Caenorhabditis elegans gene coq-2, encoding COenzyme Q (ubiquinone) biosynthesis enzyme.
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SUMMARY back to top
Summary
[Wormbase] coq-2 encodes a putative para-hydroxybenzoate-polyprenyl transferase (UbiA prenyltransferase), orthologous to S. cerevisiae COQ2; COQ-2 is required for ubiquinone (coenzyme Q9) biosynthesis and for normally short lifespan; coq-2 mutants have slowed pharyngeal pumping, and eventually arrest as paralysed larvae before dying; coq-2(RNAi) animals have reduced levels of coenzyme Q9 and superoxide, and have abnormally long lifespans; coq-2 mutants are not rescued by dietary coenzyme Q.
Wormbase predicts 5 models
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AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 2.1 times the average gene in this release, at all stages of development [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 7%, L1 or L2 larvae 15%, L3 to adult (including dauer) 79%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 11 cDNA clones and 16 elements defined by RNA-seq, some from mixed (seen 6 times), l1 (2), embryo (once). We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 12 distinct gt-ag introns. Transcription produces at least 6 different mRNAs, 5 alternatively spliced variants and 1 unspliced form. Variant a is transpliced to SL1, SL2, SL3, SL4, SL5, b to SL1, SL8, d to SL3, e to SL1. There are 2 probable alternative promotors, 2 non overlapping alternative last exons and 8 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 3 cassette exons, overlapping exons with different boundaries, splicing versus retention of one intron. 180 bp of this gene are antisense to spliced gene 3I26, raising the possibility of regulated alternate expression.
2 variants were isolated in vivo, despite the fact that they are predicted targets of nonsense mediated mRNA decay (NMD).
Function: There is one article specifically referring to this gene in PubMed. Proteins are expected to have molecular function (prenyltransferase activity) and to localize in various compartments (endoplasmic reticulum membrane, integral to membrane). No phenotype has yet been reported to our knowledge: this gene's in vivo function is yet unknown.
Protein coding potential: The 5 spliced and the unspliced mRNAs putatively encode good proteins, altogether 6 different isoforms (3 complete, 2 COOH complete, 1 partial), some containing UbiA prenyltransferase domain [Pfam], some transmembrane domains [Psort2].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome III, links to other databases and other names
Map: This gene coq-2 maps on chomosome III at position -0.92 (interpolated). In AceView, it covers 4.18 kb, from 6935903 to 6940081 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 3I27, in Wormbase by its cosmid.number name F57B9.4, in NextDB, the Nematode expression pattern database, as CEYK6809.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene sorfla (e=10-17)
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the Flash version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
a 1938 bp 370 aa 15 bp 810 bp 2kb including Promoter 4178 bp 1kb
b 1246 bp 370 aa 15 bp 118 bp 2kb including Promoter 3486 bp 1kb
c 866 bp 80 aa 622 bp 2kb 2651 bp 1kb
d 1086 bp 203 aa 15 bp 459 bp 2kb including Promoter 3460 bp 1kb
e 303 bp 95 aa 18 bp 2kb including Promoter 303 bp 1kb
f 261 bp 57 aa 87 bp 2kb 939 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
ZOOM OUT                 D:disease, C:conserved, I:interactions, R:regulation, P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography back to top
Please see this 1 article in PubMed.
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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