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 |
|---|---|---|---|---|---|---|---|---|
| 2048-YBR067C | YBR067C | TIP1 | putative lipase | Major cell wall mannoprotein with possible lipase activity; transcription is induced by heat- and cold-shock; member of the Srp1p/Tip1p family of serine-alanine-rich proteins | Accessory | Ancestral | NA | NA |
| 2049-YBR069C_NumOfGenes_3 | YBR069C | TAT1 | amino acid transporter TAT1|VAP1|TAP1 | Amino acid transporter for valine, leucine, isoleucine, and tyrosine; low-affinity tryptophan and histidine transporter; overexpression confers FK506 and FTY720 resistance; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2050-YBR070C_NumOfGenes_2 | YBR070C | ALG14 | N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase anchoring subunit ALG14 | Component of UDP-GlcNAc transferase; required for second step of dolichyl-linked oligosaccharide synthesis; anchors catalytic subunit Alg13p to ER membrane; similar to bacterial and human glycosyltransferases; both human homologs ALG13 and ALG14 are required to complement yeast alg14 mutant | Core | NA | NA | NA |
| 2051-YBR071W_NumOfGenes_2 | YBR071W | NA | NA | Protein of unknown function found in the cytoplasm and bud neck; mRNA expression may be regulated by the cell cycle and/or cell wall stress; overexpression of YBR071W affects endocytic protein trafficking | Core | NA | NA | NA |
| 2052-YBR072C-A | YBR072C-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Accessory | Unknown | NA | NA |
| 2053-YBR072W_NumOfGenes_2 | YBR072W | HSP26 | chaperone protein HSP26 | Small heat shock protein (sHSP) with chaperone activity; forms hollow, sphere-shaped oligomers that suppress unfolded proteins aggregation; long-lived protein that is preferentially retained in mother cells and forms cytoplasmic foci; oligomer activation requires heat-induced conformational change; also has mRNA binding activity | Core | NA | NA | NA |
| 2054-YBR073W | YBR073W | RDH54 | DNA-dependent ATPase RDH54|TID1 | DNA-dependent ATPase; DNA recombination/repair translocase, supercoils DNA and promotes DNA strand opening; stimulates strand exchange by modifying dsDNA topology; involved in recombinational repair of DNA double-strand breaks (DSBs) during mitosis and meiosis; phosphorylated in Mec1p-, Rad53p-dependent way in response to one DSB; contributes to remodelling of nucleosomes; proposed to be involved in crossover interference; interacts with Dmc1p; stimulates Dmc1p and Rad51p | Accessory | Ancestral | NA | NA |
| 2055-YBR074W | YBR074W | PFF1 | YBR075W | Multi-spanning vacuolar membrane protease; glycosylated transmembrane protein bearing homology to the M28 family of metalloproteases; has a lumenal-facing protease domain; proposed role in vacuole physiology | Accessory | Ancestral | NA | NA |
| 2056-YBR076C-A | YBR076C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps verified gene ECM8; identified by fungal homology and RT-PCR | Accessory | Unknown | NA | NA |
| 2057-YBR076W | YBR076W | ECM8 | NA | Non-essential protein of unknown function | Accessory | Ancestral | NA | NA |
| 2058-YBR077C | YBR077C | SLM4 | GSE1|NIR1|EGO3 | Component of the EGO and GSE complexes; essential for integrity and function of EGO; EGO is involved in the regulation of microautophagy and GSE is required for proper sorting of amino acid permease Gap1p; gene exhibits synthetic genetic interaction with MSS4 | Accessory | Ancestral | NA | NA |
| 2059-YBR078W | YBR078W | ECM33 | NA | GPI-anchored protein of unknown function; possible role in apical bud growth; GPI-anchoring on the plasma membrane crucial to function; phosphorylated in mitochondria; similar to Sps2p; ECM33 has a paralog, PST1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2060-YBR079C | YBR079C | RPG1 | translation initiation factor eIF3 core subunit a|TIF32 | eIF3a subunit of the eukaryotic translation initiation factor 3 (eIF3); subunit of the core complex of eIF3; essential for translation; part of a Prt1p-Rpg1p-Nip1p subcomplex that stimulates binding of mRNA and tRNA(i)Met to ribosomes; involved in translation reinitiation; eIF3 is also involved in programmed stop codon readthrough | Accessory | Ancestral | NA | NA |
| 2061-YBR080C | YBR080C | SEC18 | AAA family ATPase SEC18|ANU4 | AAA ATPase and SNARE disassembly chaperone; required for vesicular transport between ER and Golgi, the 'priming' step in homotypic vacuole fusion, autophagy, and protein secretion; releases Sec17p from SNAP complexes; has similarity to mammalian N-ethylmaleimide-sensitive factor (NSF) | Core | NA | NA | NA |
| 2062-YBR081C | YBR081C | SPT7 | SAGA histone acetyltransferase complex subunit SPT7|GIT2 | Subunit of the SAGA transcriptional regulatory complex; involved in proper assembly of the complex; also present as a C-terminally truncated form in the SLIK/SALSA transcriptional regulatory complex | Core | NA | NA | NA |