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 |
|---|---|---|---|---|---|---|---|---|
| 2738-YDR048C | YDR048C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps ORF VMS1/YDR049W | Accessory | Ancestral | NA | NA |
| 2739-YDR049W_NumOfGenes_2 | YDR049W | VMS1 | NA | Component of a Cdc48p-complex involved in protein quality control; exhibits cytosolic and ER-membrane localization, with Cdc48p, during normal growth, and contributes to ER-associated degradation (ERAD) of specific substrates at a step after their ubiquitination; forms a mitochondrially-associated complex with Cdc48p and Npl4p under oxidative stress that is required for ubiquitin-mediated mitochondria-associated protein degradation (MAD); conserved in C. elegans and humans | Core | NA | NA | NA |
| 2740-YDR050C_NumOfGenes_2 | YDR050C | TPI1 | triose-phosphate isomerase TPI1 | Triose phosphate isomerase, abundant glycolytic enzyme; mRNA half-life is regulated by iron availability; transcription is controlled by activators Reb1p, Gcr1p, and Rap1p through binding sites in the 5' non-coding region; inhibition of Tpi1p activity by PEP (phosphoenolpyruvate) stimulates redox metabolism in respiring cells; E104D mutation in human homolog TPI1 causes a rare autosomal disease; human TPI1 can complement yeast null mutant | Core | NA | NA | NA |
| 2741-YDR051C | YDR051C | DET1 | acid phosphatase DET1 | Acid phosphatase; involved in the non-vesicular transport of sterols in both directions between the endoplasmic reticulum and plasma membrane; deletion confers sensitivity to nickel | Accessory | Ancestral | NA | NA |
| 2742-YDR052C_NumOfGenes_2 | YDR052C | DBF4 | protein serine/threonine kinase activating protein DBF4|DNA52|LSD7 | Regulatory subunit of Cdc7p-Dbf4p kinase complex; required for Cdc7p kinase activity and initiation of DNA replication; phosphorylates the Mcm2-7 family of proteins; cell cycle regulated; relative distribution to the nucleus increases upon DNA replication stress; co-expression of human CDC7 and DBF4 complements single cdc7 or dbf4 null mutations or the cdc7 dbf4 double null mutation | Accessory | Ancestral | NA | NA |
| 2743-YDR054C | YDR054C | CDC34 | SCF E2 ubiquitin-protein ligase catalytic subunit CDC34|UBC3|DNA6 | Ubiquitin-conjugating enzyme (E2); catalytic subunit of SCF ubiquitin-protein ligase complex (together with Skp1p, Rbx1p, Cdc53p, and an F-box protein) that regulates cell cycle progression by targeting key substrates for degradation; protein abundance increases in response to DNA replication stress; human CDC34 functionally complements the thermosensitivity of the cdc34-2 mutant | Accessory | Ancestral | NA | NA |
| 2744-YDR055W | YDR055W | PST1 | HPF2 | Cell wall protein that contains a putative GPI-attachment site; secreted by regenerating protoplasts; up-regulated by activation of the cell integrity pathway, as mediated by Rlm1p; upregulated by cell wall damage via disruption of FKS1; PST1 has a paralog, ECM33, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2745-YDR056C | YDR056C | EMC10 | NA | Putative protein of unknown function; subunit of evolutionarily conserved EMC (Endoplasmic Reticulum Membrane Complex) implicated in ERAD (ER-associated degradation) and proper assembly of multi-pass transmembrane (TM) proteins; EMC acts in yeast as an ER-mitochondria tether that interacts with outer membrane protein Tom5p of TOM (Translocase of the Mitochondrial Outer Membrane) complex; YDR056C is not an essential protein | Accessory | Ancestral | NA | NA |
| 2746-YDR057W | YDR057W | YOS9 | NA | ER quality-control lectin; integral subunit of the HRD ligase; participates in efficient ER retention of misfolded proteins by recognizing them and delivering them to Hrd1p; binds to glycans with terminal alpha-1,6 linked mannose on misfolded N-glycosylated proteins and participates in targeting proteins to ERAD; member of the OS-9 protein family | Accessory | Ancestral | NA | NA |
| 2747-YDR058C | YDR058C | TGL2 | triglyceride lipase | Triacylglycerol lipase that is localized to the mitochondria; has lipolytic activity towards triacylglycerols and diacylglycerols when expressed in E. coli | Accessory | Ancestral | NA | NA |
| 2748-YDR059C | YDR059C | UBC5 | E2 ubiquitin-conjugating protein UBC5 | Ubiquitin-conjugating enzyme; mediates selective degradation of short-lived, abnormal, or excess proteins, including histone H3; central component of the cellular stress response; expression is heat inducible; protein abundance increases in response to DNA replication stress; UBC5 has a paralog, UBC4, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2749-YDR060W | YDR060W | MAK21 | RNA-binding ribosome biosynthesis protein MAK21|NOC1 | Constituent of 66S pre-ribosomal particles; required for large (60S) ribosomal subunit biogenesis; acts as part of a Mak21p-Noc2p-Rrp5p module that associates with nascent pre-rRNA during transcription and has a role in bigenesis of the large ribosomal subunit; involved in nuclear export of pre-ribosomes; required for maintenance of dsRNA virus; homolog of human CAATT-binding protein | Core | NA | NA | NA |
| 2750-YDR061W | YDR061W | NA | NA | Protein with similarity to ABC transporter family members; lacks predicted membrane-spanning regions; transcriptionally activated by Yrm1p along with genes involved in multidrug resistance | Core | NA | NA | NA |
| 2751-YDR062W | YDR062W | LCB2 | serine C-palmitoyltransferase LCB2|TSC1|SCS1 | Component of serine palmitoyltransferase; responsible along with Lcb1p for the first committed step in sphingolipid synthesis, which is the condensation of serine with palmitoyl-CoA to form 3-ketosphinganine | Core | NA | NA | NA |
| 2752-YDR063W | YDR063W | AIM7 | GMF1|GMF | Protein that interacts with Arp2/3 complex; interacts with Arp2/3 complex to stimulate actin filament debranching and inhibit actin nucleation; has similarity to Cof1p and also to human glia maturation factor (GMF); null mutant displays elevated mitochondrial genome loss | Core | NA | NA | NA |