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 |
|---|---|---|---|---|---|---|---|---|
| 2768-YDR079C-A | YDR079C-A | TFB5 | TFIIH complex subunit TFB5 | Component of RNA polymerase II general transcription factor TFIIH; involved in transcription initiation and in nucleotide-excision repair; relocalizes to the cytosol in response to hypoxia; homolog of Chlamydomonas reinhardtii REX1-S protein involved in DNA repair | Core | NA | NA | NA |
| 2769-YDR079W | YDR079W | PET100 | NA | Chaperone that facilitates the assembly of cytochrome c oxidase; integral to the mitochondrial inner membrane; interacts with a subcomplex of subunits VII, VIIa, and VIII (Cox7p, Cox9p, and Cox8p) but not with the holoenzyme | Core | NA | NA | NA |
| 2770-YDR080W | YDR080W | VPS41 | VPL20|VAM2|SVL2|FET2|CVT8 | Subunit of the HOPS endocytic tethering complex; vacuole membrane protein that functions as a Rab GTPase effector, interacting specifically with the GTP-bound conformation of Ypt7p, facilitating tethering, docking and promoting membrane fusion events at the late endosome and vacuole; required for both membrane and protein trafficking; Yck3p-mediated phosphorylation regulates the organization of vacuolar fusion sites | Core | NA | NA | NA |
| 2771-YDR081C | YDR081C | PDC2 | NA | Transcription factor for thiamine-regulated genes; required for expression of the two isoforms of pyruvate decarboxylase (PDC1 and PDC5) along with thiamine biosynthetic genes; binds a DNA sequence in the PDC5 promoter; mutant fails to grow on 2% glucose and thus is scored as inviable under standard conditions | Core | NA | NA | NA |
| 2772-YDR082W | YDR082W | STN1 | NA | Telomere end-binding and capping protein; plays a key role with Pol12p in linking telomerase action with completion of lagging strand synthesis, and in a regulatory step required for telomere capping; similar to human Stn1 | Core | NA | NA | NA |
| 2773-YDR083W | YDR083W | RRP8 | 25S rRNA (adenine645-N1)-methyltransferase | Nucleolar S-adenosylmethionine-dependent rRNA methyltransferase; methylates adenine (m1A) of the large subunit (LSU) rRNA at position 645; involved in pre-rRNA cleavage at site A2; mutation is synthetically lethal with a gar1 mutation; deletion disrupts telomere maintenance by influencing the expression of neighboring gene STN1 | Core | NA | NA | NA |
| 2774-YDR084C | YDR084C | TVP23 | NA | Integral membrane protein; localized to late Golgi vesicles along with the v-SNARE Tlg2p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern | Core | NA | NA | NA |
| 2775-YDR085C | YDR085C | AFR1 | NA | Protein required for pheromone-induced projection (shmoo) formation; regulates septin architecture during mating; has an RVXF motif that mediates targeting of Glc7p to mating projections; interacts with Cdc12p; AFR1 has a paralog, YER158C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2776-YDR086C | YDR086C | SSS1 | translocon subunit SSS1 | Subunit of the Sec61p translocation complex (Sec61p-Sss1p-Sbh1p); this complex forms a channel for passage of secretory proteins through the endoplasmic reticulum membrane, and of the Ssh1p complex (Ssh1p-Sbh2p-Sss1p); interacts with Ost4p and Wbp1p | Core | NA | NA | NA |
| 2777-YDR087C | YDR087C | RRP1 | NA | Essential evolutionarily conserved nucleolar protein; necessary for biogenesis of 60S ribosomal subunits and for processing of pre-rRNAs to mature rRNA; associated with several distinct 66S pre-ribosomal particles | Core | NA | NA | NA |
| 2778-YDR088C | YDR088C | SLU7 | mRNA splicing protein SLU7|SLT17 | RNA splicing factor; required for ATP-independent portion of 2nd catalytic step of spliceosomal RNA splicing; interacts with Prp18p; contains zinc knuckle domain | Core | NA | NA | NA |
| 2779-YDR089W | YDR089W | VTC5 | NA | Novel subunit of the vacuolar transporter chaperone complex; vacuolar transmembrane protein that regulates biosynthesis of polyphosphate; deletion reduces and overexpression increases polyP accumulation; SPX domain (Syg1, Pho81, Xpr1)-containing protein involved in phosphate homeostasis; relocalizes from vacuole to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 2780-YDR090C | YDR090C | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 2781-YDR091C | YDR091C | RLI1 | Fe-S cluster-binding ribosome biosynthesis protein | Essential Fe-S protein; required for ribosome biogenesis, translation initiation/termination; facilitates binding of multifactor complex (MFC) of initiation factors to small ribosomal subunit; Dom34-Hbs1 complex and Rli1p work in dissociating inactive ribosomes, thereby facilitating translation restart; forms complex with Lto1p and Yae1p; dependency on ROS-labile FeS clusters, activity in nuclear ribosomal-subunit export impaired by mild oxidative stress | Core | NA | NA | NA |
| 2782-YDR092W | YDR092W | UBC13 | E2 ubiquitin-conjugating protein UBC13 | E2 ubiquitin-conjugating enzyme; involved in the error-free DNA postreplication repair pathway; interacts with Mms2p to assemble ubiquitin chains at the Ub Lys-63 residue; DNA damage triggers redistribution from the cytoplasm to the nucleus | Core | NA | NA | NA |