[Wormbase] fos-1 encodes two basic region-leucine zipper (bZip) transcription factors, FOS-1A and FOS-1B, that are the sole C. elegans orthologs of the fos bZip transcription factor family; during hermaphrodite development, FOS-1A activity is required cell autonomously in the gonadal anchor cell for basement-membrane removal and subsequent anchor cell invasion of the vulval epithelium; in addition, fos-1 activity is also required for proper vulval and uterine development, fertility, and oogenesis; in late-L3 larvae, a FOS-1A translational fusion protein is expressed at high levels in the anchor cell nucleus and at lower levels in uterine cells, while a FOS-1B reporter is expressed at low levels in the anchor cell, uterine, and vulval cells; transcriptional reporters additionally reveal that fos-1b is expressed in most cells of late L3 larvae; in affecting anchor cell invasion, FOS-1A appears to act by regulating the expression of three AC-expressed genes: cdh-3/cadherin, him-4/hemicentin, and zmp-1/matrix metalloproteinase, which likely function together to promote anchor cell invasion.
Wormbase predicts 2 models from 2 genes, 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 11 spliced variants.
AceView synopsis, each blue text links to tables and details Expression: According to AceView, this gene is expressed at very high level, 5.6 times the average gene in this release, In the L3 larva, fos-1a is expressed transcriptionally and translationally mainly in the anchor cell and less strongly in the neighboring uterine cells. It is absent from the vulval precursor cells. This is in contrast to fos-1b which at that stage is expressed in most cells (peak in phasmids and some central nerve cells). FOS-1b protein would be made in many cells including the vulval precursor cells (caveat: the CFP was inserted in first exon, way ahead of the predicted ATG) [from Sherwood et al, 2005]. 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 5%, L3 to adult 77%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 41 cDNA clones and 33 elements defined by RNA-seq, some from mixed (seen 9 times), embryo (5), l4 (once). Alternative mRNA variants and regulation: The gene contains 22 distinct gt-ag introns. Transcription produces at least 11 alternatively spliced mRNAs. There are 7 probable alternative promotors, 4 non overlapping alternative last exons and 8 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 11 cassette exons, overlapping exons with different boundaries. 855 bp of this gene are antisense to spliced gene rpt-2, 376 to 5G484, raising the possibility of regulated alternate expression. Function: There are 5 articles specifically referring to this gene in PubMed. In addition we point below to 2 abstracts. This essential gene is associated to a phenotype (abnormal Eversion of VuLva, fragile animal, may explode at vulva, Protruding VuLva, Sterile adult, defect in invasion of vulval cells by anchor cell). 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 various compartments (extracellular space, nucleus). The gene interacts with 5 other genes (CDH-3, EGL-43, HIM-4, LIN-3, ZMP-1). Protein coding potential: 8 spliced mRNAs putatively encode good proteins, altogether 8 different isoforms (4 complete, 2 COOH complete, 2 partial), some containing domains bZIP transcription factor, bZIP-1, basic leucine zipper [Pfam], a coiled coil stretch [Psort2]; 2 of the 4 complete proteins appear to be secreted. The remaining 3 mRNA variants (3 spliced; 2 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 V, links to other databases and other names Map: This essential gene fos-1 maps on chomosome V at position -0.80 (interpolated). In AceView, it covers 20.65 kb, from 5995771 to 6016419 (WS190), on the direct strand. Links to:WormBase, NextDB, RNAiDB.
as Other names: The gene is also known evl-5, in Wormgenes/AceView by its positional name 5G495, in Wormbase by its cosmid.number name F29G9.4, in NextDB, the Nematode expression pattern database, as CEYK4146. Closest AceView homologs in other species ? The closest human genes, according to BlastP, are the AceView genes ATF2andCHN1, ATF7, GALNT7. The closest mouse genes, according to BlastP, are the AceView genes Atf2 (e=10-05), Junb (e=6 10-04)
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. Read more...
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.
Introns 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.
Exons: 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
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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