Caenorhabditis elegans gene clk-1, CLocK (biological timing) abnormality, encoding COenzyme Q (ubiquinone) biosynthesis enzyme required for lipoprotein metabolim; involved in response to dietary restriction; adversely influences biological rhythms, lifespan and fertility.
SUMMARY back to top
[Wormbase] clk-1 encodes the C. elegans ortholog of COQ7/CAT5, a highly conserved demethoxyubiquinone (DMQ) hydroxylase that is necessary for the biosynthesis of ubiquinone (coenzyme Q, Q9) from 5-demethoxyubiquinone (DMQ9); in C. elegans, CLK-1 activity is required for normal physiological rates of growth, development, behavior, and aging, as well as for normal brood sizes.
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 very high level, 8.5 times the average gene in this release, only in embryos, L1, L2 and L3 larvae [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 28%, L1 or L2 larvae 57%, L3 to adult 15%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 7 cDNA clones and 105 elements defined by RNA-seq, some from l2 (seen 4 times), embryo (2).
Alternative mRNA variants and regulation: The gene contains 5 distinct gt-ag introns. Transcription produces 3 alternatively spliced mRNAs. Variant a is transpliced to SL6, SL2, SL3, SL4, b to SL1. There are 2 probable alternative promotors and 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by overlapping exons with different boundaries, splicing versus retention of one intron.
Note that mRNA .b was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
Function: There are 57 articles specifically referring to this gene in PubMed. In addition we point below to 40 abstracts. This gene is associated to a phenotype (CLocK (biological timing) abnormality, maternal rescue, regulates metabolic activity, slow embryonic cell division, SLow growth, extends adult lifespan, reduced fertility, DEfecation Cycle abnormal). Functionally, the gene has been proposed to participate in processes (protein metabolism, ubiquinone biosynthesis). Proteins are expected to localize in various compartments (cytoplasm, mitochondrion). The gene interacts with 13 other genes (APR-1, ARK-1, CTL-1, CTL-2, CUX-7+CLK-2, DAF-2, DAF-16, DSC-4, EAT-2, GRO-1, ITR-1, LET-60, SOD-1).
Protein coding potential: The 3 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (2 complete, 1 partial), some containing Ubiquinone biosynthesis protein COQ7 domain [Pfam].

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 clk-1 maps on chomosome III at position -1.88 (interpolated). In AceView, it covers 1.46 kb, from 5277853 to 5279314 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
as Other names: The gene is also known coq-7, in Wormgenes/AceView by its positional name 3G369, in Wormbase by its cosmid.number name ZC395.2, in NextDB, the Nematode expression pattern database, as CEYK5490.
          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 clk-1 5' 3' encoded on plus strand of chromosome III from 5,277,853 to 5,279,314 a b c 500bp 0 136 bp exon 447 bp [gt-ag] intron 7 GenBank accessions 141 bp exon 84 bp [gt-ag] intron 8 GenBank accessions 96 bp exon 60 bp [gt-ag] intron 7 GenBank accessions 113 bp exon 120 bp [gt-ag] intron 8 GenBank accessions 265 bp exon 110 accessions, some from l2 (seen 4 times) embryo (once) Transpliced 5' end, 4 accessions Validated 3' end, 54 accessions Validated 3' end, 535 accessions 265 bp exon 141 bp exon 141 bp exon 84 bp [gt-ag] intron 8 GenBank accessions 269 bp exon 269 bp exon 120 bp [gt-ag] intron 8 GenBank accessions 1 accession from embryo Transpliced 5' end, 1 accession Validated 3' end, 41 accessions Validated 3' end, 437 accessions 255 bp exon 136 bp exon 96 bp [gt-ag] intron 1 GenBank accession 1 accession 77 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 751 bp 187 aa 187 bp 2kb including Promoter 1462 bp 1kb
b 665 bp 73 aa 29 bp 414 bp 2kb including Promoter 869 bp 1kb
c 213 bp 71 aa 2kb 309 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
gop-1 D C R P gop-2 D C I P gop-3 D C R P hap-1 C I P gro-1 D C I P 3G357 C 3G359 C toc-1 D C R P clk-1 D C I R P 3G387 C I P 3G374 3G382 C 3G350 D C I R P ztf-8 D C P 3G364 C 3G388 5kb 0 gop-1, 31 accessions, 6 variants gop-2, 138 accessions 2 variants gop-3, 48 accessions, 3 variants hap-1, 0 accession gro-1, 33 accessions, 6 variants 3G357, 37 accessions, 3 variants 3G359, 7 accessions, 2 variants toc-1, 46 accessions, 5 variants clk-1, 112 accessions 3 variants 3G387, 44 accessions, 7 variants 3G395, 25 accessions, 2 variants 3G356, 4 accessions, 2 variants 3G362, 5 accessions 3G374, 0 accession 3G382, 0 accession 3G340, 67 accessions, 5 variants 3G350, 6 accessions, 3 variants ztf-8, 50 accessions, 5 variants 3G364, 74 accessions, 2 variants 3G388, 15 accessions 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 57 articles in PubMed.
In addition we found 40 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

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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