Caenorhabditis elegans gene bli-2, BLIstered cuticle, encoding nematode cuticle collagen.
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] A cuticle collagen involved in strut assembly in the adult cuticle.
Wormbase predicts one model

AceView synopsis, each blue text links to tables and details
According to AceView, this gene is well expressed, 0.5 times the average gene in this release, down regulated in dauer [SAGE, Jones et al, 2001]. The sequence of this gene is defined by 4 cDNA clones and 2 elements defined by RNA-seq, some from l4 (seen 2 times). We annotate structural defects or features in 2 cDNA clones.
The gene contains 1 gt-ag intron. Transcription produces one mRNA.
Function: There are 6 articles specifically referring to this gene in PubMed. In addition we point below to 12 abstracts. This gene is associated to a phenotype (BLIstered cuticle, SMAll body size). Proteins are expected to have molecular function (structural constituent of cuticle). The gene interacts with BLI-1.
The spliced mRNA putatively encodes a good protein, 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 II, links to other databases and other names
Map: This gene bli-2 maps on chomosome II at position -1.02 (interpolated). In AceView, it covers 1.06 kb, from 5652422 to 5651365 (WS190), on the reverse strand.
Links to: WormBase, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 2F940, in Wormbase by its cosmid.number name F59E12.12.
          Complete gene on genome diagram: back to top
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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-2 5' 3' encoded on minus strand of chromosome II from 5,652,417 to 5,651,371 a 100 200bp 0 100 bp exon 100 bp exon 47 bp [gt-ag] intron 4 GenBank accessions 911 bp exon 6 accessions, some from l4 (seen 2 times) Validated 3' end, 25 accessions 911 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 1011 bp 311 aa 29 bp 46 bp 2kb possibly including promoter 1058 bp 1kb

Gene neighbors and Navigator on chromosome II back to top
2F929 C R zyg-1 D C I P 2F947 C R 2F953 D C R P C 2F955 C R C R P 2F918 C 2F924 C I P 2F930 D C I P ddl-1 D C I P bli-2 C P fut-3 C R 2F950 C R 2F956 5kb 0 npl-4.2+npl-4.1, 153 accessions 11 variants 2F929, 7 accessions zyg-1, 49 accessions, 3 variants 2F947, 72 accessions, 2 variants 2F953, 28 accessions, 5 variants 2F953b, 6 accessions, 2 variants 2F955, 7 accessions 2F947a, 1 accession 2F958, 3 accessions, 2 variants 2F918, 104 accessions 18 variants 2F924, 0 accession 2F930, 55 accessions, 2 variants ddl-1, 51 accessions, 5 variants bli-2, 6 accessions fut-3, 41 accessions, 3 variants 2F950, 37 accessions, 4 variants 2F956, 29 accessions, 3 variants 2F960, 44 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 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 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 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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