Caenorhabditis elegans essential gene bli-1, encoding nematode cuticle collagen, BLIstered cuticle.
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] The bli-1 gene encodes an unusual cuticular collagen that is required for proper strut formation within the unique medial layer of the adult cuticle; bli-1 interacts genetically with other cuticular collagens such as bli-2 and rol-1, and may be processed for secretion by BLI-4, a Kex2/subtilisin serine endoproteinase; consistent with its role in adult cuticle formation, bli-1 mRNA is highly expressed only during the L4 larval stage.
Wormbase predicts one model

AceView synopsis, each blue text links to tables and details
According to AceView, this gene is expressed at high level, 1.5 times the average gene in this release, in L3, L4 larvae and in adult [Kohara and Riddle cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: L1 or L2 larvae 1%, L3 to adult 98%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 12 cDNA clones and 8 elements defined by RNA-seq, some from l4 (seen 4 times), mixed (once). We annotate structural defects or features in 3 cDNA clones.
The gene contains 4 distinct gt-ag introns. Transcription produces one spliced mRNA, 1 alternatively spliced variant and 1 unspliced form. Variant a is transpliced to SL1. There are 2 validated alternative polyadenylation sites (see the diagram). 723 bp of this gene are antisense to spliced gene dph-2, raising the possibility of regulated alternate expression.
Function: There are 6 articles specifically referring to this gene in PubMed. In addition we point below to 12 abstracts. This essential gene is associated to a phenotype (BLIstered cuticle, Embryonic Lethal, Sterile adult). Functionally, the gene has been proposed to participate in a process (sporulation (sensu Bacteria)). Proteins are expected to have molecular function (structural constituent of cuticle) and to localize in various compartments (extracellular space, forespore). The gene interacts with 3 other genes (BLI-2, BLI-4, SC109).
Protein coding potential: The spliced and the unspliced mRNAs putatively encode good proteins, altogether 2 different isoforms (1 complete, 1 COOH complete), some containing domains collagen triple helix repeat, nematode cuticle collagen, N-terminal, Small acid-soluble spore protein, SspO [Pfam]; the complete protein appears to be secreted.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome II, links to other databases and other names
Map: This essential gene bli-1 maps on chomosome II at position +2.65 (interpolated). In AceView, it covers 3.20 kb, from 10708882 to 10712084 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 2L1, in Wormbase by its cosmid.number name C09G5.6, in NextDB, the Nematode expression pattern database, as CEYK4882.
          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 bli-1 5' 3' encoded on plus strand of chromosome II from 10,708,882 to 10,712,081 a b 500bp 0 198 bp exon 198 bp exon 46 bp [gt-ag] intron 3 GenBank accessions 274 bp exon 45 bp [gt-ag] intron 3 GenBank accessions 2123 bp exon 49 bp [gt-ag] intron 3 GenBank accessions 106 bp exon 47 bp [gt-ag] intron 3 GenBank accessions 315 bp exon 19 accessions, some from l4 (seen 4 times) Transpliced 5' end, 1 accession Validated 3' end, 33 accessions 315 bp exon 2326 bp exon 2326 bp exon 1 accession from mixed 2326 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 3016 bp 948 aa 54 bp 115 bp 2kb including Promoter 3203 bp 1kb
b 2326 bp 619 aa 464 bp 2kb 2326 bp 1kb

Gene neighbors and Navigator on chromosome II back to top
ggr-1 C P col-79 C P col-39 C P col-80 C P bli-1 D C I P 2L5 C 2L19 C R C P gbh-1 C I P dph-2 D C R P glb-12 5kb 0 ptb-1, 37 accessions, 8 variants ggr-1, 10 accessions, 3 variants col-79, 0 accession col-39, 0 accession col-80, 0 accession bli-1, 20 accessions, 2 variants 2L5, 7 accessions 2L19, 22 accessions, 3 variants 2L9, 12 accessions gbh-1, 25 accessions, 2 variants dph-2, 32 accessions, 10 variants glb-12, 7 accessions, 2 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 6 articles in PubMed.
In addition we found 12 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b 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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