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 |
|---|---|---|---|---|---|---|---|---|
| 1868-YAR068W_NumOfGenes_3 | YAR068W | NA | NA | Fungal-specific protein of unknown function; induced in respiratory-deficient cells; YAR068W has a paralog, YHR214W-A, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 1869-YAR070C_NumOfGenes_2 | YAR070C | NA | NA | Dubious open reading frame; unlikely to encode a protein, based on available experimental and comparative sequence data; YAR070C has a paralog, YHR214C-B, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 1870-YBL001C | YBL001C | ECM15 | NA | Non-essential protein of unknown function; likely exists as tetramer, may be regulated by the binding of small-molecule ligands (possibly sulfate ions), may have a role in yeast cell-wall biogenesis | Core | NA | NA | NA |
| 1871-YBL002W | YBL002W | HTB2 | histone H2B | Histone H2B; core histone protein required for chromatin assembly and chromosome function; nearly identical to HTB1; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates reassembly after DNA replication, transcriptional activation, meiotic DSB formation and H3 methylation | Core | NA | NA | NA |
| 1872-YBL003C | YBL003C | HTA2 | histone H2A|H2A2 | Histone H2A; core histone protein required for chromatin assembly and chromosome function; one of two nearly identical (see also HTA1) subtypes; DNA damage-dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by Nat4p | Core | NA | NA | NA |
| 1873-YBL004W | YBL004W | UTP20 | NA | Component of the small-subunit (SSU) processome; SSU processome is involved in the biogenesis of the 18S rRNA | Core | NA | NA | NA |
| 1874-YBL005W | YBL005W | PDR3 | drug-responsive transcription factor PDR3|TPE2|AMY2 | Transcriptional activator of the pleiotropic drug resistance network; regulates expression of ATP-binding cassette (ABC) transporters through binding to cis-acting PDRE sites (PDR responsive elements); has a role in response to drugs and organic solvents; post-translationally up-regulated in cells lacking functional mitochondrial genome; involved in diauxic shift; relative distribution to nucleus increases upon DNA replication stress; APCC(Cdh1) substrate | Core | NA | NA | NA |
| 1875-YBL006C_NumOfGenes_2 | YBL006C | LDB7 | RSC14 | Component of the RSC chromatin remodeling complex; interacts with Rsc3p, Rsc30p, Npl6p, and Htl1p to form a module important for a broad range of RSC functions | Core | NA | NA | NA |
| 1876-YBL007C | YBL007C | SLA1 | cytoskeletal protein-binding protein SLA1 | Cytoskeletal protein binding protein; required for assembly of the cortical actin cytoskeleton; interacts with proteins regulating actin dynamics and proteins required for endocytosis; found in the nucleus and cell cortex; has 3 SH3 domains | Core | NA | NA | NA |
| 1877-YBL008W | YBL008W | HIR1 | NA | Subunit of the HIR complex; HIR is a nucleosome assembly complex involved in regulation of histone gene transcription; contributes to nucleosome formation, heterochromatic gene silencing, and formation of functional kinetochores | Core | NA | NA | NA |
| 1878-YBL008W-A | YBL008W-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Core | NA | NA | NA |
| 1879-YBL009W | YBL009W | ALK2 | protein kinase ALK2 | Protein kinase; along with its paralog, ALK1, required for proper spindle positioning and nuclear segregation following mitotic arrest, proper organization of cell polarity factors in mitosis, proper localization of formins and polarity factors, and survival in cells that activate spindle assembly checkpoint; phosphorylated in response to DNA damage; ALK2 has a paralog, ALK1, that arose from the whole genome duplication; similar to mammalian haspins | Core | NA | NA | NA |
| 1880-YBL010C | YBL010C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein colocalizes with clathrin-coated vesicles | Core | NA | NA | NA |
| 1881-YBL011W | YBL011W | SCT1 | bifunctional glycerol-3-phosphate/glycerone-phosphate O-acyltransferase SCT1|GAT2 | Glycerol 3-phosphate/dihydroxyacetone phosphate sn-1 acyltransferase; dual substrate-specific acyltransferase of the glycerolipid biosynthesis pathway; prefers 16-carbon fatty acids; similar to Gpt2p; gene is constitutively transcribed | Core | NA | NA | NA |
| 1882-YBL012C | YBL012C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |