Gene FGF6TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS
Compact gene diagram
According to AceView, this gene is expressed at low level
, only 5.5% of the average gene in this release. The sequence
of this gene is defined by 7 GenBank accessions
, some from pectoral muscle (after mastectomy) (seen once). We annotate structural defects or features
in one cDNA clone.
Alternative mRNA variants and regulation:
The gene contains 4 distinct gt-ag introns
. Transcription produces 3 alternatively spliced mRNAs
. There are 3 probable alternative promotors
(see the diagram
). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, overlapping exons with different boundaries.
There are 15 articles
specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases
(Cell Transformation, Neoplastic; Mesothelioma; Prostatic Intraepithelial Neoplasia; Prostatic Neoplasms; Translocation, Genetic), proposed to participate in pathways
(MAPK signaling pathway, Melanoma, Pathways in cancer, Regulation of actin cytoskeleton) and processes
(cell proliferation, cell-cell signaling, fibroblast growth factor receptor signaling pathway, positive regulation of cell proliferation, signal transduction and 6 others
). Proteins are expected to have molecular function
(growth factor activity) and to localize
in various compartments (extracellular region, membrane, extracellular space, sarcolemma). Putative protein interactors
have been described (FGFR1, FGFR2, FGFR3, FGFR4).
Protein coding potential:
The spliced mRNAs putatively encode a good protein
, containing Fibroblast growth factor domain
[Pfam], some transmembrane domains [Psort2]
. The remaining 2 mRNA variants (2 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
7 supporting clones for gene FGF6
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
Links to the sequence
most 5' clones
(with AA variation)
relative to genome
|BC121097 ||PCR rescued clones ||.a ||1 to 747 ||1 to 747 ||exact ||tiling clone, || ||747/747 |
| 7 diff|
|BC121098 ||PCR rescued clones ||.a ||1 to 747 ||1 to 747 ||exact || || ||747/747 |
| 6 diff|
|NM_020996.1 || ||.a ||5 to 748 ||1 to 744 ||exact ||RefSeq, || ||744/744 |
| 2 diff|
|X63454 || ||.a ||5 to 748 ||1 to 744 ||exact ||tiling clone, || ||744/744 |
| 2 diff|
|AA781411 || ||.b ||1 to 466 ||467 to 2 ||exact ||tiling clone, || ||466/467 |
| 0 diff|
|F22806 ||pectoral muscle (after mastectomy) ||.c ||1 to 335 ||1 to 335 ||exact ||tiling clone, || ||335/335 |
| 2 diff|
|AI217705 ||pooled ||Gene FGF6, variant not shown || || || || ||This clone was ignored || || |