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 |
|---|---|---|---|---|---|---|---|---|
| 3008-YDR318W | YDR318W | MCM21 | CTF5 | Component of the kinetochore sub-complex COMA; COMA (Ctf19p, Okp1p, Mcm21p, Ame1p) bridges kinetochore subunits in contact with centromeric DNA with subunits bound to microtubules during kinetochore assembly; involved in minichromosome maintenance; modified by sumoylation; orthologous to human centromere constitutive-associated network (CCAN) subunit CENP-O and fission yeast mal2 | Core | NA | NA | NA |
| 3009-YDR319C | YDR319C | YFT2 | FIT2A | Protein required for normal ER membrane biosynthesis; member of the highly conserved FIT family of proteins involved in triglyceride droplet biosynthesis and homologous to human FIT2; interacts with Sst2p and Hsp82p in high-throughput two-hybrid screens | Core | NA | NA | NA |
| 3010-YDR320C | YDR320C | SWA2 | BUD24|AUX1 | Auxilin-like protein involved in vesicular transport; clathrin-binding protein required for uncoating of clathrin-coated vesicles | Core | NA | NA | NA |
| 3011-YDR320C-A | YDR320C-A | DAD4 | HSK2 | Essential subunit of the Dam1 complex (aka DASH complex); complex couples kinetochores to the force produced by MT depolymerization thereby aiding in chromosome segregation; is transferred to the kinetochore prior to mitosis | Core | NA | NA | NA |
| 3012-YDR320W-B | YDR320W-B | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps the verified gene DAD4/YDR320C-A | Core | NA | NA | NA |
| 3013-YDR321W | YDR321W | ASP1 | asparaginase ASP1 | Cytosolic L-asparaginase, involved in asparagine catabolism; catalyzes hydrolysis of L-asparagine to aspartic acid and ammonia; important enzyme for the treatment of acute lymphoblastic leukemia; has low glutaminase activity and dependence; synthesized constitutively | Core | NA | NA | NA |
| 3014-YDR322C-A | YDR322C-A | TIM11 | F1F0 ATP synthase subunit e|ATP21 | Subunit e of mitochondrial F1F0-ATPase; ATPase is a large, evolutionarily conserved enzyme complex required for ATP synthesis; essential for the dimeric and oligomeric state of ATP synthase, which in turn determines the shape of inner membrane cristae | Core | NA | NA | NA |
| 3015-YDR322W | YDR322W | MRPL35 | mitochondrial 54S ribosomal protein YmL35|YmL35 | Mitochondrial ribosomal protein of the large subunit | Core | NA | NA | NA |
| 3016-YDR323C | YDR323C | PEP7 | VPT19|VPS19|VPL21|VAC1 | Adaptor protein involved in vesicle-mediated vacuolar protein sorting; multivalent adaptor protein; facilitates vesicle-mediated vacuolar protein sorting by ensuring high-fidelity vesicle docking and fusion, which are essential for targeting of vesicles to the endosome; required for vacuole inheritance | Core | NA | NA | NA |
| 3017-YDR324C | YDR324C | UTP4 | NA | Subunit of U3-containing 90S preribosome and SSU processome complexes; involved in production of 18S rRNA and assembly of small ribosomal subunit; member of t-Utp subcomplex involved with transcription of 35S rRNA transcript; Small Subunit processome is also known as SSU processome | Core | NA | NA | NA |
| 3018-YDR325W | YDR325W | YCG1 | condensin subunit YCG1|YCS5|TIE1 | Subunit of the condensin complex; required for establishment and maintenance of chromosome condensation, chromosome segregation and chromatin binding by the complex; required for tRNA genes clustering at the nucleolus; required for replication slow zone breakage following Mec1p inactivation; transcription is cell cycle regulated, peaking in mitosis and declining in G1; protein is constitutively degraded by the proteasome; rate limiting for condensin recruitment to chromatin | Core | NA | NA | NA |
| 3019-YDR326C | YDR326C | YSP2 | LAM2|LTC4 | Sterol-binding protein; has a probable role in retrograde transport of sterols from the plasma membrane to the ER; contains two StART-like domains that bind sterols and a GRAM domain; co-localizes to puncta in the cortical ER with Sip3p; one of six StART-like domain-containing proteins in yeast that may be involved in sterol transfer between intracellular membranes; conserved across eukaryotes | Core | NA | NA | NA |
| 3020-YDR327W | YDR327W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene SKP1 | Accessory | Ancestral | NA | NA |
| 3021-YDR328C | YDR328C | SKP1 | SCF ubiquitin ligase subunit SKP1|CBF3D|MGO1 | Evolutionarily conserved kinetochore protein; part of multiple protein complexes, including the SCF ubiquitin ligase complex, the CBF3 complex that binds centromeric DNA, and the RAVE complex that regulates assembly of the V-ATPase; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3022-YDR329C | YDR329C | PEX3 | PAS3 | Peroxisomal membrane protein (PMP); required for proper localization and stability of PMPs; anchors peroxisome retention factor Inp1p at the peroxisomal membrane; interacts with Pex19p | Core | NA | NA | NA |