Caenorhabditis elegans essential gene fos-1, encoding basic leucine zipper transcription factor, ortholog of vertebrate fos, promotes basement membrane removal during cell invasion, abnormal Eversion of VuLva evl-5.
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SUMMARY back to top
Summary
[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)
          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 fos-1 5' 3' encoded on plus strand of chromosome V from 5,995,771 to 6,016,419 a d b f g c k j e h i 5kb 0 113 bp exon 113 bp exon 519 bp [gt-ag] intron 1 GenBank accession 171 bp exon 51 bp [gt-ag] intron 18 GenBank accessions 164 bp exon 42 bp [gt-ag] intron 17 GenBank accessions 350 bp exon 48 bp [gt-ag] intron 6 GenBank accessions 283 bp exon 45 bp [gt-ag] intron 5 GenBank accessions 180 bp exon 102 bp [gt-ag] intron 5 GenBank accessions 230 bp exon 82 bp [gt-ag] intron 6 GenBank accessions 607 bp exon 113 bp [gt-ag] intron 7 GenBank accessions 489 bp exon 17 accessions, some from mixed (seen 2 times) embryo (once) Validated 3' end, 8 accessions Validated 3' end, 12 accessions 489 bp exon 388 bp exon 388 bp exon 2277 bp [gt-ag] intron 2 GenBank accessions 70 bp exon 45 bp [gt-ag] intron 4 GenBank accessions 137 bp exon 2157 bp [gt-ag] intron 4 GenBank accessions 114 bp exon 595 bp [gt-ag] intron 5 GenBank accessions 501 bp exon 53 bp [gt-ag] intron 4 GenBank accessions 202 bp exon 595 bp [gt-ag] intron 6 GenBank accessions 867 bp exon 23 accessions Validated 3' end, 5 accessions Validated 3' end, 10 accessions 867 bp exon 249 bp exon 51 bp [gt-ag] intron 18 GenBank accessions 164 bp exon 42 bp [gt-ag] intron 17 GenBank accessions 350 bp exon 48 bp [gt-ag] intron 6 GenBank accessions 283 bp exon 45 bp [gt-ag] intron 5 GenBank accessions 180 bp exon 102 bp [gt-ag] intron 5 GenBank accessions 230 bp exon 82 bp [gt-ag] intron 6 GenBank accessions 607 bp exon 113 bp [gt-ag] intron 7 GenBank accessions 451 bp exon 8 accessions, some from mixed (seen 5 times) Validated 3' end, 8 accessions 451 bp exon 400 bp exon 400 bp exon 102 bp uORF 400 bp exon 400 bp exon 113 bp [gt-ag] intron 1 GenBank accession 70 bp exon 70 bp exon 1 accession 70 bp exon 592 bp exon 592 bp exon 21 bp uORF 592 bp exon 592 bp exon 1000 bp [gt-ag] intron 1 GenBank accession 107 bp exon 107 bp exon 1 accession 107 bp exon 205 bp exon 205 bp exon 51 bp [gt-ag] intron 18 GenBank accessions 164 bp exon 42 bp [gt-ag] intron 17 GenBank accessions 350 bp exon 48 bp [gt-ag] intron 6 GenBank accessions 283 bp exon 45 bp [gt-ag] intron 5 GenBank accessions 180 bp exon 102 bp [gt-ag] intron 5 GenBank accessions 230 bp exon 82 bp [gt-ag] intron 6 GenBank accessions 687 bp exon 8 accessions, some from embryo (seen 3 times) l4 (once), mixed (once) Validated 3' end, 8 accessions 687 bp exon 68 bp exon 1118 bp [gt-ag] intron 1 GenBank accession 324 bp exon 324 bp exon 45 bp uORF 324 bp exon 324 bp exon 5988 bp [gt-ag] intron 1 GenBank accession 70 bp exon 70 bp exon 2 accessions 70 bp exon 113 bp exon 113 bp exon 619 bp [gt-ag] intron 1 GenBank accession 67 bp exon 1 accession 67 bp exon 70 bp exon 7430 bp [gt-ag] intron 3 GenBank accessions 70 bp exon 45 bp [gt-ag] intron 4 GenBank accessions 137 bp exon 137 bp exon 2157 bp [gt-ag] intron 4 GenBank accessions 114 bp exon 595 bp [gt-ag] intron 5 GenBank accessions 501 bp exon 53 bp [gt-ag] intron 4 GenBank accessions 202 bp exon 595 bp [gt-ag] intron 6 GenBank accessions 501 bp exon 10 accessions, some from embryo (seen once) mixed (once) Validated 3' end, 5 accessions 501 bp exon 158 bp exon 47 bp [gt-ag] intron 1 GenBank accession 344 bp exon 1 accession 344 bp exon 113 bp exon 113 bp exon 17609 bp [gt-ag] intron 1 GenBank accession 107 bp exon 1 accession 107 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 2587 bp 818 aa 20 bp 110 bp 2kb possibly including promoter 3589 bp 1kb
b 2514 bp 813 aa 72 bp 2kb 2997 bp 1kb
c 2099 bp 657 aa 49 bp 76 bp 2kb probably including promoter 2469 bp 1kb
d 2279 bp 467 aa 130 bp 745 bp 2kb possibly including promoter 8001 bp 1kb
e 1595 bp 331 aa 220 bp 379 bp 2kb probably including promoter 12470 bp 1kb
f 470 bp 51 aa 316 bp 99 bp 2kb 583 bp 1kb
g 699 bp 48 aa 553 bp 18 bp 2kb possibly including promoter 1699 bp 1kb
h 502 bp 64 aa 307 bp 2kb 549 bp 1kb
i 220 bp 66 aa 20 bp 2kb possibly including promoter 17829 bp 1kb
j 180 bp 52 aa 20 bp 2kb 799 bp 1kb
k 462 bp 39 aa 344 bp 42 bp 2kb probably including promoter 7568 bp 1kb

Gene neighbors and Navigator on chromosome V back to top
dhs-16 C R P fos-1 D C I R P cpg-4 C P aps-1C D C I R P C R 5G466 C R P fut-8 D C I R P rpt-2 dhs-17 5kb 0 acy-2, 27 accessions dhs-16, 19 accessions fos-1, 74 accessions, 11 variants cpg-4, 0 accession aps-1C, 151 accessions 7 variants 5G484, 4 accessions, 2 variants 5G466, 7 accessions fut-8, 22 accessions, 3 variants rpt-2, 53 accessions dhs-17, 16 accessions 2 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 5 articles in PubMed.
In addition we found 2 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j, .k Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

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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