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 |
|---|---|---|---|---|---|---|---|---|
| 2468-YDL017W | YDL017W | CDC7 | serine/threonine protein kinase CDC7|SAS1|LSD6 | DDK (Dbf4-dependent kinase) catalytic subunit; required for origin firing and replication fork progression in mitotic S phase through phosphorylation of Mcm2-7p complexes and Cdc45p; kinase activity correlates with cyclical DBF4 expression; required for pre-meiotic DNA replication, meiotic DSB formation, recruitment of monopolin complex to kinetochores during meiosis I, regulation of meiosis-specific Ndt80p; mutation complemented by human CDC7 and DBF4 co-expression | Core | NA | NA | NA |
| 2469-YDL018C | YDL018C | ERP3 | NA | Protein with similarity to Emp24p and Erv25p; member of the p24 family involved in ER to Golgi transport | Core | NA | NA | NA |
| 2470-YDL019C | YDL019C | OSH2 | oxysterol-binding protein related protein OSH2 | Member of an oxysterol-binding protein family with seven members; in S. cerevisiae, family members have overlapping, redundant functions in sterol metabolism and collectively perform a function essential for viability; contains FFAT motif; interacts with ER anchor Scs2p at patches at the plasma membrane and at the nuclear envelope; regulated by sterol binding; OSH2 has a paralog, SWH1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2471-YDL020C | YDL020C | RPN4 | stress-regulated transcription factor RPN4|UFD5|SON1 | Transcription factor that stimulates expression of proteasome genes; Rpn4p levels are in turn regulated by the 26S proteasome in a negative feedback control mechanism; RPN4 is transcriptionally regulated by various stress responses; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 2472-YDL021W | YDL021W | GPM2 | phosphoglycerate mutase family protein GPM2 | Homolog of Gpm1p phosphoglycerate mutase; converts 3-phosphoglycerate to 2-phosphoglycerate in glycolysis; may be non-functional; GPM2 has a paralog, GPM3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2473-YDL022C-A | YDL022C-A | NA | NA | Protein of unknown function; SWAT-GFP and mCherry fusion proteins localize to the cytosol; partially overlaps the verified gene DIA3; identified by fungal homology and RT-PCR; mRNA identified as translated by ribosome profiling data | Core | NA | NA | NA |
| 2474-YDL022W_NumOfGenes_2 | YDL022W | GPD1 | glycerol-3-phosphate dehydrogenase (NAD(+)) GPD1|OSR5|OSG1|HOR1|DAR1 | NAD-dependent glycerol-3-phosphate dehydrogenase; key enzyme of glycerol synthesis, essential for growth under osmotic stress; expression regulated by high-osmolarity glycerol response pathway; protein abundance increases in response to DNA replication stress; constitutively inactivated via phosphorylation by the protein kinases Ypk1p and Ypk2p, dephosphorylation increases catalytic activity; forms a heterodimer with Pnc1p to facilitate its peroxisomal import | Core | NA | NA | NA |
| 2475-YDL024C | YDL024C | DIA3 | putative acid phosphatase DIA3 | Protein of unknown function; involved in invasive and pseudohyphal growth | Core | NA | NA | NA |
| 2476-YDL025C_NumOfGenes_2 | YDL025C | RTK1 | putative serine/threonine protein kinase RTK1 | Putative protein kinase, potentially phosphorylated by Cdc28p; interacts with ribosome biogenesis factors, Cka2, Gus1 and Arc1; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2477-YDL026W | YDL026W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Unknown | NA | NA |
| 2478-YDL027C | YDL027C | MRX9 | NA | Protein that associates with mitochondrial ribosome; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YDL027C is not an essential gene | Core | NA | NA | NA |
| 2479-YDL028C | YDL028C | MPS1 | serine/threonine/tyrosine protein kinase MPS1|PAC8|RPK1 | Dual-specificity kinase; autophosphorylation required for function; required for spindle pole body (SPB) duplication and spindle checkpoint function; contributes to bi-orientation by promoting formation of force-generating kinetochore-microtubule attachments in meiosis I; substrates include SPB proteins Spc42p, Spc110p, and Spc98p, mitotic exit network protein Mob1p, kinetochore protein Cnn1p, and checkpoint protein Mad1p; substrate of APCC(Cdh1); similar to human Mps1p | Core | NA | NA | NA |
| 2480-YDL029W | YDL029W | ARP2 | actin-related protein 2|ACT2 | Essential component of the Arp2/3 complex; Arp2/3 is a highly conserved actin nucleation center required for the motility and integrity of actin patches; involved in endocytosis and membrane growth and polarity; required for efficient Golgi-to-ER trafficking in COPI mutants | Core | NA | NA | NA |
| 2481-YDL030W | YDL030W | PRP9 | SF3a splicing factor complex subunit PRP9 | Subunit of the SF3a splicing factor complex; required for spliceosome assembly; acts after the formation of the U1 snRNP-pre-mRNA complex | Core | NA | NA | NA |
| 2482-YDL031W | YDL031W | DBP10 | putative ATP-dependent RNA helicase DBP10 | Putative ATP-dependent RNA helicase of the DEAD-box protein family; constituent of 66S pre-ribosomal particles; essential protein involved in ribosome biogenesis | Core | NA | NA | NA |