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 |
|---|---|---|---|---|---|---|---|---|
| 3818-YGL176C | YGL176C | NA | NA | Putative protein of unknown function; deletion mutant is viable and has no detectable phenotype | Core | NA | NA | NA |
| 3819-YGL178W_NumOfGenes_2 | YGL178W | MPT5 | UTH4|PUF5|HTR1 | mRNA-binding protein of the PUF family; binds to specific mRNAs, often in the 3' UTR; has broad specificity and binds to more than 1000 mRNAs (16% of the transcriptome); recruits the CCR4-NOT deadenylase complex to mRNAs along with Dhh1p and Dcp1p to promote deadenylation, decapping, and decay; also interacts with the Caf20p translational initiation repressor, affecting its mRNA target specificity | Core | NA | NA | NA |
| 3820-YGL179C | YGL179C | TOS3 | serine/threonine protein kinase TOS3 | Protein kinase; related to and functionally redundant with Elm1p and Sak1p for the phosphorylation and activation of Snf1p; functionally orthologous to LKB1, a mammalian kinase associated with Peutz-Jeghers cancer-susceptibility syndrome; TOS3 has a paralog, SAK1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3821-YGL180W | YGL180W | ATG1 | serine/threonine protein kinase ATG1|APG1|CVT10|AUT3 | Protein serine/threonine kinase; required for vesicle formation in autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; structurally required for phagophore assembly site formation; during autophagy forms a complex with Atg13p and Atg17p; essential for cell cycle progression from G2/M to G1 under nitrogen starvation | Core | NA | NA | NA |
| 3822-YGL181W | YGL181W | GTS1 | LSR1|FHT1 | Protein involved in Arf3p regulation and in transcription regulation; localizes to the nucleus and to endocytic patches; contains an N-terminal Zn-finger and ArfGAP homology domain, a C-terminal glutamine-rich region, and a UBA (ubiquitin associated) domain; gts1 mutations affect budding, cell size, heat tolerance, sporulation, life span, ultradian rhythms, endocytosis; expression oscillates in a pattern similar to metabolic oscillations | Core | NA | NA | NA |
| 3823-YGL182C | YGL182C | 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 MND1/YGL183C | Core | NA | NA | NA |
| 3824-YGL183C | YGL183C | MND1 | NA | Protein required for recombination and meiotic nuclear division; forms a complex with Hop2p, which is involved in chromosome pairing and repair of meiotic double-strand breaks | Core | NA | NA | NA |
| 3825-YGL184C | YGL184C | STR3 | cystathionine beta-lyase STR3 | Peroxisomal cystathionine beta-lyase; converts cystathionine into homocysteine; may be redox regulated by Gto1p; involved in the release of the aromatic thiol 3-mercaptohexanol during wine fermentation | Core | NA | NA | NA |
| 3826-YGL185C | YGL185C | NA | putative hydroxyacid dehydrogenase | Putative protein with sequence similar to hydroxyacid dehydrogenases; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm | Core | NA | NA | NA |
| 3827-YGL186C | YGL186C | TPN1 | NA | Plasma membrane pyridoxine (vitamin B6) transporter; member of the purine-cytosine permease subfamily within the major facilitator superfamily; proton symporter with similarity to Fcy21p, Fcy2p, and Fcy22p | Core | NA | NA | NA |
| 3828-YGL187C | YGL187C | COX4 | cytochrome c oxidase subunit IV | Subunit IV of cytochrome c oxidase; the terminal member of the mitochondrial inner membrane electron transport chain; precursor N-terminal 25 residues are cleaved during mitochondrial import; phosphorylated; spermidine enhances translation | Core | NA | NA | NA |
| 3829-YGL188C | YGL188C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 3830-YGL188C-A | YGL188C-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 3831-YGL189C | YGL189C | RPS26A | eS26|ribosomal 40S subunit protein S26A|S26e|S26A|RPS26 | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S26, no bacterial homolog; RPS26A has a paralog, RPS26B, that arose from the whole genome duplication; human homolog can partially complement an RPS26A, RPS26B double null mutant; mutations in the human gene are associated with Diamond-Blackfan anemia | Core | NA | NA | NA |
| 3832-YGL190C | YGL190C | CDC55 | TMR4|protein phosphatase 2A regulatory subunit CDC55 | Regulatory subunit B of protein phosphatase 2A (PP2A); Zds1p/2p-dependent localization to cytoplasm promotes mitotic entry; localization to nucleus prevents mitotic exit; required for correct nuclear division, chromosome segregation during achiasmate meiosis; maintains nucleolar sequestration of Cdc14p during early meiosis; limits formation of PP2A-Rts1p holocomplexes to ensure timely dissolution of sister chromosome cohesion; homolog of mammalian B55 | Core | NA | NA | NA |