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 |
|---|---|---|---|---|---|---|---|---|
| 3158-YDR469W | YDR469W | SDC1 | SAF19|CPS25 | Subunit of the COMPASS (Set1C) complex; COMPASS methylates lysine 4 of histone H3 and is required in chromatin silencing at telomeres; contains a Dpy-30 domain that mediates interaction with Bre2p; similar to C. elegans and human DPY-30 | Core | NA | NA | NA |
| 3159-YDR470C | YDR470C | UGO1 | NA | Outer membrane component of the mitochondrial fusion machinery; binds to Fzo1p and Mgm1p to link these two GTPases during mitochondrial fusion; involved in fusion of both the outer and inner membranes; facilitates dimerization of Fzo1p during fusion; import into the outer membrane is mediated by Tom70p and Mim1p; has similarity to carrier proteins but likely not a transporter; similar to human SLC25A46 implicated in optic atroprophy spectrum disorder | Core | NA | NA | NA |
| 3160-YDR471W | YDR471W | RPL27B | eL27|ribosomal 60S subunit protein L27B|L27e|L27B | Ribosomal 60S subunit protein L27B; homologous to mammalian ribosomal protein L27, no bacterial homolog; RPL27B has a paralog, RPL27A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3161-YDR472W | YDR472W | TRS31 | TRAPP subunit TRS31 | Core component of transport protein particle (TRAPP) complexes I-III; TRAPP complexes are related multimeric guanine nucleotide-exchange factor for the GTPase Ypt1p, regulating ER-Golgi traffic (TRAPPI), intra-Golgi traffic (TRAPPII), endosome-Golgi traffic (TRAPPII and III) and autophagy (TRAPPIII) | Core | NA | NA | NA |
| 3162-YDR473C | YDR473C | PRP3 | U4/U6-U5 snRNP complex subunit PRP3|RNA3 | Splicing factor; component of the U4/U6-U5 snRNP complex | Core | NA | NA | NA |
| 3163-YDR475C | YDR475C | JIP4 | YDR474C | Protein of unknown function; previously annotated as two separate ORFs, YDR474C and YDR475C, which were merged as a result of corrections to the systematic reference sequence; JIP4 has a paralog, YOR019W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3164-YDR476C | YDR476C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YDR476C is not an essential gene | Core | NA | NA | NA |
| 3165-YDR477W | YDR477W | SNF1 | AMP-activated serine/threonine-protein kinase catalytic subunit SNF1|PAS14|HAF3|GLC2|CCR1|CAT1 | AMP-activated S/T protein kinase; forms a complex with Snf4p and members of the Sip1p/Sip2p/Gal83p family; required for transcription of glucose-repressed genes, thermotolerance, sporulation, and peroxisome biogenesis; regulates nucleocytoplasmic shuttling of Hxk2p; regulates filamentous growth and acts as a non-canonical GEF, activating Arf3p during invasive growth; SUMOylation by Mms21p inhibits its function and targets Snf1p for destruction via the Slx5-Slx8 Ub ligase | Core | NA | NA | NA |
| 3166-YDR478W | YDR478W | SNM1 | NA | Ribonuclease MRP complex subunit; ribonuclease (RNase) MRP cleaves pre-rRNA and has a role in cell cycle-regulated degradation of daughter cell-specific mRNAs; binds to the NME1 RNA subunit of RNase MRP | Core | NA | NA | NA |
| 3167-YDR479C | YDR479C | PEX29 | NA | ER-resident protein involved in peroxisomal biogenesis; ER-localized protein that associates with peroxisomes; interacts with Pex30p and reticulons Rtn1p and Yop1p to regulate peroxisome biogenesis from the ER; role in peroxisomal-destined vesicular flow from the ER; regulates peroxisomal size, number and distribution; Pex28p and Pex29p may act at steps upstream of those mediated by Pex30p, Pex31p, and Pex32p; forms ER foci upon DNA replication stress | Core | NA | NA | NA |
| 3168-YDR480W | YDR480W | DIG2 | RST2 | MAP kinase-responsive inhibitor of the Ste12p transcription factor; involved in the regulation of mating-specific genes and the invasive growth pathway; related regulators Dig1p and Dig2p bind to Ste12p; DIG2 has a paralog, DIG1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3169-YDR481C | YDR481C | PHO8 | alkaline phosphatase PHO8|phoH | Repressible vacuolar alkaline phosphatase; regulated by levels of Pi and by Pho4p, Pho9p, Pho80p, Pho81p and Pho85p; dephosphorylates phosphotyrosyl peptides; contributes to NAD+ metabolism by producing nicotinamide riboside from NMN | Core | NA | NA | NA |
| 3170-YDR482C | YDR482C | CWC21 | U2-type spliceosomal complex subunit CWC21 | Protein involved in RNA splicing by the spliceosome; component of a complex containing Cef1p; interacts genetically with ISY1 and BUD13; may bind RNA; has similarity to S. pombe Cwf21p | Core | NA | NA | NA |
| 3171-YDR483W | YDR483W | KRE2 | alpha-1,2-mannosyltransferase KRE2|MNT1 | Alpha1,2-mannosyltransferase of the Golgi; involved in protein mannosylation; KRE2 has a paralog, KTR6, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3172-YDR484W | YDR484W | VPS52 | SAC2 | Component of the GARP (Golgi-associated retrograde protein) complex; GARP is required for the recycling of proteins from endosomes to the late Golgi, and for mitosis after DNA damage induced checkpoint arrest; involved in localization of actin and chitin; members of the GARP complex are Vps51p-Vps52p-Vps53p-Vps54p | Core | NA | NA | NA |