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 |
|---|---|---|---|---|---|---|---|---|
| 3443-YER114C | YER114C | BOI2 | BEB1 | Protein implicated in polar growth, functionally redundant with Boi1p; interacts with bud-emergence protein Bem1p; contains an SH3 (src homology 3) domain and a PH (pleckstrin homology) domain; BOI2 has a paralog, BOI1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3444-YER115C | YER115C | SPR6 | NA | Protein of unknown function; expressed during sporulation; not required for sporulation, but gene exhibits genetic interactions with other genes required for sporulation | Core | NA | NA | NA |
| 3445-YER116C | YER116C | SLX8 | SUMO-targeted ubiquitin ligase complex subunit SLX8 | Subunit of Slx5-Slx8 SUMO-targeted ubiquitin ligase (STUbL) complex; role in proteolysis of spindle positioning protein Kar9, DNA repair proteins Rad52p and Rad57p; stimulated by SUMO-modified substrates; contains a C-terminal RING domain; forms nuclear foci upon DNA replication stress; required for maintenance of genome integrity like human ortholog RNF | Core | NA | NA | NA |
| 3446-YER117W | YER117W | RPL23B | uL14|ribosomal 60S subunit protein L23B|L14|YL32|L23B|L17aB | Ribosomal 60S subunit protein L23B; homologous to mammalian ribosomal protein L23 and bacterial L14; RPL23B has a paralog, RPL23A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3447-YER118C | YER118C | SHO1 | osmosensor SHO1|SSU81 | Transmembrane osmosensor for filamentous growth and HOG pathways; involved in activation of the Cdc42p- and MAP kinase-dependent filamentous growth pathway and the high-osmolarity glycerol (HOG) response pathway; phosphorylated by Hog1p; interacts with Pbs2p, Msb2p, Hkr1p, and Ste11p | Core | NA | NA | NA |
| 3448-YER119C | YER119C | AVT6 | aspartate/glutamate transporter | Vacuolar aspartate and glutamate exporter; member of a family of seven genes (AVT1-7) related to vesicular GABA-glycine transporters; involved in compartmentalizing acidic amino acids in response to nitrogen starvation; AVT6 has a paralog, AVT5, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3449-YER119C-A | YER119C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; not conserved in closely related Saccharomyces species; deletion mutation blocks replication of Brome mosaic virus in S. cerevisiae, but this is likely due to effects on the overlapping gene SCS2 | Core | NA | NA | NA |
| 3450-YER120W | YER120W | SCS2 | phosphatidylinositol-binding protein SCS2 | Integral ER membrane protein, regulates phospholipid metabolism; one of 6 proteins (Ist2p, Scs2p, Scs22p, Tcb1p, Tcb2p, Tcb3p) that connect ER to plasma membrane (PM) and regulate PI4P levels by controlling access of Sac1p phosphatase to substrate PI4P in the PM; interacts with FFAT motifs in Opi1p, Swh1p, Osh2p, and Osh3p; involved in telomeric silencing; VAP homolog; SCS2 has a paralog, SCS22, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3451-YER121W | YER121W | NA | NA | Putative protein of unknown function; may be involved in phosphatase regulation and/or generation of precursor metabolites and energy | Core | NA | NA | NA |
| 3452-YER122C | YER122C | GLO3 | ADP-ribosylation factor GTPase-activating protein | ADP-ribosylation factor GTPase activating protein (ARF GAP); involved in ER-Golgi transport; shares functional similarity with Gcs1p | Core | NA | NA | NA |
| 3453-YER123W | YER123W | YCK3 | casein kinase YCK3|CKI3 | Palmitoylated vacuolar membrane-localized casein kinase I isoform; negatively regulates vacuole fusion during hypertonic stress via phosphorylation of Vps41p; shares essential functions with Hrr25p; regulates vesicle fusion in AP-3 pathway | Core | NA | NA | NA |
| 3454-YER124C | YER124C | DSE1 | NA | Daughter cell-specific protein; may regulate cross-talk between the mating and filamentation pathways; deletion affects cell separation after division and sensitivity to alpha-factor and drugs affecting the cell wall; relocalizes from bud neck to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 3455-YER125W | YER125W | RSP5 | NEDD4 family E3 ubiquitin-protein ligase|SMM1|UBY1|NPI1|MUT2|MDP1 | NEDD4 family E3 ubiquitin ligase; regulates processes including: MVB sorting, the heat shock response, transcription, endocytosis and ribosome stability; ubiquitinates Sec23p, Sna3p, Ste4p, Nfi1p, Rpo21p and Sem1p; autoubiquitinates; deubiquitinated by Ubp2p; regulated by SUMO ligase Siz1p, in turn regulates Siz1p SUMO ligase activity; required for efficient Golgi-to-ER trafficking in COPI mutants; mutant tolerates aneuploidy; human homolog implicated in Liddle syndrome | Core | NA | NA | NA |
| 3456-YER126C | YER126C | NSA2 | rRNA-processing protein NSA2 | Protein constituent of 66S pre-ribosomal particles; contributes to processing of the 27S pre-rRNA; recruited by ribosomal proteins L17, L35, and L37 to assembling ribosomes after 27SB pre-rRNA is generated, immediately preceding removal of ITS2 | Core | NA | NA | NA |
| 3457-YER127W | YER127W | LCP5 | NA | Essential protein involved in maturation of 18S rRNA; depletion leads to inhibited pre-rRNA processing and reduced polysome levels; localizes primarily to the nucleolus | Core | NA | NA | NA |