfGenes_2 | YKR028W | SAP190 | NA | Protein that forms a complex with the Sit4p protein phosphatase; required for Sit4p function; member of a family of similar proteins including Sap4p, Sap155p, and Sap185p; SAP190 has a paralog, SAP185, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5322-YKR029C_NumOfGenes_2 | YKR029C | SET3 | histone-binding protein SET3 | Defining member of the SET3 histone deacetylase complex; which is a meiosis-specific repressor of sporulation genes; necessary for efficient transcription by RNAPII; one of two yeast proteins that contains both SET and PHD domains; SET3 has a paralog, SET4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5323-YKR030W_NumOfGenes_2 | YKR030W | GMH1 | MSG1 | Golgi membrane protein of unknown function; interacts with Gea1p and Gea2p; required for localization of Gea2p; computational analysis suggests a possible role in either cell wall synthesis or protein-vacuolar targeting | Core | NA | NA | NA |
| 5324-YKR031C_NumOfGenes_2 | YKR031C | SPO14 | phospholipase D|PLD1 | Phospholipase D; catalyzes the hydrolysis of phosphatidylcholine, producing choline and phosphatidic acid; involved in Sec14p-independent secretion; required for meiosis and spore formation; differently regulated in secretion and meiosis; participates in transcription initiation and/or early elongation of specific genes; interacts with "foot domain" of RNA polymerase II; deletion results in abnormal CTD-Ser5 phosphorylation of RNA polymerase II at specific promoter regions | Core | NA | NA | NA |
| 5325-YKR032W | YKR032W | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains | Core | NA | NA | NA |
| 5326-YKR034W_NumOfGenes_3 | YKR034W | DAL80 | UGA43 | Negative regulator of genes in multiple nitrogen degradation pathways; expression is regulated by nitrogen levels and by Gln3p; member of the GATA-binding family, forms homodimers and heterodimers with Gzf3p; DAL80 has a paralog, GZF3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5327-YKR035W-A_NumOfGenes_3 | YKR035W-A | DID2 | VPL30|VPS46|CHM1|FTI1 | Class E protein of the vacuolar protein-sorting (Vps) pathway; binds Vps4p and directs it to dissociate ESCRT-III complexes; forms a functional and physical complex with Ist1p; human ortholog may be altered in breast tumors | Core | NA | NA | NA |
| 5328-YKR036C_NumOfGenes_3 | YKR036C | CAF4 | NA | WD40 repeat-containing protein associated with the CCR4-NOT complex; interacts in a Ccr4p-dependent manner with Ssn2p; also interacts with Fis1p, Mdv1p and Dnm1p and plays a role in mitochondrial fission; CAF4 has a paralog, MDV1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5329-YKR037C_NumOfGenes_2 | YKR037C | SPC34 | NA | Essential subunit of the Dam1 complex (aka DASH complex); complex couples kinetochores to the force produced by MT depolymerization thereby aiding in chromosome segregation; also localized to nuclear side of spindle pole body | Core | NA | NA | NA |
| 5330-YKR038C_NumOfGenes_2 | YKR038C | KAE1 | tRNA N6-adenosine threonylcarbamoyltransferase | Highly conserved ATPase of HSP70/DnaK family; essential functional component of the EKC/KEOPS complex, with Bud32p, Cgi121p, Pcc1p, and Gon7p; EKC/KEOPS complex is required for t6A tRNA modification and telomeric TG1-3 recombination; may have role in transcription | Accessory | Ancestral | NA | NA |
| 5331-YKR039W_NumOfGenes_2 | YKR039W | GAP1 | amino acid permease GAP1 | General amino acid permease; Gap1p senses the presence of amino acid substrates to regulate localization to the plasma membrane when needed; essential for invasive growth | Accessory | Ancestral | NA | NA |
| 5332-YKR040C | YKR040C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YKR041W | Accessory | Ancestral | NA | NA |