Summary
[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, 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 2 spliced variants.

AceView summary
Expression: According to AceView, this gene is well expressed, 0.5 times the average gene in this release, only in embryos, L1, L2 and L3 larvae [Kohara cDNAs]. The sequence of this gene is defined by 7 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 4 distinct gt-ag introns. Transcription produces 2 alternatively spliced mRNAs. There are 2 probable alternative promotors and 2 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by 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).
Protein coding potential: The 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (2 complete, 1 COOH complete), some containing Ubiquinone biosynthesis protein COQ7 domain [Pfam].
Function: There are 56 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).

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12

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.

The closest human gene, according to BlastP, is the AceView gene COQ7 (e=5 10^-55).
The closest mouse gene, according to BlastP, is the AceView gene Coq7 (e=10^-55)

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 cDNA clones supporting each intron. Superimposed introns of the same color are identical, of different colors are different.
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. Details on tissue of origin for each intron and exon is available from the intron and exons table. Good predicted proteins are in pink, yellow proteins may be partial or unconvincing, green are uORFs. Proteins supported by a single continuous GenBank accession lead to underlining the name/ending of the variant. Names not underlined result from cDNA concatenation in the coding region and should be experimentally checked.
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