Caenorhabditis elegans essential gene icl-1, encoding ICLn ion channel homolog, nucleotide-sensitive chloride conductance regulator.
SUMMARY back to top
[Wormbase] The icl-1 gene encodes, through alternative splicing, two alternative forms (ICL-1A, or 'IClnN1', and ICL-1B, or 'IClnN2'), with distinct electrophysiological properties, of an anion channel homolog.
Wormbase predicts 2 models, 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 3 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 7.3 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 19%, L1 or L2 larvae 36%, L3 to adult (including dauer) 45%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 6 cDNA clones and 90 elements defined by RNA-seq, some from embryo (seen once), l1 (once), l2 (once), mixed (once).
Alternative mRNA variants and regulation: The gene contains 7 distinct gt-ag introns. Transcription produces 3 alternatively spliced mRNAs. Variant a is transpliced to SL1, SL2, SL3, SL4, SL5, SL7, SL8, b to SL7, SL2. There are 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by presence or absence of a cassette exon, overlapping exons with different boundaries.
Function: There are 5 articles specifically referring to this gene in PubMed. In addition we point below to 2 abstracts. This essential gene is associated to a phenotype (Embryonic Lethal, SLow growth). Functionally, the gene has been proposed to participate in processes (chloride transport, regulation of cell volume). Proteins are expected to localize in cytoplasm. These proteins appear to interact with other proteins (SNR-1, SNR-3, SNR-6, SNR-7).
Protein coding potential: The 3 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (2 complete, 1 partial), some containing Nucleotide-sensitive chloride conductance regulator domain [Pfam], a second peroximal domain, a vacuolar domain, 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 IV, links to other databases and other names
Map: This essential gene icl-1 maps on chomosome IV at position +4.63 (interpolated). In AceView, it covers 1.12 kb, from 9095633 to 9094515 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 4J860, in Wormbase by its cosmid.number name C01F6.8, in NextDB, the Nematode expression pattern database, as CEYK6358.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene CLNS1A (e=3 10-09).
The closest mouse gene, according to BlastP, is the AceView gene Clns1a (e=6 10-11).
The closest A.thaliana gene, according to BlastP, is the AceView gene AT5G62290 (e=3 10-05)
          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 icl-1 5' 3' encoded on minus strand of chromosome IV from 9,095,633 to 9,094,515 a b c 1kb 0 124 bp exon 124 bp exon 44 bp [gt-ag] intron 7 GenBank accessions 143 bp exon 44 bp [gt-ag] intron 3 GenBank accessions 60 bp exon 59 bp [gt-ag] intron 3 GenBank accessions 102 bp exon 42 bp [gt-ag] intron 7 GenBank accessions 149 bp exon 74 bp [gt-ag] intron 7 GenBank accessions 278 bp exon 90 accessions, some from l2 (seen once) Transpliced 5' end, 2 accessions Validated 3' end, 159 accessions Validated 3' end, 190 accessions 278 bp exon 124 bp exon 124 bp exon 44 bp [gt-ag] intron 7 GenBank accessions 143 bp exon 163 bp [gt-ag] intron 5 GenBank accessions 102 bp exon 42 bp [gt-ag] intron 7 GenBank accessions 149 bp exon 74 bp [gt-ag] intron 7 GenBank accessions 260 bp exon 5 accessions, some from embryo (seen once) l1 (once), mixed (once) Transpliced 5' end, 2 accessions Validated 3' end, 131 accessions 260 bp exon 122 bp exon 122 bp exon 49 bp [gt-ag] intron 1 GenBank accession 138 bp exon 1 accession 138 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 856 bp 225 aa 8 bp 170 bp 2kb including Promoter 1119 bp 1kb
b 778 bp 205 aa 8 bp 152 bp 2kb including Promoter 1101 bp 1kb
c 260 bp 66 aa 61 bp 2kb probably including promoter 309 bp 1kb

Gene neighbors and Navigator on chromosome IV back to top
C R P mppb-1 C I R P twk-8 C R P 4J855 C R C I R P 4J865 C P fem-3 D C I P aly-1 D C I P D C R P 4J842 D C R P lpl-1 D C I R P icl-1 D C I R P 4J862 C R P cyp-31A1 5kb 0 nhr-11, 48 accessions 5 variants mppb-1, 135 accessions 2 variants twk-8, 32 accessions, 6 variants 4J855, 67 accessions, 4 variants 4J863, 74 accessions, 6 variants 4J865, 0 accession fem-3, 24 accessions, 4 variants aly-1, 21 accessions 4J868, 0 accession 4J842, 28 accessions, 4 variants lpl-1, 48 accessions, 7 variants icl-1, 96 accessions, 3 variants 4J862, 169 accessions cyp-31A1, 41 accessions 9 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 5 articles in PubMed.
In addition we found 2 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c 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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