Caenorhabditis elegans gene dpy-7, DumPY : shorter than wild-type, encoding cuticle collagen.
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Complete gene on genome diagram:
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 are thought to form trimers or higher order polymers. They can be grouped into subfamilies according to homology (Johnstone, 2000). 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. During cuticle synthesis, the genes are expressed in a distinct temporal series, reiterated at each molt, and the temporal groups contribute distinct discrete substructure of the extracellular matrix: The early group of cuticle collagen genes is required for the formation of annuli, it includes DPY-2, 3, 7, 8 and 10, and peaks in mRNA abundance about 4 h before the new cuticle is secreted; these 5 proteins localise in the annuli of the outermost layer of cuticle, right above the actin bundles in the epidermal cell. The intermediate group includes DPY-5 and DPY-13, peaks about 2 hours later, and these collagens go below and in between the annuli (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 the DPY genes above, loss of function causes a change in body shape (dumpy, squat or long), or leads to animals that roll when moving (alae helically twisted), or to male ray morphology defects. Some collagens that participate in the inner basement membranes are essential for viability, or play a critical role in synaptogenesis, 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: Iain Johnstone and Jim Kramer; Don Riddle, Ann Rose, Bob Horvitz, Sidney Brenner][Wormbase] dpy-7 encodes a cuticular collagen; DPY-7 functions as a structural constituent of the extracellular cuticle whose activity is required for normal cuticular morphology and hence, proper body form.
Map on chromosome X, links to other databases and other names
This gene dpy-7 maps on chomosome X at position -1.65 (measured by recombination), -1.34 (interpolated).
Links to: WormBase
The gene is also known in Wormgenes/AceView by its positional name XI156, in Wormbase by its cosmid.number name F46C8.6.
Closest AceView homologs in other species
The closest mouse gene
, according to BlastP, is the AceView gene C1qc
Compact gene diagram
Sequences: click on the numbers to get the DNA
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.
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Details on tissue of origin for each intron and exon is available from the intron and exons table
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. Proteins supported by a single continuous cDNA sequence 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.
are depicted by broken lines; the height of the top of each intron reflects the relative number of clones supporting this intron. ]^[ A pink broken line
denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron). ] ^ ] A blue broken line
denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries. ]-[ Pink
and ] - ] blue
straight lines represent 'fuzzy' introns of the standard and non-standard types respectively, those introns do not follow the 16 bp rule. Black straight lines ]-[denote gaps in the alignments.
Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). Flags identify validated endings: cap site on the 5' side, polyadenylation site on the 3' side. Filled flags correspond to frequent events while empty flags have lesser supporting cDNAs (yet all are validated); at the 3' side, black flags are associated to the main AATAAA signal, blue flags
to any single letter variant of the main . More explanations are given in the gene help file
Summaries of AceView transcripts and proteins
Predicted protein properties
The predicted CDS is fully annotated here
Gene neighbors and Navigator on chromosome X
This table allows to see at a glance from the last column if an isoform has its exonic structure fully supported by a single clone (the variant identifier a, b, c under such mRNA is underlined in the gene diagrams), or if it requires concatenation of two or more cDNA clones (identifier not underlined).
Extends from ||
318 aa |
nematode cuticle collagen, N-terminal, collagen triple helix repeat ||
COOH complete ||
Met (ATG) |
1 to 957 |
Please see these 16 articles in PubMed
In addition we found 43 papers for which we do not have a PubMed identifier
- [wbg5.2p41] genetic studies of mutants that reiterate cell lineages: lin-4 II and unc-86 III.
- [wbg9.3p47] y9: an XO-specific lethal mutation that suppresses the known XX-specific lethal mutations.
- [wbg9.3p46] suppressors of bli-6(mn4) IV.
- [wbg10.1p35] molecular cloning of the unc-6 gene.
- [wbg10.1p99] a little uncoordinated genetics.
- [wbg10.1p30] progress towards cloning the deg-1 gene.
