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 |
|---|---|---|---|---|---|---|---|---|
| 2588-YDL142C | YDL142C | CRD1 | cardiolipin synthase|CLS1 | Cardiolipin synthase; produces cardiolipin, which is a phospholipid of the mitochondrial inner membrane that is required for normal mitochondrial membrane potential and function and for correct integration of membrane-multispanning proteins into the mitochondrial outer membrane; required to maintain tubular mitochondrial morphology and functions in mitochondrial fusion; also required for normal vacuolar ion homeostasis | Core | NA | NA | NA |
| 2589-YDL143W | YDL143W | CCT4 | chaperonin-containing T-complex subunit CCT4|ANC2|TCP4 | 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 |
| 2590-YDL144C | YDL144C | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YDL144C is not an essential gene; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2591-YDL145C | YDL145C | COP1 | coatomer subunit alpha|SOO1|RET1|SEC33 | Alpha subunit of COPI vesicle coatomer complex; complex surrounds transport vesicles in the early secretory pathway | Core | NA | NA | NA |
| 2592-YDL146W | YDL146W | LDB17 | NA | Protein involved in the regulation of endocytosis; transiently recruited to actin cortical patches in a SLA1-dependent manner after late coat component assembly; GFP-fusion protein localizes to the periphery, cytoplasm, bud, and bud neck | Core | NA | NA | NA |
| 2593-YDL147W | YDL147W | RPN5 | proteasome regulatory particle lid subunit RPN5|NAS5 | Subunit of the CSN and 26S proteasome lid complexes; similar to mammalian p55 subunit and to another S. cerevisiae regulatory subunit, Rpn7p; Rpn5p is an essential protein; the COP9 signalosome is also known as the CSN | Core | NA | NA | NA |
| 2594-YDL148C | YDL148C | NOP14 | snoRNA-binding rRNA-processing protein NOP14|UTP2 | Nucleolar protein; forms a complex with Noc4p that mediates maturation and nuclear export of 40S ribosomal subunits; also present in the small subunit processome complex, which is required for processing of pre-18S rRNA | Core | NA | NA | NA |
| 2595-YDL149W | YDL149W | ATG9 | autophagy protein ATG9|CVT6|APG9|CVT7|AUT9 | Transmembrane protein involved in forming Cvt and autophagic vesicles; cycles between the phagophore assembly site (PAS) and other cytosolic punctate structures, not found in autophagosomes; may be involved in membrane delivery to the PAS | Core | NA | NA | NA |
| 2596-YDL150W_NumOfGenes_2 | YDL150W | RPC53 | DNA-directed RNA polymerase III subunit C53|C53|RPC4 | RNA polymerase III subunit C53 | Core | NA | NA | NA |
| 2597-YDL152W | YDL152W | 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 SAS10/YDL153C, a component of the small ribosomal subunit processosome | Core | NA | NA | NA |
| 2598-YDL153C | YDL153C | SAS10 | rRNA-processing protein SAS10|UTP3 | Subunit of U3-containing Small Subunit (SSU) processome complex; involved in production of 18S rRNA and assembly of small ribosomal subunit; disrupts silencing when overproduced; mutant has increased aneuploidy tolerance; essential gene | Core | NA | NA | NA |
| 2599-YDL154W | YDL154W | MSH5 | MutS family protein MSH5 | Protein of the MutS family; forms a dimer with Msh4p that facilitates crossovers between homologs during meiosis; msh5-Y823H mutation confers tolerance to DNA alkylating agents; homologs present in C. elegans and humans | Core | NA | NA | NA |
| 2600-YDL155W | YDL155W | CLB3 | B-type cyclin CLB3 | B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the G2/M transition; may be involved in DNA replication and spindle assembly; accumulates during S phase and G2, then targeted for ubiquitin-mediated degradation; relative distribution to the nucleus increases upon DNA replication stress; CLB3 has a paralog, CLB4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2601-YDL156W | YDL156W | CMR1 | NA | Nuclear protein with a role in protein quality control; localizes to the intranuclear quality control compartment (INQ) in response to proteasome inhibition or DNA replication stress; INQ likely sequesters proteins involved in DNA metabolism for degradation or re-folding; DNA-binding protein with preference for UV-damaged DNA; contains three WD domains (WD-40 repeat); human ortholog WDR76 also exhibits perinuclear localization under similar stress conditions | Core | NA | NA | NA |
| 2602-YDL157C | YDL157C | NA | NA | Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Accessory | Ancestral | NA | NA |