Caenorhabditis elegans essential gene arx-7, encoding actin Related protein 2/3 compleX component.
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SUMMARY back to top
Summary
[Wormbase] arx-7 encodes the C. elegans ortholog of the p16Arc subunit of the actin-related protein (Arp)2/3 complex.
Wormbase predicts 4 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 12 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 10.0 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 17%, L1 or L2 larvae 27%, L3 to adult 56%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 57 cDNA clones and 75 elements defined by RNA-seq, some from l1 (seen 11 times), mixed (11), embryo (9), l2 (3), l4 (3). We annotate structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 23 distinct introns (22 gt-ag, 1 gc-ag). Transcription produces at least 13 different mRNAs, 12 alternatively spliced variants and 1 unspliced form. Variant a is transpliced to SL2, b to SL2, SL9, c to SL3, SL2, SL1, SL4, j to SL1, SL2, SL3. There are 3 probable alternative promotors, 4 non overlapping alternative last exons and 13 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 6 cassette exons, overlapping exons with different boundaries, splicing versus retention of 2 introns. 427 bp of this gene are antisense to spliced gene 1D637, raising the possibility of regulated alternate expression.
2 variants were isolated in vivo, despite the fact that they are predicted targets of nonsense mediated mRNA decay (NMD).
Function: There are 2 articles specifically referring to this gene in PubMed. This essential gene is associated to a phenotype (Embryonic Lethal, Larval arrest, unhealthy, defective hypodermal enclosure). Functionally, the gene has been proposed to participate in a process (regulation of actin polymerization). Proteins are expected to localize in various compartments (nucleus, cytoskeleton).
Protein coding potential: 10 spliced mRNAs putatively encode good proteins, altogether 10 different isoforms (3 complete, 3 COOH complete, 4 partial), some containing ARP2/3 complex 16 kDa subunit (p16-Arc) domain [Pfam], a coiled coil stretch [Psort2]. The remaining 3 mRNA variants (2 spliced, 1 unspliced; 3 partial) appear not to encode good proteins.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome I, links to other databases and other names
Map: This essential gene arx-7 maps on chomosome I at position -4.88 (interpolated). In AceView, it covers 15.56 kb, from 3084875 to 3069316 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 1D638, in Wormbase by its cosmid.number name M01B12.3, M01B12.4, in NextDB, the Nematode expression pattern database, as CEYK2106.
          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 arx-7 5' 3' encoded on minus strand of chromosome I from 3,084,875 to 3,069,316 a b c f d m e k g h i j l 1 2kb 0 52 bp exon 52 bp exon 759 bp [gt-ag] intron 16 GenBank accessions 107 bp exon 730 bp [gt-ag] intron 17 GenBank accessions 283 bp exon 946 bp [gt-ag] intron 3 GenBank accessions 30 bp exon 1213 bp [gt-ag] intron 3 GenBank accessions 295 bp exon 1528 bp [gt-ag] intron 19 GenBank accessions 614 bp exon 1303 bp [gt-ag] intron 10 GenBank accessions 451 bp exon 1296 bp [gt-ag] intron 7 GenBank accessions 132 bp exon 2163 bp [gt-ag] intron 16 GenBank accessions 107 bp exon 594 bp [gt-ag] intron 21 GenBank accessions 107 bp exon 107 bp exon 640 bp [gt-ag] intron 36 GenBank accessions 18 accessions, some from l1 (seen 5 times) embryo (3), l4 (3), l2 (once) mixed (once) Transpliced 5' end, 1 accession Validated 3' end, 3 accessions Validated 3' end, 1 accession 549 bp exon 52 bp exon 52 bp exon 759 bp [gt-ag] intron 16 GenBank accessions 107 bp exon 730 bp [gt-ag] intron 17 GenBank accessions 283 bp exon 2189 bp [gt-ag] intron 21 GenBank accessions 295 bp exon 1528 bp [gt-ag] intron 19 