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 |
|---|---|---|---|---|---|---|---|---|
| 2903-YDR211W | YDR211W | GCD6 | translation initiation factor eIF2B catalytic subunit epsilon | Catalytic epsilon subunit of the translation initiation factor eIF2B; eIF2B is the guanine-nucleotide exchange factor for eIF2; activity subsequently regulated by phosphorylated eIF2; first identified as a negative regulator of GCN4 expression; forms cytoplasmic foci upon DNA replication stress | Core | NA | NA | NA |
| 2904-YDR212W | YDR212W | TCP1 | chaperonin-containing T-complex alpha subunit TCP1|CCT1 | Alpha subunit of chaperonin-containing T-complex; complex mediates protein folding in the cytosol; involved in actin cytoskeleton maintenance; overexpression in neurons suppresses formation of pathogenic conformations of huntingtin protein | Accessory | Ancestral | NA | NA |
| 2905-YDR213W | YDR213W | UPC2 | MOX4 | Sterol regulatory element binding protein; induces sterol biosynthetic genes, upon sterol depletion; acts as a sterol sensor, binding ergosterol in sterol rich conditions; relocates from intracellular membranes to perinuclear foci upon sterol depletion; redundant activator of filamentation with ECM22, up-regulating the expression of filamentous growth genes; contains a Zn[2]-Cys[6] binuclear cluster; UPC2 has a paralog, ECM22, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2906-YDR214W | YDR214W | AHA1 | NA | Co-chaperone that binds Hsp82p and activates its ATPase activity; plays a role in determining prion variants; similar to Hch1p; expression is regulated by stresses such as heat shock; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2907-YDR215C | YDR215C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; null mutant displays elevated sensitivity to expression of a mutant huntingtin fragment or of alpha-synuclein | Core | NA | NA | NA |
| 2908-YDR216W | YDR216W | ADR1 | DNA-binding transcription factor ADR1 | Carbon source-responsive zinc-finger transcription factor; required for transcription of the glucose-repressed gene ADH2, of peroxisomal protein genes, and of genes required for ethanol, glycerol, and fatty acid utilization | Core | NA | NA | NA |
| 2909-YDR217C | YDR217C | RAD9 | chromatin-binding protein RAD9 | DNA damage-dependent checkpoint protein; required for cell-cycle arrest in G1/S, intra-S, and G2/M, plays a role in postreplication repair (PRR) pathway; transmits checkpoint signal by activating Rad53p and Chk1p; hyperphosphorylated by Mec1p and Tel1p; multiple cyclin dependent kinase consensus sites and the C-terminal BRCT domain contribute to DNA damage checkpoint activation; Rad9p Chk1 Activating Domain (CAD) is phosphorylated at multiple sites by Cdc28p/Clb2p | Core | NA | NA | NA |
| 2910-YDR218C | YDR218C | SPR28 | septin SPR28 | Sporulation-specific homolog of the CDC3/10/11/12 family of genes; meiotic septin expressed at high levels during meiotic divisions and ascospore formation; the yeast CDC3/10/11/12 family is a family of bud neck microfilament genes | Core | NA | NA | NA |
| 2911-YDR219C | YDR219C | MFB1 | NA | Mitochondria-associated F-box protein; involved in maintenance of normal mitochondrial morphology; interacts with Skp1p through the F-box motif; preferentially localizes to the mother cell during budding | Core | NA | NA | NA |
| 2912-YDR220C | YDR220C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; null mutant exhibits synthetic phenotype with alpha-synuclein | Core | NA | NA | NA |
| 2913-YDR221W | YDR221W | GTB1 | NA | Glucosidase II beta subunit, forms a complex with alpha subunit Rot2p; involved in removal of two glucose residues from N-linked glycans during glycoprotein biogenesis in the ER; relocalizes from ER to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 2914-YDR222W | YDR222W | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern; YDR222W has a paralog, YLR225C, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2915-YDR223W | YDR223W | CRF1 | NA | Transcriptional corepressor; involved in repression of ribosomal protein (RP) gene transcription via the TOR signaling pathway which promotes accumulation of Crf1p in the nucleus; role in repression of RP genes varies by strain; CRF1 has a paralog, IFH1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2916-YDR224C | YDR224C | HTB1 | histone H2B|SPT12 | Histone H2B; core histone protein required for chromatin assembly and chromosome function; nearly identical to HTB2; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates reassembly after DNA replication, transcriptional activation, meiotic DSB formation and H3 methylation | Core | NA | NA | NA |
| 2917-YDR225W | YDR225W | HTA1 | histone H2A|SPT11|H2A1 | Histone H2A; core histone protein required for chromatin assembly and chromosome function; one of two nearly identical subtypes (see also HTA2); DNA damage-dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by Nat4p; N-terminally propionylated in vivo | Core | NA | NA | NA |