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 |
|---|---|---|---|---|---|---|---|---|
| 7793-YPR174C | YPR174C | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nuclear periphery; potential Cdc28p substrate; binds phosphatidylinositols and phosphatidylethanolamine in a large-scale study; relative distribution to foci at the nuclear periphery increases upon DNA replication stress; YPR174C has a paralog, NBP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7794-YPR175W | YPR175W | DPB2 | DNA polymerase epsilon noncatalytic subunit | Second largest subunit of DNA polymerase II (DNA polymerase epsilon); required for maintenance of fidelity of chromosomal replication; essential motif in C-terminus is required for formation of the four-subunit Pol epsilon; expression peaks at the G1/S phase boundary; Cdc28p substrate | Core | NA | NA | NA |
| 7795-YPR176C | YPR176C | BET2 | Rab geranylgeranyltransferase BET2 | Beta subunit of Type II geranylgeranyltransferase; required for vesicular transport between the endoplasmic reticulum and the Golgi; provides a membrane attachment moiety to Rab-like proteins Ypt1p and Sec4p; human homolog RABGGTB can complement yeast BET2 mutant | Core | NA | NA | NA |
| 7796-YPR178W_NumOfGenes_2 | YPR178W | PRP4 | U4/U6-U5 snRNP complex subunit PRP4|RNA4 | Splicing factor; component of the U4/U6-U5 snRNP complex | Core | NA | NA | NA |
| 7797-YPR179C | YPR179C | HDA3 | PLO1 | Subunit of the HDA1 histone deacetylase complex; possibly tetrameric trichostatin A-sensitive class II histone deacetylase complex contains Hda1p homodimer and an Hda2p-Hda3p heterodimer; required for the activity of the complex; relocalizes to the cytosol in response to hypoxia; similar to Hda2p | Core | NA | NA | NA |
| 7798-YPR180W | YPR180W | AOS1 | E1 ubiquitin-activating protein AOS1|RHC31 | Subunit of heterodimeric nuclear SUMO activating enzyme E1 with Uba2p; activates Smt3p (SUMO) before its conjugation to proteins (sumoylation), which may play a role in protein targeting; essential for viability; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 7799-YPR181C | YPR181C | SEC23 | GTPase-activating protein SEC23 | GTPase-activating protein, stimulates the GTPase activity of Sar1p; component of the Sec23p-Sec24p heterodimer of the COPII vesicle coat, involved in ER to Golgi transport; substrate of Ubp3/Bre5 complex; ubiquitylated by Ub-ligase Rsp5p; proteasome-mediated degradation of Sec23p is regulated by Cdc48p | Core | NA | NA | NA |
| 7800-YPR182W | YPR182W | SMX3 | mRNA splicing protein SMX3|Sm F|SmF | Core Sm protein Sm F; part of heteroheptameric complex (with Smb1p, Smd1p, Smd2p, Smd3p, Sme1p, and Smx2p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; homolog of human Sm F | Core | NA | NA | NA |
| 7801-YPR183W | YPR183W | DPM1 | dolichyl-phosphate beta-D-mannosyltransferase|SED3 | Dolichol phosphate mannose (Dol-P-Man) synthase of ER membrane; catalyzes formation of Dol-P-Man from Dol-P and GDP-Man; required for biosynthesis of glycosyl phosphatidylinositol (GPI) membrane anchor, as well as O-mannosylation and protein N- and O-linked glycosylation; human homolog DPM1 can complement yeast mutant strains | Core | NA | NA | NA |
| 7802-YPR184W | YPR184W | GDB1 | bifunctional 4-alpha-glucanotransferase/amylo-alpha-1,6-glucosidase | Glycogen debranching enzyme; contains glucanotranferase and alpha-1,6-amyloglucosidase activities; required for glycogen degradation; phosphorylated in mitochondria; activity is inhibited by Igd1p; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 7803-YPR185W | YPR185W | ATG13 | serine/threonine protein kinase regulatory subunit ATG13|APG13 | Regulatory subunit of the Atg1p signaling complex; stimulates Atg1p kinase activity; required for vesicle formation during autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; contains a HORMA domain required for autophagy and for recruitment of the phosphatidylinositol 3-kinase complex subunit Atg14p to the pre-autophagosomal structure | Core | NA | NA | NA |
| 7804-YPR186C | YPR186C | PZF1 | TFC2 | Transcription factor IIIA (TFIIIA); essential DNA binding protein required for transcription of 5S rRNA by RNA polymerase III; not involved in transcription of other RNAP III genes; nine conserved zinc fingers; may also bind 5S rRNA | Core | NA | NA | NA |
| 7805-YPR187W | YPR187W | RPO26 | DNA-directed RNA polymerase core subunit RPO26|ABC23|RPB6 | RNA polymerase subunit ABC23; common to RNA polymerases I, II, and III; part of central core; similar to bacterial omega subunit | Core | NA | NA | NA |
| 7806-YPR188C | YPR188C | MLC2 | NA | Regulatory light chain for the type II myosin Myo1p; binds to an IQ motif of Myo1p, localization to the bud neck depends on Myo1p; involved in the disassembly of the Myo1p ring | Core | NA | NA | NA |
| 7807-YPR189W | YPR189W | SKI3 | SKI complex subunit tetratricopeptide repeat protein SKI3|SKI5 | Ski complex component and TPR protein; mediates 3'-5' RNA degradation by the cytoplasmic exosome; null mutants have superkiller phenotype of increased viral dsRNAs and are synthetic lethal with mutations in 5'-3' mRNA decay; mutations in the human ortholog, TTC37, causes Syndromic diarrhea/Trichohepatoenteric (SD/THE) syndrome | Core | NA | NA | NA |