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 |
|---|---|---|---|---|---|---|---|---|
| 4703-YJL003W | YJL003W | COX16 | NA | Mitochondrial inner membrane protein; required for assembly of cytochrome c oxidase | Core | NA | NA | NA |
| 4704-YJL004C | YJL004C | SYS1 | NA | Integral membrane protein of the Golgi; required for targeting of the Arf-like GTPase Arl3p to the Golgi; multicopy suppressor of ypt6 null mutation | Core | NA | NA | NA |
| 4705-YJL005W | YJL005W | CYR1 | adenylate cyclase|FIL1|TSM0185|SRA4|HSR1|CDC35 | Adenylate cyclase; required for cAMP production and cAMP-dependent protein kinase signaling; the cAMP pathway controls a variety of cellular processes, including metabolism, cell cycle, stress response, stationary phase, and sporulation | Core | NA | NA | NA |
| 4706-YJL006C | YJL006C | CTK2 | NA | Beta subunit of C-terminal domain kinase I (CTDK-I); which phosphorylates both RNA pol II subunit Rpo21p to affect transcription and pre-mRNA 3' end processing, and ribosomal protein Rps2p to increase translational fidelity; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 4707-YJL007C | YJL007C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains | Core | NA | NA | NA |
| 4708-YJL008C | YJL008C | CCT8 | chaperonin-containing T-complex subunit CCT8 | Subunit of the cytosolic chaperonin Cct ring complex; related to Tcp1p, required for the assembly of actin and tubulins in vivo | Core | NA | NA | NA |
| 4709-YJL009W | YJL009W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps CCT8/YJL008C, a verified gene encoding a subunit of the cytosolic chaperonin Cct ring complex | Accessory | Ancestral | NA | NA |
| 4710-YJL010C | YJL010C | NOP9 | RNA-binding RNA processing protein NOP9 | Essential subunit of U3-containing 90S preribosome; involved in production of 18S rRNA and assembly of small ribosomal subunit; also part of pre-40S ribosome and required for its export into cytoplasm; binds RNA and contains pumilio domain | Core | NA | NA | NA |
| 4711-YJL011C | YJL011C | RPC17 | DNA-directed RNA polymerase III subunit RPC17|C17 | RNA polymerase III subunit C17; physically interacts with C31, C11, and TFIIIB70; may be involved in the recruitment of pol III by the preinitiation complex; protein abundance increases in response to DNA replication stress; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 4712-YJL012C | YJL012C | VTC4 | YJL012C-A|PHM3 | Vacuolar membrane polyphosphate polymerase; subunit of the vacuolar transporter chaperone (VTC) complex involved in synthesis and transfer of polyP to the vacuole; regulates membrane trafficking; role in non-autophagic vacuolar fusion; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4713-YJL013C | YJL013C | MAD3 | NA | Subunit of spindle-assembly checkpoint complex; involved in delaying anaphase onset in cells with defects in mitotic spindle assembly; pseudosubstrate inhibitor of APC(Cdc20), the anaphase promoting complex involved in securin (Pds1p) turnover; MAD3 has a paralog, BUB1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4714-YJL014W | YJL014W | CCT3 | chaperonin-containing T-complex subunit CCT3|TCP3|BIN2 | Subunit of the cytosolic chaperonin Cct ring complex; related to Tcp1p, required for the assembly of actin and tubulins in vivo; capable of binding Q/N rich proteins and mediating their folding | Core | NA | NA | NA |
| 4715-YJL015C | YJL015C | NA | NA | Dubious open reading frame unlikely to encode a functional protein; expression if heat-inducible; located in promoter region of essential CCT3 gene encoding a subunit of the cytosolic chaperonin Cct ring complex, overlaps ORF YJL016W | Accessory | Ancestral | NA | NA |
| 4716-YJL016W | YJL016W | TPH3 | YJL017W | Putative protein of unknown function; GFP-fusion protein localizes to the cytoplasm; contains two adjacent PH-like domains; conserved in closely related Saccharomyces species | Accessory | Ancestral | NA | NA |
| 4717-YJL019W | YJL019W | MPS3 | YJL018W|NEP98 | Nuclear envelope protein; required for SPB insertion, SPB duplication, Kar5p localization near the SPB and nuclear fusion; interacts with Mps2p to tether half-bridge to core SPB; N-terminal acetylation by Eco1p regulates its role in nuclear organization; localizes to the SPB half bridge and telomeres during meiosis; required with Ndj1p and Csm4p for meiotic bouquet formation and telomere-led rapid prophase movement; member of the SUN protein family (Sad1-UNC-84 homology) | Core | NA | NA | NA |