- [wbg10.3p104] a story of two kinky mup's.
- [wm89p135] use of YACs to identify and clone putative collagen genes in the region of dpy-6/dpy-7.
- [wbg11.5p72] The effect of him mutations on recombination and segregation.
- [wm91p174] THE REGULATION OF CUTICLE SYNTHESIS IN C. elegans.
- [wm93p138] Cloning and analysis of the dpy-7 homologue from C. briggsae.
- [wbg13.1p46] Mapping the Alpha1 and Beta Subunits of the C. elegans Voltage-Gated CalciumChannel
- [wm93p226] Molecular analysis of the collagen gene dpy-7.
- [wbg13.3p72] Dominant Ivermectin Resistance Mutations
- [wm95p234] REGULATION OF THE CUTICULAR COLLAGEN GENE dpy-7
- [wm95p209] TIME FOR SOME RESULTS: MOLECULAR CHARACTERISATION OF THE CLK-1 LOCUS.
- [wm95p294] CUTICULAR COLLAGEN GENES ARE EXPRESSED IN AN ELABORATE SEQUENTIAL PATTERN.
- [wm95p398] SUPPRESSION OF emb-5 BY MUTATIONS IN GENES ENCODING EXTRACELLULAR MATRIX PROTEINS
- [wbg14.4p22] Partial rescue and further characterization of him-3.
- [wcwm96p104] Suppressors of let-60 Dominant Negative Mutations
- [wbg14.3p20] Regulation of cell and stage specific expression of the cuticle collagen gene dpy-7.
- [wbg14.3p21] elt-3: a new GATA transcription factor from C.elegans
- [wm97e496] CHARACTERIZATION OF THE ELUSIVE UNC-10 GENE
- [wm97e398] PUTATIVE MORPHOGENIC MUTANTS IN C.ELEGANS
- [wm97e60] GENES REQUIRED FOR ELONGATION OF THE EMBRYO
- [ewm98pp12] The use of Green Fluorescent Protein to identify genes involved in aspects of hypodermal function in Caenorhabditis elegans.
- [wcwm98p197] The dim-1 gene encodes a novel protein required for myofilament stability
- [wbg15.2p22] unc-10 encodes the C. elegans homolog of the rab3 effector Rim
- [wbg15.4p23] The dim-1 gene encodes a novel protein required for myofilament stability and unc-112 encodes a homolog of the human MIG-2 protein
- [wcwm98p160] GENES THAT CONTROL NMDA RECEPTOR EXPRESSION IN THE PVC COMMAND INTERNEURONS
- [ewm98pp56] Screen for body size mutants in C. elegans
- [ewm98pt44] lin-26 and lir-1 are involved in defining the epithelial identity.
- [ewm98pp37] A screening for morphogenetic mutants by insertional mutagenesis.
- [wm99p336] The role of the GATA factor elt-3 in hypodermal development
- [wm99p717] The unc-112 and dim-1 genes encode novel proteins required for myofilament lattice assembly and stability
- [wm99p712] Genetic analysis of genes involved in hypodermal function in Caenorhabditis elegans
- [euwm2000ab43] Assembly of cuticle collagens
- [ecwm2000p201] Further progress in understanding unc-98, a gene important for intermediate filament protein organization in nematode muscle
- [euwm2000ab126] A C. elegans mutant defective in cuticle synthesis, possibly identifies a SEC-23 homologue
- [wm2001p722] The structural role and interactions of the DPY-7 cuticular collagen in the exoskeleton of Caenorhabditis elegans.
- [wm2001p516] GATA factor function and hypodermal development.
- [wm2001p190] Nuclear hormone receptor nhr-23(CHR3) is a critical regulator of all four larval molts of Caenorhabditis elegans
- [wm2001p721] CHARACTERISATION OF MUTANT ALLELES INVOLVED IN C.ELEGANS CUTICLE FUNCTION
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 see the mRNA diagram, sequence and annotation, click the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.
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