Caenorhabditis elegans gene adr-2, encoding double-stranded RNA adenosine-deaminase, editase.
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SUMMARY back to top
Summary
The gene adr-1 encodes two isoforms of double stranded RNA adenosine-deaminase (editase) and is well expressed at all stages of development [Hough et al, 1999; Kohara cDNAs], mostly in neurons and in the developing vulva [Tonkin et al, 2002]. It is one of two closely related genes. RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans, as shown by the study of null deletion alleles [Tonkin et al, 2002]. Some ADAR function is required to prevent gene silencing in somatic tissue: transgenes expressed in the somatic tissues of wild-type animals are silenced in strains with deletions in the two genes encoding ADARs, adr-1 and adr-2 [Knight and Bass, 2002]. It lies second in a six gene operon including in that order an essential gene 3I324 (NADH:ubiquinone oxidoreductase complex I, 23.9 kD mitochondrial subunit), gene 3I320 (haloacid dehalogenase-like hydrolase, GS1-like protein), gene 3I318, gene 3I314 (heat shock protein 75) and gene 3I312 (NADH oxidoreductase complex)[Wormbase] adr-2 encodes an adenosine deaminase that acts on RNA (ADAR); ADARs are RNA-editing enzymes that deaminate adenosines to create inosines in double-stranded RNA (dsRNA); adr-2 is expressed ubiquitously in early embryos, as well as in the germline of early adults; ADR-2 is required for ADAR activity in vivo, and for normal chemotaxis.
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
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AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 3.0 times the average gene in this release, at all stages of development [Kohara cDNAs], mostly in neurons and in the developing vulva [Tonkin et al, 2002]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 7%, L1 or L2 larvae 67%, L3 to adult 26%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 19 cDNA clones and 21 elements defined by RNA-seq, some from l2 (seen 7 times), l1 (4), embryo (once), l4 (once). We annotate structural defects or features in 4 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 4 distinct gt-ag introns. Transcription produces 2 alternatively spliced mRNAs. Variant a is transpliced to SL1, SL2, SL3, SL4, SL8, SL5, SL9, b to SL3. There are 5 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ splicing versus retention of one intron.
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant b).
Function: There are 6 articles specifically referring to this gene in PubMed. In addition we point below to 3 abstracts. This gene is associated to a phenotype (abnormal CHEmotaxis, required for normal behaviour). Functionally, the gene has been proposed to participate in a process (RNA processing). Proteins are expected to have molecular functions (adenosine deaminase activity, double-stranded RNA binding activity) and to localize in various compartments (cytoplasm, intracellular). These proteins appear to interact with another protein (ADBP-1).
Protein coding potential: The 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (2 complete), some containing domains Adenosine deaminase/editase, double-stranded RNA binding [Pfam].

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 gene adr-2 maps on chomosome III at position -0.74 (interpolated). In AceView, it covers 1.94 kb, from 7232811 to 7230877 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 3I322, in Wormbase by its cosmid.number name T20H4.4, in NextDB, the Nematode expression pattern database, as CEYK6994.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes ADARB1 (e=4 10-53), ADAR (e=4 10-53), ADARB2 (e=2 10-47).
The closest mouse genes, according to BlastP, are the AceView genes Adarb1 (e=3 10-55), Adar (e=3 10-55).
The closest A.thaliana gene, according to BlastP, is the AceView gene AT1G01760 (e=8 10-25)
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the Flash version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
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.
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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 uORF Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
a 1713 bp 495 aa 225 bp 2kb including Promoter 1935 bp 1kb
b 1666 bp 367 aa 437 bp 125 bp 483 bp 2kb including Promoter 1835 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
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 3 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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