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 |
|---|---|---|---|---|---|---|---|---|
| 6263-YMR196W | YMR196W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YMR196W is not an essential gene | Core | NA | NA | NA |
| 6264-YMR197C | YMR197C | VTI1 | v-SNARE protein VTI1 | Protein involved in cis-Golgi membrane traffic; v-SNARE that interacts with two t-SNARES, Sed5p and Pep12p; required for multiple vacuolar sorting pathways; human homolog VTI1A can complement yeast null mutant | Core | NA | NA | NA |
| 6265-YMR198W | YMR198W | CIK1 | NA | Kinesin-associated protein; required for both karyogamy and mitotic spindle organization, interacts stably and specifically with Kar3p and may function to target this kinesin to a specific cellular role; locus encodes a long and short transcript with differing functions; CIK1 has a paralog, VIK1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6266-YMR199W | YMR199W | CLN1 | cyclin CLN1 | G1 cyclin involved in regulation of the cell cycle; activates Cdc28p kinase to promote the G1 to S phase transition; late G1 specific expression depends on transcription factor complexes, MBF (Swi6p-Mbp1p) and SBF (Swi6p-Swi4p); CLN1 has a paralog, CLN2, that arose from the whole genome duplication; cell cycle arrest phenotype of the cln1 cln2 cln3 triple null mutant is complemented by any of human cyclins CCNA2, CCNB1, CCNC, CCND1, or CCNE1 | Core | NA | NA | NA |
| 6267-YMR200W | YMR200W | ROT1 | NA | Molecular chaperone involved in protein folding in ER; mutation causes defects in cell wall synthesis and lysis of autophagic bodies, suppresses tor2 mutations, and is synthetically lethal with kar2-1 and with rot2 mutations; involved in N-linked glycosylation and O-mannosylation; transmembrane helix Ser250 is essential for Rot1p to interact with other membrane components and exert its functional role, avoiding exposure of Ser H-bonding group at lipid-exposed surface | Core | NA | NA | NA |
| 6268-YMR201C | YMR201C | RAD14 | NA | Protein that recognizes and binds damaged DNA during NER; subunit of Nucleotide Excision Repair Factor 1 (NEF1); contains zinc finger motif; homolog of human XPA protein; NER stands for nucleotide excision repair | Core | NA | NA | NA |
| 6269-YMR202W | YMR202W | ERG2 | C-8 sterol isomerase ERG2|END11 | C-8 sterol isomerase; catalyzes isomerization of delta-8 double bond to delta-7 position at an intermediate step in ergosterol biosynthesis; transcriptionally down-regulated when ergosterol is in excess; mutation is functionally complemented by human EBP | Core | NA | NA | NA |
| 6270-YMR203W | YMR203W | TOM40 | MOM38|ISP42 | Component of the TOM (translocase of outer membrane) complex; responsible for recognition and initial import steps for all mitochondrially directed proteins; constitutes the core element of the protein conducting pore; pre-Tom40p is phosphorylated by PKA, which impairs its import into mitochondria under non-respiratory conditions | Core | NA | NA | NA |
| 6271-YMR204C | YMR204C | INP1 | NA | Peripheral membrane protein of peroxisomes; involved in peroxisomal inheritance; recruitment to peroxisomes is mediated by interaction with Pex3p at the peroxisomal membrane | Core | NA | NA | NA |
| 6272-YMR205C | YMR205C | PFK2 | 6-phosphofructokinase subunit beta | Beta subunit of heterooctameric phosphofructokinase; involved in glycolysis; indispensable for anaerobic growth; activated by fructose-2,6-bisphosphate and AMP; mutation inhibits glucose induction of cell cycle-related genes | Core | NA | NA | NA |
| 6273-YMR206W | YMR206W | NA | NA | Putative protein of unknown function; not an essential gene; YMR206W has a paralog, YNR014W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6274-YMR207C | YMR207C | HFA1 | acetyl-CoA carboxylase HFA1 | Mitochondrial acetyl-coenzyme A carboxylase; catalyzes production of malonyl-CoA in mitochondrial fatty acid biosynthesis; relocalizes from mitochondrion to cytoplasm upon DNA replication stress; genetic and comparative analysis suggests that translation begins at a non-canonical (Ile) start codon at -372 relative to the annotated start codon | Core | NA | NA | NA |
| 6275-YMR208W | YMR208W | ERG12 | mevalonate kinase|RAR1 | Mevalonate kinase; acts in the biosynthesis of isoprenoids and sterols, including ergosterol, from mevalonate; human MVK functionally complements the lethality of the erg12 null mutation | Core | NA | NA | NA |
| 6276-YMR209C | YMR209C | NA | NA | Putative S-adenosylmethionine-dependent methyltransferase; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum and vacuole respectively; YMR209C is not an essential gene | Core | NA | NA | NA |
| 6277-YMR210W | YMR210W | MGL2 | putative carboxylic ester hydrolase | Monoacylglycerol lipase; palmitoyl monoacylglycerol is the preferred substrate; role in triacylglycerol catabolism; minor role in medium-chain fatty acid ethyl ester biosynthesis; contains an alpha/beta hydrolase domain and a typical lipase motif; has similarity to acyltransferases, Eeb1p and Eht1p, and human ABHD1 | Core | NA | NA | NA |