GenBank accessions 614 bp exon 1303 bp [gt-ag] intron 10 GenBank accessions 451 bp exon 1296 bp [gt-ag] intron 7 GenBank accessions 132 bp exon 2163 bp [gt-ag] intron 16 GenBank accessions 107 bp exon 594 bp [gt-ag] intron 21 GenBank accessions 107 bp exon 107 bp exon 640 bp [gt-ag] intron 36 GenBank accessions 5 accessions, some from l1 (seen 3 times) l2 (once) Transpliced 5' end, 2 accessions Validated 3' end, 3 accessions Validated 3' end, 1 accession 550 bp exon 52 bp exon 52 bp exon 759 bp [gt-ag] intron 16 GenBank accessions 107 bp exon 730 bp [gt-ag] intron 17 GenBank accessions 283 bp exon 2189 bp [gt-ag] intron 21 GenBank accessions 295 bp exon 1528 bp [gt-ag] intron 19 GenBank accessions 614 bp exon 1303 bp [gt-ag] intron 10 GenBank accessions 451 bp exon 3591 bp [gt-ag] intron 7 GenBank accessions 107 bp exon 594 bp [gt-ag] intron 21 GenBank accessions 107 bp exon 107 bp exon 640 bp [gt-ag] intron 36 GenBank accessions 92 accessions, some from mixed (seen 7 times) embryo (6), l1 (3), l2 (once) Transpliced 5' end, 5 accessions Validated 3' end, 3 accessions Validated 3' end, 1 accession Validated 3' end, 168 accessions 578 bp exon 102 bp exon 102 bp exon 724 bp [gt-ag] intron 1 GenBank accession 1 accession 283 bp exon 147 bp exon 147 bp exon 1528 bp [gt-ag] intron 19 GenBank accessions 614 bp exon 1303 bp [gt-ag] intron 10 GenBank accessions 451 bp exon 3591 bp [gt-ag] intron 7 GenBank accessions 107 bp exon 594 bp [gt-ag] intron 21 GenBank accessions 107 bp exon 107 bp exon 640 bp [gt-ag] intron 36 GenBank accessions 317 bp exon 1057 bp [gt-ag] intron 1 GenBank accession 95 bp exon 84 bp [gt-ag] intron 5 GenBank accessions 122 bp exon 102 bp [gt-ag] intron 6 GenBank accessions 7 accessions, some from mixed (seen 3 times) Validated 3' end, 3 accessions Validated 3' end, 1 accession Validated 3' end, 62 accessions Validated 3' end, 6 accessions 427 bp exon 193 bp exon 1 accession 193 bp exon 371 bp exon 371 bp exon 198 bp exon 1 accession 198 bp exon 54 bp exon 54 bp exon 1308 bp [gt-ag] intron 1 GenBank accession 1 accession 116 bp exon 46 bp exon 46 bp exon 1596 bp [gt-ag] intron 1 GenBank accession 1 accession 277 bp exon 171 bp exon 62 bp [gt-ag] intron 1 GenBank accession 56 bp exon 1 accession 56 bp exon 89 bp exon 89 bp exon 1948 bp [gc-ag] intron 1 GenBank accession 552 bp exon 1 accession 552 bp exon 95 bp exon 95 bp exon 87 bp [gt-ag] intron 1 GenBank accession 109 bp exon 2 accessions Transpliced 5' end, 1 accession 109 bp exon 54 bp exon 54 bp exon 1311 bp [gt-ag] intron 1 GenBank accession 1 accession 113 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.
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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 Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
a 2727 bp 688 aa 37 bp 623 bp 2kb including Promoter 13899 bp 1kb
b 2698 bp 678 aa 37 bp 624 bp 2kb including Promoter 13900 bp 1kb
c 2594 bp 634 aa 37 bp 652 bp 2kb including Promoter 13928 bp 1kb
d 2387 bp 449 aa 1035 bp 2kb 11286 bp 1kb
e 569 bp 164 aa 72 bp 2kb 612 bp 1kb
f 385 bp 128 aa 2kb 1109 bp 1kb
g 323 bp 94 aa 41 bp 2kb probably including promoter 1919 bp 1kb
h 227 bp 75 aa 2kb 289 bp 1kb
i 641 bp 61 aa 454 bp 2kb 2589 bp 1kb
j 204 bp 64 aa 10 bp 2kb including Promoter 291 bp 1kb
k 170 bp 56 aa 2kb 1478 bp 1kb
l 167 bp 55 aa 2kb 1478 bp 1kb
m 193 bp 44 aa 58 bp 2kb 193 bp 1kb

Gene neighbors and Navigator on chromosome I back to top
1D637 C R 1D655 D C P ztf-23 D C R P arx-7 D C R P riok-1 5kb 0 1D637, 26 accessions, 3 variants 1D655, 0 accession ztf-23, 32 accessions 2 variants arx-7, 132 accessions 13 variants riok-1, 33 accessions 5 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, .c, .d, .e, .f, .g, .h, .i, .j, .k, .l, .m 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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