Caenorhabditis elegans gene col-34, abnormal RAy Morphology ram-4, encoding COLlagen structural gene.
SUMMARY back to top
Cuticle and basement membrane collagens are extracellular matrix components encoded by a family of about 160 genes known to be expressed to which this gene belongs. Collagens have short interrupted blocks of Gly-X-Y sequence flanked by conserved cysteine residues, akin to vertebrate fibril-associated collagens with interrupted triple helix, and form trimers or higher order polymers. They have been grouped into five main subfamilies. The Caenorhabditis elegans cuticle is a complex multilayered extracellular matrix, consisting predominantly of cuticle collagens and synthesised by the underlying epidermal cell layer (called hypodermis). It is secreted five times during development, in embryos and before each molt, and is slightly different from stage to stage. During cuticle synthesis, the genes are expressed in a distinct temporal series, and the temporal groups contribute distinct discrete substructure of the extracellular matrix (McMahon et al, 2003). For a small number of collagen genes, with no distinctive sequence feature, but certainly critical to assembly or function of the extracellular matrix, such as dpy-2, 3, 7, 8, 10, 5 or 13, sqt-3, lon-3, bli-1, bli-2 or ram-4, loss of function causes a change in body shape (dumpy, squat, long, blistered), or leads to animals that roll when moving (helically twisted), or to male ray morphology defects. Some collagens that participate in the inner basement membranes such as let-2, emb-9, cle-1, mec-5 or unc-122 are essential for viability, or play critical roles in synaptogenesis or synaptic transmission, muscle attachment, cell migration and process guidance. But most other collagens probably have a redundant role, since loss of their function is apparently wild type, and alleles with visible effects in these genes are gain of function mutations. [Main specialists: Jim Kramer and Iain Johnstone][Wormbase] col-34 encodes a cuticle collagen protein and is a critical component of male tail cuticle organization affecting ray morphology.
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 4 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 8.6 times the average gene in this release, in L3, L4 larvae and in adult [Kohara and Riddle cDNAs]. The sequence of this gene is defined by 3 cDNA clones and 110 elements defined by RNA-seq, some from mixed (seen once). We annotate structural defects or features in 3 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 5 distinct gt-ag introns. Transcription produces 4 alternatively spliced mRNAs. The mRNAs appear to differ by presence or absence of 2 cassette exons, overlapping exons with different boundaries, splicing versus retention of 3 introns. 369 bp of this gene are antisense to spliced gene anticol-34artefact, raising the possibility of regulated alternate expression.
Function: There are 4 articles specifically referring to this gene in PubMed. In addition we point below to 7 abstracts. This gene is associated to a phenotype (abnormal RAy Morphology). Proteins are expected to have molecular function (structural constituent of cuticle).
Protein coding potential: The 4 spliced mRNAs putatively encode good proteins, altogether 4 different isoforms (1 COOH complete, 3 partial), some containing domains collagen triple helix repeat, nematode cuticle collagen, N-terminal [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome IV, links to other databases and other names
Map: This gene col-34 maps on chomosome IV at position +0.03 (interpolated). In AceView, it covers 1.07 kb, from 4244603 to 4243537 (WS190), on the reverse strand.
Links to: WormBase, RNAiDB.
as Other names: The gene is also known ram-4, in Wormgenes/AceView by its positional name 4F8, in Wormbase by its cosmid.number name F36A4.10.
          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 col-34 5' 3' encoded on minus strand of chromosome IV from 4,244,603 to 4,243,537 a b c d 500bp 0 104 bp exon 104 bp exon 54 bp [gt-ag] intron 3 GenBank accessions 646 bp exon 48 bp [gt-ag] intron 4 GenBank accessions 215 bp exon 110 accessions, some from mixed (seen once) Validated 3' end, 624 accessions 215 bp exon 235 bp exon 135 bp [gt-ag] intron 1 GenBank accession 1 accession 113 bp exon 235 bp exon 366 bp [gt-ag] intron 1 GenBank accession 1 accession 44 bp exon 235 bp exon 339 bp [gt-ag] intron 1 GenBank accession 1 accession 14 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 3' UTR Upstream sequence Transcription
Downstream sequence
a 965 bp 306 aa 42 bp 2kb 1067 bp 1kb
b 348 bp 116 aa 2kb 483 bp 1kb
c 279 bp 93 aa 2kb 645 bp 1kb
d 249 bp 83 aa 2kb 588 bp 1kb

Gene neighbors and Navigator on chromosome IV back to top
dpy-13 D C I P ttr-20 C ama-1 D C I R P col-33 C P 4F31 C 4F33 4F3 4F10 C 4E982 C C srbc-70 C 4E994 P D C P col-34 5kb 0 dpy-13, 538 accessions 2 variants ttr-20, 13 accessions ama-1, 54 accessions, 5 variants col-33, 31 accessions 9 variants 4F31, 6 accessions, 2 variants 4F33, 16 accessions 4F3, 0 accession srbc-72, 0 accession 4F2, 2 accessions 4F4, 1 accession 4F10, 0 accession 4E982, 6 accessions srbc-71, 4 accessions 2 variants srbc-70, 0 accession 4E994, 31 accessions, 4 variants 4F6, 3 accessions col-34, 113 accessions 4 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 4 articles in PubMed.
In addition we found 7 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d 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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