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 |
|---|---|---|---|---|---|---|---|---|
| 3953-YGR053C | YGR053C | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 3954-YGR054W | YGR054W | NA | NA | Eukaryotic initiation factor eIF2A; associates specifically with both 40S subunits and 80 S ribosomes, and interacts genetically with both eIF5b and eIF4E; homologous to mammalian eIF2A | Core | NA | NA | NA |
| 3955-YGR055W | YGR055W | MUP1 | NA | High affinity methionine permease; integral membrane protein with 13 putative membrane-spanning regions; also involved in cysteine uptake | Core | NA | NA | NA |
| 3956-YGR056W | YGR056W | RSC1 | RSC subunit protein RSC1 | Component of the RSC chromatin remodeling complex; required for expression of mid-late sporulation-specific genes; contains two essential bromodomains, a bromo-adjacent homology (BAH) domain, and an AT hook; RSC1 has a paralog, RSC2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3957-YGR057C | YGR057C | LST7 | NA | Subunit of the Lst4p-Lst7p GTPase activating protein complex for Gtr2p; stimulates the GTPase activity of Rag family GTPase Gtr2p, within the context of the Gtr1p-Gtr2p heterodimer, after amino acid stimulation; required for activation of TORC1 in response to amino acid stimulation; recruited to the vacuolar membrane during amino acid starvation and released from the membrane by TORC1; required for the transport of amino acid permease Gap1p from the Golgi to the cell surface | Core | NA | NA | NA |
| 3958-YGR058W | YGR058W | PEF1 | NA | Penta-EF-hand protein; required for polar bud growth and cell wall abscission; binds calcium and zinc with different affinity; localizes to bud site in G1, bud neck in G2; binds to Sec31p and modulates COPII coat assembly | Core | NA | NA | NA |
| 3959-YGR059W | YGR059W | SPR3 | septin SPR3 | Sporulation-specific homolog of the CDC3/10/11/12 family of genes; septin protein involved in sporulation; regulated by ABFI; the yeast CDC3/10/11/12 family is a family of bud neck microfilament genes | Core | NA | NA | NA |
| 3960-YGR060W | YGR060W | ERG25 | methylsterol monooxygenase | C-4 methyl sterol oxidase; catalyzes the first of three steps required to remove two C-4 methyl groups from an intermediate in ergosterol biosynthesis; mutants accumulate the sterol intermediate 4,4-dimethylzymosterol; human MSMO1 functionally complements the growth defect caused by repression of ERG25 expression | Core | NA | NA | NA |
| 3961-YGR061C | YGR061C | ADE6 | phosphoribosylformylglycinamidine synthase | Formylglycinamidine-ribonucleotide (FGAM)-synthetase; catalyzes a step in the 'de novo' purine nucleotide biosynthetic pathway | Core | NA | NA | NA |
| 3962-YGR062C | YGR062C | COX18 | membrane insertase COX18|OXA2 | Protein required for membrane insertion of C-terminus of Cox2p; mitochondrial integral inner membrane protein; interacts genetically and physically with Mss2p and Pnt1p; similar to S. cerevisiae Oxa1, N. crassa Oxa2p, and E. coli YidC; respiratory defect of the null mutant is functionally complemented by human COX18 carrying the N-terminal 54 amino acids of S. cerevisiae Cox18p | Core | NA | NA | NA |
| 3963-YGR063C | YGR063C | SPT4 | transcription elongation factor SPT4 | Spt4p/5p (DSIF) transcription elongation factor complex subunit; the Spt4/5 complex binds to ssRNA in a sequence-specific manner, and along with RNAP I and II has multiple roles regulating transcriptional elongation, RNA processing, quality control, and transcription-coupled repair; localizes to kinetochores and heterochromatin, influencing chromosomal dynamics and silencing; required for transcription through long trinucleotide repeats in ORFs and non-protein coding regions | Accessory | Ancestral | NA | NA |
| 3964-YGR064W | YGR064W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF SPT4/YGR063C | Accessory | Ancestral | NA | NA |
| 3965-YGR065C | YGR065C | VHT1 | NA | High-affinity plasma membrane H+-biotin (vitamin H) symporter; mutation results in fatty acid auxotrophy; 12 transmembrane domain containing major facilitator subfamily member; mRNA levels negatively regulated by iron deprivation and biotin | Core | NA | NA | NA |
| 3966-YGR066C | YGR066C | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 3967-YGR067C | YGR067C | NA | NA | Putative protein of unknown function; contains a zinc finger motif similar to that of Adr1p | Core | NA | NA | NA |