Caenorhabditis elegans gene atf-7, encoding cAMP-dependent Transcription Factor-like.
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SUMMARY back to top
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Wormbase predicts 3 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 8 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 17.2 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 18%, L1 or L2 larvae 45%, L3 to adult 37%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 89 cDNA clones and 138 elements defined by RNA-seq, some from l1 (seen 23 times), embryo (14), l2 (14), mixed (8), l4 (4), whole animal (once). We annotate structural defects or features in 4 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 11 distinct gt-ag introns. Transcription produces at least 8 alternatively spliced mRNAs. Variant b is transpliced to SL1, c to SL1, d to SL1, SL2, SL3, SL4, e to SL2, SL1, g to SL1. There are 3 probable alternative promotors and 34 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, presence or absence of 2 cassette exons, overlapping exons with different boundaries, splicing versus retention of 3 introns.
Note that mRNA .h was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
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 d, e, g).
Function:. Functionally, the gene has been proposed to participate in a process (regulation of transcription, DNA-dependent). Proteins are expected to have molecular functions (protein dimerization activity, transcription factor activity) and to localize in nucleus.
Protein coding potential: The 8 spliced mRNAs putatively encode good proteins, altogether 7 different isoforms (6 complete, 1 COOH complete), some containing basic leucine zipper domain [Pfam], 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 III, links to other databases and other names
Map: This gene atf-7 maps on chomosome III at position -2.94 (interpolated). In AceView, it covers 7.42 kb, from 4499011 to 4491589 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 3F582, in Wormbase by its cosmid.number name C07G2.2, in NextDB, the Nematode expression pattern database, as CEYK3651.
          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 atf-7 5' 3' encoded on minus strand of chromosome III from 4,499,011 to 4,491,589 a b c d e f g h 1kb 0 332 bp exon 332 bp exon 94 bp [gt-ag] intron 7 GenBank accessions 414 bp exon 117 bp [gt-ag] intron 45 GenBank accessions 404 bp exon 56 bp [gt-ag] intron 14 GenBank accessions 292 bp exon 41 bp [gt-ag] intron 18 GenBank accessions 117 bp exon 235 bp [gt-ag] intron 38 GenBank accessions 322 bp exon 2 accessions, some from l1 (seen 2 times) Validated 3' end, 6 accessions Validated 3' end, 3 accessions Validated 3' end, 1 accession 322 bp exon 264 bp exon 264 bp exon 94 bp [gt-ag] intron 7 GenBank accessions 414 bp exon 117 bp [gt-ag] intron 45 GenBank accessions 404 bp exon 56 bp [gt-ag] intron 14 GenBank accessions 292 bp exon 41 bp [gt-ag] intron 18 GenBank accessions 117 bp exon 235 bp [gt-ag] intron 38 GenBank accessions 787 bp exon 12 accessions, some from l2 (seen 4 times) l1 (3), mixed (2), l4 (once) Transpliced 5' end, 4 accessions Validated 3' end, 1 accession Validated 3' end, 34 accessions Validated 3' end, 2 accessions Validated 3' end, 1 accession Validated 3' end, 744 accessions 787 bp exon 264 bp exon 264 bp exon 94 bp [gt-ag] intron 7 GenBank accessions 414 bp exon 117 bp [gt-ag] intron 45 GenBank accessions 404 bp exon 56 bp [gt-ag] intron 14 GenBank accessions 292 bp exon 50 bp [gt-ag] intron 6 GenBank accessions 108 bp exon 235 bp [gt-ag] intron 38 GenBank accessions 618 bp exon 1 accession from l1 Transpliced 5' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 34 accessions Validated 3' end, 2 accessions 618 bp exon 84 bp exon 84 bp exon 36 bp uORF 84 bp exon 406 bp [gt-ag] intron 36 GenBank accessions 63 bp exon 63 