Caenorhabditis elegans essential gene byn-1, encoding mammalian BYstiN (adhesion protein) related.
SUMMARY back to top
[Wormbase] byn-1 encodes a homolog of mammalian BYSTIN-LIKE (BYSL; OMIM:603871).
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 2 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 6.0 times the average gene in this release, at all stages of development [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 12%, L1 or L2 larvae 70%, L3 to adult 18%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 63 cDNA clones and 16 elements defined by RNA-seq, some from l1 (seen 36 times), l2 (13), embryo (6), l4 (2), mixed (2). We annotate structural defects or features in 5 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 9 distinct gt-ag introns. Transcription produces 2 alternatively spliced mRNAs. Variant a is transpliced to SL1, SL2, SL3, SL4, SL5, SL7, SL6, SL10, SL12. There are 2 non overlapping alternative last exons and 3 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 3' end.
Function: There are 2 articles specifically referring to this gene in PubMed. This essential gene is associated to a phenotype (Embryonic Lethal, Protruding VuLva, SLow growth, Sterile adult).
Protein coding potential: The spliced mRNAs putatively encode a good protein, containing Bystin domain [Pfam]. The remaining mRNA variant (spliced; partial) appears not to encode a good protein.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome III, links to other databases and other names
Map: This essential gene byn-1 maps on chomosome III at position -0.92 (interpolated). In AceView, it covers 3.88 kb, from 6931937 to 6935819 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 3I25, in Wormbase by its cosmid.number name F57B9.5, in NextDB, the Nematode expression pattern database, as CEYK6101.
          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 byn-1 5' 3' encoded on plus strand of chromosome III from 6,931,937 to 6,935,799 a b 1 2kb 0 154 bp exon 154 bp exon 69 bp [gt-ag] intron 52 GenBank accessions 113 bp exon 47 bp [gt-ag] intron 51 GenBank accessions 106 bp exon 52 bp [gt-ag] intron 51 GenBank accessions 156 bp exon 46 bp [gt-ag] intron 50 GenBank accessions 134 bp exon 48 bp [gt-ag] intron 47 GenBank accessions 90 bp exon 51 bp [gt-ag] intron 49 GenBank accessions 145 bp exon 46 bp [gt-ag] intron 55 GenBank accessions 96 bp exon 48 bp [gt-ag] intron 58 GenBank accessions 234 bp exon 1892 bp [gt-ag] intron 62 GenBank accessions 356 bp exon 77 accessions, some from l1 (seen 36 times) l2 (13), embryo (6), l4 (2) mixed (2) Transpliced 5' end, 44 accessions Validated 3' end, 5 accessions Validated 3' end, 73 accessions 356 bp exon 153 bp exon 153 bp exon 46 bp [gt-ag] intron 50 GenBank accessions 134 bp exon 134 bp exon 48 bp [gt-ag] intron 47 GenBank accessions 2 accessions Validated 3' end, 2 accessions 76 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 1584 bp 449 aa 4 bp 230 bp 2kb including Promoter 3883 bp 1kb
b 363 bp 58 aa 185 bp 2kb 457 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
inf-1 D C I R P byn-1 D C P coq-2 C R P 3I29 D C P let-711 D C I R P C R pdf-1 C I R P flap-1 C P 3I24 R C R pqn-46 5kb 0 inf-1, 179 accessions 4 variants byn-1, 79 accessions, 2 variants coq-2, 27 accessions, 6 variants 3I29, 14 accessions let-711, 21 accessions 3 variants pdf-1, 131 accessions 4 variants flap-1, 43 accessions 4 variants 3I24, 16 accessions 3I26, 1 accession pqn-46, 27 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 2 articles in PubMed.
? Gene Summary Gene on genome mRNA:.a, .b 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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