Caenorhabditis elegans gene deg-1, gain of function leads to DEGeneration of certain neurons, encoding putative ion channel.
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SUMMARY back to top
Summary
[Wormbase] deg-1 encodes a putative ion channel for which altered function induces necrotic cell death of neurons required for mechanosensory behavior; expressed in the ASH, IL1, AVD, AVG, and PVC neurons in addition to some muscle cells.
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 6 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 2.6 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 4 cDNA clones and 30 elements defined by RNA-seq, some from mixed (seen once). We annotate structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 25 distinct gt-ag introns. Transcription produces at least 6 alternatively spliced mRNAs. Variant a is transpliced to SL1. There are 3 probable alternative promotors and 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, presence or absence of 5 cassette exons, overlapping exons with different boundaries. 290 bp of this gene are antisense to spliced gene mec-7, raising the possibility of regulated alternate expression.
Function: There are 17 articles specifically referring to this gene in PubMed. In addition we point below to 47 abstracts. This gene is associated to a phenotype (gain of function leads to DEGeneration of certain neurons). Functionally, the gene has been proposed to participate in a process (sodium ion transport). Proteins are expected to have molecular function (sodium channel activity) and to localize in membrane. The gene interacts with 7 other genes (ASP-3, ASP-4, CLP-1, CNX-1, MEC-6, SUP-41, TRA-3).
Protein coding potential: The 6 spliced mRNAs putatively encode good proteins, altogether 6 different isoforms (1 complete, 5 partial), some containing Na+ channel, amiloride-sensitive domain [Pfam], some transmembrane domains, a coiled coil stretch [Psort2].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome X, links to other databases and other names
Map: This gene deg-1 maps on chomosome X at position -1.29 (measured by recombination), -0.98 (interpolated). In AceView, it covers 21.14 kb, from 7753935 to 7775079 (WS190), on the direct strand.
Links to: WormBase, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name XI393, in Wormbase by its cosmid.number name C47C12.6.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes SCNN1B, SCNN1G, SCNN1A, bybleeby.
The closest mouse gene, according to BlastP, is the AceView gene Scnn1g (e=2 10-37).
The closest A.thaliana gene, according to BlastP, is the AceView gene AT5G51400 (e=0.27)
          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 deg-1 5' 3' encoded on plus strand of chromosome X from 7,753,931 to 7,775,079 a b c f d e 5kb 0 355 bp exon 355 bp exon 44 bp [gt-ag] intron 3 GenBank accessions 99 bp exon 126 bp [gt-ag] intron 3 GenBank accessions 213 bp exon 64 bp [gt-ag] intron 3 GenBank accessions 99 bp exon 42 bp [gt-ag] intron 3 GenBank accessions 65 bp exon 867 bp [gt-ag] intron 3 GenBank accessions 136 bp exon 323 bp [gt-ag] intron 2 GenBank accessions 118 bp exon 187 bp [gt-ag] intron 2 GenBank accessions 54 bp exon 539 bp [gt-ag] intron 2 GenBank accessions 62 bp exon 44 bp [gt-ag] intron 2 GenBank accessions 158 bp exon 48 bp [gt-ag] intron 2 GenBank accessions 262 bp exon 50 bp [gt-ag] intron 3 GenBank accessions 217 bp exon 45 bp [gt-ag] intron 3 GenBank accessions 149 bp exon 404 bp [gt-ag] intron 3 GenBank accessions 72 bp exon 6291 bp [gt-ag] intron 3 GenBank accessions 103 bp exon 46 bp [gt-ag] intron 4 GenBank accessions 647 bp exon 24 accessions, some from mixed (seen once) Transpliced 5' end, 1 accession Validated 3' end, 3 accessions Validated 3' end, 47 accessions Validated 3' end, 3 accessions Validated 3' end, 4 accessions 647 bp exon 83 bp exon 83 bp exon 670 bp [gt-ag] intron 1 GenBank accession 138 bp exon 314 bp [gt-ag] intron 1 GenBank accession 54 bp exon 8356 bp [gt-ag] intron 1 GenBank accession 3 accessions 99 bp exon 136 bp exon 136 bp exon 68 bp [gt-ag] intron 1 GenBank accession 30 bp exon 225 bp [gt-ag] intron 1 GenBank accession 118 bp exon 780 bp [gt-ag] intron 1 GenBank accession 58 bp exon 3 accessions 58 bp exon 146 bp exon 146 bp exon 6767 bp [gt-ag] intron 1 GenBank accession 1 accession 96 bp exon 107 bp exon 107 bp exon 568 bp [gt-ag] intron 1 GenBank accession 1 accession 274 bp exon 52 bp exon 86 bp [gt-ag] intron 1 GenBank accession 168 bp exon 285 bp [gt-ag] intron 1 GenBank accession 58 bp exon 2 accessions 58 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.
Read more...
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
unit
pre-mRNA		 Downstream sequence
a 2809 bp 778 aa 10 bp 462 bp 2kb including Promoter 11929 bp 1kb
b 374 bp 124 aa 2kb 9714 bp 1kb
c 342 bp 113 aa 2kb 1415 bp 1kb
d 381 bp 108 aa 57 bp 2kb possibly including promoter 949 bp 1kb
e 278 bp 92 aa 2kb 649 bp 1kb
f 242 bp 80 aa 2kb 7009 bp 1kb

Gene neighbors and Navigator on chromosome X back to top
ref-2 D C I P deg-1 D C I R P XI365 P XI399 C XI383 XI387 XI378 XI388t C XI366 D C I R P mec-7 C XI396 C P XI402 5kb 0 ref-2, 15 accessions, 4 variants deg-1, 34 accessions, 6 variants XI365, 0 accession XI399, 14 accessions XI353, 0 accession XI383, 0 accession XI387, 0 accession XI378, 7 accessions, 2 variants XI388t, 0 accession XI366, 5 accessions mec-7, 118 accessions 2 variants XI396, 14 accessions, 3 variants XI402, 26 accessions 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 17 articles in PubMed.
In addition we found 47 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f 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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