Caenorhabditis elegans gene coq-1, encoding COenzyme Q (ubiquinone) biosynthesis enzyme.
SUMMARY back to top
[Wormbase] coq-1 encodes a putative hexaprenyl pyrophosphate synthetase, orthologous to S. cerevisiae COQ1; COQ-1 is required for ubiquinone (coenzyme Q9) biosynthesis and for normally short lifespan; coq-1 mutants have slowed pharyngeal pumping, and eventually arrest as paralysed larvae before dying; coq-1(RNAi) animals have reduced levels of coenzyme Q9 and superoxide, and have abnormally long lifespans; coq-1 mutants are not rescued by dietary coenzyme Q.
Wormbase predicts one model, but Caenorhabditis elegans cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 3 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 2.2 times the average gene in this release, mostly from L1 larvae to adult [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 2%, L1 or L2 larvae 57%, L3 to adult 42%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 14 cDNA clones and 15 elements defined by RNA-seq, some from l1 (seen 4 times), l2 (3), l4 (2).
Alternative mRNA variants and regulation: The gene contains 11 distinct gt-ag introns. Transcription produces 3 alternatively spliced mRNAs. Variant a is transpliced to SL1, SL2, SL3, SL4, SL9. There are 2 probable alternative promotors and 2 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, overlapping exons with different boundaries.
Function: There are 2 articles specifically referring to this gene in PubMed. This gene is associated to a phenotype (RNAi enhances human tau induced Unc phenotype). Functionally, the gene has been proposed to participate in a process (isoprenoid biosynthesis). Proteins are expected to localize in mitochondrion.
Protein coding potential: 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (1 complete, 1 partial), some containing Polyprenyl synthetase domain [Pfam]. The remaining mRNA variant (spliced; partial) appears not to encode a good protein.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome I, links to other databases and other names
Map: This gene coq-1 maps on chomosome I at position -0.02 (interpolated). In AceView, it covers 2.83 kb, from 5415666 to 5412841 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 1F982, in Wormbase by its cosmid.number name C24A11.9, in NextDB, the Nematode expression pattern database, as CEYK9282.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene PDSS1 (e=4 10-08).
The closest mouse gene, according to BlastP, is the AceView gene Pdss1 (e=5 10-08).
The closest A.thaliana gene, according to BlastP, is the AceView gene GPPS\/GPS1 (e=7 10-09)
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene coq-1 5' 3' encoded on minus strand of chromosome I from 5,415,666 to 5,412,845 a c b 1 2kb 0 138 bp exon 138 bp exon 50 bp [gt-ag] intron 11 GenBank accessions 97 bp exon 53 bp [gt-ag] intron 10 GenBank accessions 114 bp exon 47 bp [gt-ag] intron 10 GenBank accessions 77 bp exon 317 bp [gt-ag] intron 9 GenBank accessions 92 bp exon 45 bp [gt-ag] intron 10 GenBank accessions 104 bp exon 365 bp [gt-ag] intron 11 GenBank accessions 111 bp exon 97 bp [gt-ag] intron 11 GenBank accessions 136 bp exon 46 bp [gt-ag] intron 10 GenBank accessions 144 bp exon 160 bp [gt-ag] intron 10 GenBank accessions 182 bp exon 47 bp [gt-ag] intron 10 GenBank accessions 370 bp exon 27 accessions, some from l1 (seen 4 times) l2 (3), l4 (2) Transpliced 5' end, 8 accessions Validated 3' end, 6 accessions Validated 3' end, 10 accessions 370 bp exon 172 bp exon 172 bp exon 50 bp [gt-ag] intron 11 GenBank accessions 1 accession 85 bp exon 101 bp exon 101 bp exon 369 bp [gt-ag] intron 1 GenBank accession 107 bp exon 1 accession 107 bp exon 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.
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
Downstream sequence
a 1565 bp 393 aa 94 bp 289 bp 2kb including Promoter 2792 bp 1kb
b 208 bp 68 aa 2kb probably including promoter 577 bp 1kb
c 257 bp 43 aa 128 bp 2kb 307 bp 1kb

Gene neighbors and Navigator on chromosome I back to top
1F971 C P 1F991 I P 1F995 D C R P 1F999 C R 1G3 C P 1F962 C R frm-4 D C R P coq-1 C R 1F986 D C I R P 1F990 D C I R P atp-3 D C I P dpy-5 1G2 5kb 0 1F971, 7 accessions, 2 variants 1F991, 33 accessions 1F995, 5 accessions, 2 variants 1F999, 73 accessions, 3 variants 1G3, 9 accessions 1F993, 1 accession 1F962, 0 accession frm-4, 62 accessions, 9 variants coq-1, 29 accessions, 3 variants 1F986, 48 accessions, 4 variants 1F990, 41 accessions, 7 variants atp-3, 110 accessions 4 variants dpy-5, 94 accessions 1G2, 37 accessions, 3 variants 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 these 2 articles in PubMed.
? Gene Summary Gene on genome mRNA:.a, .b, .c Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DC

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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