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, 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 7 spliced variants.

AceView summary
Expression: According to AceView, this gene is expressed at very high level, 5.5 times the average gene in this release, at all stages of development [Kohara cDNAs]. The sequence of this gene is defined by 72 cDNA clones, some from whole animal (seen 5 times). We annotate structural defects or features in 3 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 8 distinct gt-ag introns. Transcription produces at least 7 alternatively spliced mRNAs. There are 2 probable alternative promotors and 14 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by by truncation of the 5' end, overlapping exons with different boundaries, splicing versus retention of 3 introns.
Protein coding potential: The 7 spliced mRNAs putatively encode good proteins, altogether 7 different isoforms (6 complete, 3 COOH complete), some containing basic leucine zipper domain [Pfam], a vacuolar domain, a coiled coil stretch [Psort2]. 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.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12
Map on chromosome CHROMOSOME_III, links to other databases and other names back to top ?
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:               (in true scale, with colored introns) back to top
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 cDNA clones supporting each intron. Superimposed introns of the same color are identical, of different colors are different.
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. Details on tissue of origin for each intron and exon is available from the intron and exons table. Good predicted proteins are in pink, yellow proteins may be partial or unconvincing, green are uORFs. Proteins supported by a single continuous GenBank accession lead to underlining the name/ending of the variant. Names not underlined result from cDNA concatenation in the coding region and should be experimentally checked.
More legend
Sequences back to top
What is known about the gene and its neighbors on chromosome CHROMOSOME_III back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         (see the Legend)
Annotated mRNA diagrams back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function and related genes C

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function and 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 and 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 all variants, their summarized annotations, 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'.

If you know more about this gene, or found errors, please share your knowledge. Merci !