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
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
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).
. 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
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
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
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.
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.
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Details on tissue of origin for each intron and exon is available from the intron and exons table
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. Proteins supported by a single continuous cDNA sequence 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.
are depicted by broken lines; the height of the top of each intron reflects the relative number of clones supporting this intron. ]^[ A pink broken line
denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron). ] ^ ] A blue broken line
denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries. ]-[ Pink
and ] - ] blue
straight lines represent 'fuzzy' introns of the standard and non-standard types respectively, those introns do not follow the 16 bp rule. Black straight lines ]-[denote gaps in the alignments.
Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). Flags identify validated endings: cap site on the 5' side, polyadenylation site on the 3' side. Filled flags correspond to frequent events while empty flags have lesser supporting cDNAs (yet all are validated); at the 3' side, black flags are associated to the main AATAAA signal, blue flags
to any single letter variant of the main . More explanations are given in the gene help file