bp exon 63 bp exon 4398 bp [gt-ag] intron 40 GenBank accessions 414 bp exon 414 bp exon 117 bp [gt-ag] intron 45 GenBank accessions 404 bp exon 404 bp exon 56 bp [gt-ag] intron 14 GenBank accessions 292 bp exon 292 bp exon 41 bp [gt-ag] intron 18 GenBank accessions 117 bp exon 117 bp exon 235 bp [gt-ag] intron 38 GenBank accessions 795 bp exon 795 bp exon 198 accessions, some from embryo (seen 13 times) l1 (13), l2 (9), mixed (4) l4 (3) Transpliced 5' end, 20 accessions Validated 3' end, 1 accession Validated 3' end, 34 accessions Validated 3' end, 2 accessions Validated 3' end, 1 accession Validated 3' end, 744 accessions 795 bp exon 84 bp exon 84 bp exon 36 bp uORF 84 bp exon 406 bp [gt-ag] intron 36 GenBank accessions 63 bp exon 63 bp exon 63 bp exon 4398 bp [gt-ag] intron 40 GenBank accessions 414 bp exon 414 bp exon 117 bp [gt-ag] intron 45 GenBank accessions 404 bp exon 404 bp exon 56 bp [gt-ag] intron 14 GenBank accessions 292 bp exon 292 bp exon 50 bp [gt-ag] intron 6 GenBank accessions 108 bp exon 108 bp exon 235 bp [gt-ag] intron 38 GenBank accessions 785 bp exon 785 bp exon 8 accessions, some from l1 (seen 4 times) embryo (once), mixed (once) Transpliced 5' end, 2 accessions Validated 3' end, 1 accession Validated 3' end, 34 accessions Validated 3' end, 2 accessions Validated 3' end, 1 accession 785 bp exon 61 bp exon 4040 bp [gt-ag] intron 1 GenBank accession 772 bp exon 772 bp exon 117 bp [gt-ag] intron 45 GenBank accessions 404 bp exon 56 bp [gt-ag] intron 14 GenBank accessions 292 bp exon 41 bp [gt-ag] intron 18 GenBank accessions 117 bp exon 235 bp [gt-ag] intron 38 GenBank accessions 764 bp exon 3 accessions, some from mixed (seen once) Validated 3' end, 1 accession Validated 3' end, 34 accessions Validated 3' end, 2 accessions Validated 3' end, 1 accession 764 bp exon 772 bp exon 772 bp exon 408 bp uORF 408 bp uORF 772 bp exon 772 bp exon 117 bp [gt-ag] intron 45 GenBank accessions 404 bp exon 404 bp exon 56 bp [gt-ag] intron 14 GenBank accessions 450 bp exon 450 bp exon 450 bp exon 235 bp [gt-ag] intron 38 GenBank accessions 1 accession from l2 Transpliced 5' end, 1 accession Validated 3' end, 6 accessions Validated 3' end, 3 accessions Validated 3' end, 1 accession 469 bp exon 404 bp exon 94 bp [gt-ag] intron 1 GenBank accession 254 bp exon 254 bp exon 393 bp [gt-ag] intron 1 GenBank accession 2 accessions Validated 3' end, 1 accession Validated 3' end, 34 accessions Validated 3' end, 2 accessions Validated 3' end, 1 accession 784 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 uORF Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
a 1881 bp 523 aa 98 bp 211 bp 2kb possibly including promoter 2424 bp 1kb
b 2278 bp 523 aa 30 bp 676 bp 2kb including Promoter 2821 bp 1kb
c 2100 bp 520 aa 30 bp 507 bp 2kb including Promoter 2652 bp 1kb
d 2169 bp 460 aa 102 bp 684 bp 33 bp 2kb including Promoter 7422 bp 1kb
e 2150 bp 457 aa 102 bp 674 bp 33 bp 2kb including Promoter 7412 bp 1kb
f 2410 bp 441 aa 431 bp 653 bp 2kb possibly including promoter 6899 bp 1kb
g 2095 bp 373 aa 370 bp 603 bp 405 bp 2kb including Promoter 2503 bp 1kb
h 1442 bp 186 aa 881 bp 2kb 1929 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
rps-1 D C P cpg-1 D C R P 3F601 C R D C I R P pqn-45 C I R P ins-17 C R atf-7 D C I R P cct-5 5kb 0 3F561, 9 accessions, 2 variants rps-1, 1762 accessions 6 variants cpg-1, 182 accessions 3 variants 3F601, 42 accessions, 3 variants 3F562t, 0 accession 3F586, 3 accessions pqn-45, 81 accessions 5 variants ins-17, 52 accessions 2 variants atf-7, 227 accessions 8 variants cct-5, 271 accessions 6 variants ZOOM OUT                 D:disease, C:conserved, I:interactions, R:regulation, P:publications         Read more...
Annotated mRNA diagrams back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

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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