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 |
|---|---|---|---|---|---|---|---|---|
| 4478-YHR216W_NumOfGenes_6 | YHR216W | IMD2 | IMP dehydrogenase IMD2|PUR5 | Inosine monophosphate dehydrogenase; catalyzes the rate-limiting step in GTP biosynthesis, expression is induced by mycophenolic acid resulting in resistance to the drug, expression is repressed by nutrient limitation; IMD2 has a paralog, YAR073W/YAR075W, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 4479-YHR217C | YHR217C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; located in the telomeric region TEL08R | Accessory | Unknown | S. paradoxus | NA |
| 4480-YIL001W | YIL001W | NA | NA | Putative protein of unknown function; contains a BTB/POZ domain which generally function in protein interactions; deletion slightly improved competitive fitness in rich media; GFP-tagged protein is localized to the cytoplasm | Core | NA | NA | NA |
| 4481-YIL002C | YIL002C | INP51 | phosphoinositide 5-phosphatase INP51|SJL1 | Phosphatidylinositol 4,5-bisphosphate 5-phosphatase; synaptojanin-like protein with an N-terminal Sac1 domain, plays a role in phosphatidylinositol 4,5-bisphosphate homeostasis and in endocytosis; null mutation confers cold-tolerant growth | Core | NA | NA | NA |
| 4482-YIL002W-A | YIL002W-A | NA | NA | Putative protein of unknown function; identified by expression profiling and mass spectrometry | Core | NA | NA | NA |
| 4483-YIL003W | YIL003W | CFD1 | iron-sulfur cluster assembly protein CFD1|DRE3 | Highly conserved iron-sulfur cluster binding protein; localized in the cytoplasm; forms a complex with Nbp35p that is involved in iron-sulfur protein assembly in the cytosol | Core | NA | NA | NA |
| 4484-YIL004C | YIL004C | BET1 | SLY12 | Type II membrane protein required for vesicular transport; required for vesicular transport between the endoplasmic reticulum and Golgi complex; v-SNARE with similarity to synaptobrevins | Core | NA | NA | NA |
| 4485-YIL005W | YIL005W | EPS1 | protein disulfide isomerase EPS1 | ER protein with chaperone and co-chaperone activity; involved in retention of resident ER proteins; has a role in recognizing proteins targeted for ER-associated degradation (ERAD), member of the protein disulfide isomerase family | Core | NA | NA | NA |
| 4486-YIL006W | YIL006W | YIA6 | NAD+ transporter|NDT1 | Mitochondrial NAD+ transporter; involved in the transport of NAD+ into the mitochondria (see also YEA6); member of the mitochondrial carrier subfamily; disputed role as a pyruvate transporter; has putative mouse and human orthologs; YIA6 has a paralog, YEA6, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4487-YIL007C | YIL007C | NAS2 | NA | Evolutionarily conserved 19S regulatory particle assembly-chaperone; involved in assembly of the base subcomplex of the 19S proteasomal regulatory particle (RP); non-essential gene; interacts with Rpn4p; protein abundance increases in response to DNA replication stress; ortholog of human p27 | Core | NA | NA | NA |
| 4488-YIL008W | YIL008W | URM1 | ubiquitin-related modifier URM1 | Ubiquitin-like protein involved in thiolation of cytoplasmic tRNAs; receives sulfur from the E1-like enzyme Uba4p and transfers it to tRNA; also functions as a protein tag with roles in nutrient sensing and oxidative stress response | Core | NA | NA | NA |
| 4489-YIL009C-A_NumOfGenes_2 | YIL009C-A | EST3 | telomerase subunit EST3 | Component of the telomerase holoenzyme; involved in telomere replication; synthesis of the full-length protein results from a programmed +1 ribosomal frameshift | Core | NA | NA | NA |
| 4490-YIL009W | YIL009W | FAA3 | long-chain fatty acid-CoA ligase FAA3 | Long chain fatty acyl-CoA synthetase; activates imported fatty acids with a preference for C16:0-C18:0 chain lengths; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery | Core | NA | NA | NA |
| 4491-YIL010W | YIL010W | DOT5 | thioredoxin peroxidase DOT5 | Nuclear thiol peroxidase; functions as an alkyl-hydroperoxide reductase during post-diauxic growth | Accessory | Ancestral | NA | NA |
| 4492-YIL011W | YIL011W | TIR3 | YIB1 | Cell wall mannoprotein; member of Srp1p/Tip1p family of serine-alanine-rich proteins; expressed under anaerobic conditions and required for anaerobic growth; TIR3 has a paralog, TIR2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |