Special

MmuEX0048241 @ mm9

Exon Skipping

Description
tenascin C [Source:MGI Symbol;Acc:MGI:101922]
Coordinates
chr4:63643685-63654333:-
Coord C1 exon
chr4:63654061-63654333
Coord A exon
chr4:63645494-63645766
Coord C2 exon
chr4:63643685-63643957
Length
273 bp
Sequences
Splice sites
3' ss Seq
TCACTCCTCCCTTCTTTCAGAGG
3' ss Score
10.61
5' ss Seq
CAGGTATTT
5' ss Score
7.51
Exon sequences
Seq C1 exon
CCAGAGAACCTGAAATTGGAAACTTAAATGTTTCTGATGTAACTCCTAAGAGCTTCAATCTCTCCTGGACAGCTACCGACGGGATCTTCGACATGTTTACTATTGAAATTATTGATTCTAATAGGTTGCTGCAAACAGCAGAACATAATATATCTGGTGCTGAACGGACTGCCCACATCTCAGGGCTTCCACCTAGTACTGATTTCATTGTCTACCTCTCTGGAATTGCTCCCAGCATCCGTACCAAAACCATCAGTACCACGGCTACCACAG
Seq A exon
AGGCCTTGCCCCTTCTGGAAAATTTAACCATTTCCGACACTAATCCCTACGGGTTCACAGTTTCCTGGACGGCATCGGAGAATGCCTTTGACAGCTTTCTAGTAACGGTGGTGGATTCTGGGAAGCTGCTGGACCCCCAGGAATTCACACTTTCAGGAACCCAGAGGAAGCTGGAGCTTAGAGGCCTCATAACTGGCATTGGCTATGAGGTCCTGGTCTCTGGCTTCACTCAAGGGCACCAAACAAAGCCCTTGAGGGCTGAGACCATTACAG
Seq C2 exon
AAGCTGAACCGGAAGTTGACAACCTTCTAGTTTCAGATGCCACTCCAGACGGTTTCCGTCTGTCCTGGACTGCTGATGAAGGGATATTCGACAGTTTTGTTATCAGGATCAGAGATACCAAAAAGCAATCTGAGCCACAAGAAATATCCCTCCCTTCCCCCGAACGTACCAGGGACATAACAGGTCTCAGAGAGGCCACTGAGTACGAAATTGAACTCTATGGAATAAGCCGCGGAAGGCGATCCCAGCCAGTCAGTGCCATAGCAACAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028364_MULTIEX1-5/6=4-6
Average complexity
C1
Mappability confidence:
100%=100=100%
Protein Impact

Alternative protein isoforms (No Ref)

No structure available
Features
Disorder rate (Iupred):
  C1=0.168 A=0.098 C2=0.370
Domain overlap (PFAM):

C1:
PF0004116=fn3=WD(100=79.3)
A:
PF0004116=fn3=WD(100=88.0)
C2:
PF0004116=fn3=WD(100=88.0)


Main Inclusion Isoform:


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Other assemblies
Conservation
Chicken
(galGal4)
ALTERNATIVE
(TNC)
Chicken
(galGal3)
Zebrafish
(danRer10)
ALTERNATIVE
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCTCTCCTGGACAGCTACCG
R:
TCATCAGCAGTCCAGGACAGA
Band lengths:
295-568
Functional annotations
There are 10 annotated functions for this event
PMID: 12151539
Tenascin-C is a multimodular glycoprotein that possesses neurite outgrowth-stimulating properties, and one functional site has been localized to the alternatively spliced fibronectin type III domain D (encoded by HsaEX0066152). To identify the neuronal receptor that mediates this effect, neighboring pairs of fibronectin type III domains: exon A1 (HsaEX0066148), exon A2, exon B, exon C (HsaEX0066151), exon D (HsaEX0066152), were expressed as hybrid proteins fused to the Fc fragment of human immunoglobulin. These IgFc fusions were tested for neurite outgrowth-promoting properties on embryonic day 18 rat hippocampal neurons, and both the combinations BD and D6 were shown to promote the elongation of the longest process, the prospective axon. Antibodies to the cell adhesion molecule F3/contactin of the Ig superfamily blocked the BD- but not the D6-dependent effect. Biochemical studies using F3/contactin?IgFc chimeric proteins confirmed that the adhesion molecule selectively reacts with the combination BD but not with other pairs of fibronectin type III repeats of tenascin-C. The alternatively spliced BD cassettes are prominently expressed in the developing hippocampus, as shown by reverse transcription PCR, and colocalize with F3 expression during perinatal periods when axon growth and the establishment of hippocampal connections take place. Note, the exons are tested in combination with one another, e.g. B and D are tested together. The effect of individual exons are not tested in isolation.
PMID: 1725601
Three consecutive exons encoding one FN3 domain each. Modulation of binding to Fibronectin.
PMID: 1725601
Three consecutive exons encoding one FN3 domain each. Modulation of binding to Fibronectin.
PMID: 7499434
The small splice variant of tenascin-C (TNC) has eight fibronectin type III (FN3) domains (it lacks all alternatively splice exons, including: HsaEX0066148, HsaEX0066149, HsaEX0066151, and HsaEX0066152). The major large splice variant has three (in chicken) or seven (in human) additional FN3 domains (encoded by the alternative exons A1 (HsaEX0066148), A2, A3 (HsaEX0066149), A4, B,C (HsaEX0066151), D (HsaEX0066152)) inserted between domains five and six. Chiquet-Ehrismann et al. (Chiquet-Ehrismann, R., Matsuoka, Y., Hofer, U., Spring, J., Bernasconi, C., and Chiquet, M. (1991, Cell Regul. 2, 927-938) demonstrated that the small variant bound preferentially to fibronectin in enzyme-linked immunosorbent assay, and only the small variant was incorporated into the matrix by cultures of chicken fibroblasts. In this paper the authors have studied human tenascin-C, and confirmed that the small variant binds preferentially to purified fibronectin and to fibronectin-containing extracellular matrix. Thus this differential binding appears to be conserved across vertebrate species. Using bacterial expression proteins, they mapped the major binding site to the third FN3 domain of TNC. Consistent with this mapping, a monoclonal antibody against an epitope in this domain did not stain TNC segments bound to cell culture matrix fibrils. The enhanced binding of the small TN variant suggests the existence of another, weak binding site probably in FN3 domains 6-8, which is only positioned to bind fibronectin in the small splice variant. This binding of domains 6-8 may involve a third molecule present in matrix fibrils, as the enhanced binding of small TN was much more prominent to matrix fibrils than to purified fibronectin. Note, the function of individual exons were not examined.
PMID: 9348542
This study examined the in vivo expression and cell adhesive properties of two full-length recombinant tenascin-C proteins: TN-190, which contains the eight constant fibronectin type III repeats, and TN-ADC, which contains the additional AD2 (HsaEX006150), AD1, and C (HsaEX0066151) repeats. In situ hybridization with probes specific for the AD2, AD1, and C repeats shows that these splice variants are expressed at sites of active tissue modeling and fibronectin expression in the developing avian feather bud and sternum. Transcripts incorporating the AD2, AD1, and C repeats are present in embryonic day 10 wing bud but not in embryonic day 10 lung. By using a panel of nine cell lines in attachment assays, the authors have found that C2C12, G8, and S27 myoblastic cells undergo concentration-dependent adhesion to both variants, organize actin microspikes that contain the actin-bundling protein fascin, and do not assemble focal contacts. On a molar basis, TN-ADC is more active than TN-190 in promoting cell attachment and irregular cell spreading. The addition of either TN-190 or TN-ADC in solution to C2C12, COS-7, or MG-63 cells adherent on fibronectin decreases cell attachment and results in decreased organization of actin microfilament bundles, with formation of cortical membrane ruffles and retention of residual points of substratum contact that contain filamentous actin and fascin. These data establish a biochemical similarity in the processes of cell adhesion to tenascin-C and thrombospondin-1, also an ?antiadhesive? matrix component, and also demonstrate that both the adhesive and adhesion-modulating properties of tenascin-C involve similar biochemical events in the cortical cytoskeleton. In addition to these generic properties, TN-ADC is less active in adhesion modulation than TN-190.
PMID: 10367733
This study investigated the impact of cellular environment on the neurite outgrowth promoting properties of the alternatively spliced fibronectin type-III region (fnA-D) of tenascin-C. The effects of the A1-A4 region (consists of exon A1 (HsaEX0066148), A2, A3 (HsaEX0066149), and A4), B-D region (consists of exon B, exon C (HsaEX0066151), and exon D (HsaEX0066152) and the entire region A-D (all the mentioned exons) were examined. FnA-D promoted neurite outgrowth in vitro when bound to the surface of BHK cells or cerebral cortical astrocytes, but the absolute increase was greater on astrocytes. In addition, different neurite outgrowth promoting sites were revealed within fnA-D bound to the two cellular substrates. FnA-D also promoted neurite outgrowth as a soluble ligand; however, the actions of soluble fnA-D were not affected by cell type. It was hypothesized that different mechanisms of cellular binding can alter the growth promoting actions of bound fnA-D. The authors found that fnA-D utilizes two distinct sequences to bind to the BHK cell surface as opposed to the BHK extracellular matrix. In contrast, only one of these sequences is utilized to bind to the astrocyte matrix as opposed to the astrocyte surface. Furthermore, Scatchard analysis indicated two types of receptors for fnA-D on BHK cells and only one type on astrocytes. These results suggest that active sites for neurite outgrowth within fnA-D are differentially revealed depending on cell-specific fnA-D binding sites.
PMID: 10493745
Tenascin-C has been implicated in regulation of both neurite outgrowth and neurite guidance. A particular region of tenascin-C has powerful neurite outgrowth-promoting actions in vitro. This region consists of the alternatively spliced fibronectin type-III (FN-III) repeats A?D and is abbreviated fnA-D. The purpose of this study was to investigate whether fnA-D also provides neurite guidance cues and whether the same or different sequences mediate outgrowth and guidance. The examined exons were A1 (HsaEX0066148), A2, A3 (HsaEX0066149), A4, C (HsaEX0066151), and D (HsaEX0066152). The authors developed an assay to quantify neurite behavior at sharp substrate boundaries and found that neurites demonstrated a strong preference for fnA-D when given a choice at a poly-l-lysine?fnA-D interface, even when fnA-D was intermingled with otherwise repellant molecules. Furthermore, neurites preferred cells that overexpressed the largest but not the smallest tenascin-C splice variant when given a choice between control cells and cells transfected with tenascin-C. The permissive guidance cues of large tenascin-C expressed by cells were mapped to fnA-D. Using a combination of recombinant proteins corresponding to specific alternatively spliced FN-III domains and monoclonal antibodies against neurite outgrowth-promoting sites, the authors demonstrated that neurite outgrowth and guidance were facilitated by distinct sequences within fnA-D.
PMID: 11714809
Together, these 6-8 alternative exon array the encode minimal region of tenascin-C that can inhibit T cell activation. Recombinant fragments corresponding to defined regions of the molecule were tested for their ability to inhibit in vitro activation of human peripheral blood T cells induced by anti-CD3 mAbs in combination with fibronectin or IL-2. A recombinant protein encompassing the alternatively spliced fibronectin type III domains of tenascin-C (TnFnIII A1-3 and B-D) vigorously inhibited both early and late lymphocyte activation events including activation-induced TCR/CD8 down-modulation, cytokine production, and DNA synthesis. In agreement with this, full length recombinant tenascin-C containing the alternatively spliced region suppressed T cell activation, whereas tenascin-C lacking this region did not. Using a series of smaller fragments and deletion mutants issued from this region, the authors have identified the TnFnIII A1A2 domain as the minimal region suppressing T cell activation. Single TnFnIII A1 or A2 domains were no longer inhibitory, while maximal inhibition required the presence of the TnFnIII A3 domain.
PMID: 19405959
The stromal microenvironment has a profound influence on tumour cell behaviour. In tumours, the extracellular matrix (ECM) composition differs from normal tissue and allows novel interactions to influence tumour cell function. The ECM protein tenascin-C (TNC) is frequently up-regulated in breast cancer and the same authors have previously identified two novel isoforms - one containing exon 16 (TNC-16) (the exon is also called exon D (HsaEX0066152) and one containing exons 14 (exon B) plus 16 (TNC-14/16). The present study has analysed the functional significance of this altered TNC isoform profile in breast cancer. TNC-16 and TNC-14/16 splice variants were generated using PCR-ligation and over-expressed in breast cancer cells (MCF-7, T47D, MDA-MD-231, MDA-MB-468, GI101) and human fibroblasts. The effects of these variants on tumour cell invasion and proliferation were measured and compared with the effects of the large (TNC-L) (containing alternatively spliced exons A1 (HsaEX0066148), A2, A3 (HsaEX0066149), A4, B, C (HsaEX0066151), D) and fully spliced small (TNC-S) isoforms (skips all cassette exons). TNC-16 and TNC-14/16 significantly enhanced tumour cell proliferation (P < 0.05) and invasion, both directly (P < 0.01) and as a response to transfected fibroblast expression (P < 0.05) with this effect being dependent on tumour cell interaction with TNC, because TNC-blocking antibodies abrogated these responses. An analysis of 19 matrix metalloproteinases (MMPs) and tissue inhibitor of matrix metalloproteinases 1 to 4 (TIMP 1 to 4) revealed that TNC up-regulated expression of MMP-13 and TIMP-3 two to four fold relative to vector, and invasion was reduced in the presence of MMP inhibitor GM6001. However, this effect was not isoform-specific but was elicited equally by all TNC isoforms.
PMID: 32599145
The pro-inflammatory activity of an endogenous innate immune trigger is controlled by inclusion or exclusion of a novel immunomodulatory site located within domains AD2AD1 (both exons), identifying this as a mechanism that prevents unnecessary inflammation in healthy tissues but enables rapid immune cell mobilization and activation upon tissue damage, and defining how this goes awry in autoimmune disease.


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Pre-implantation embryo development
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types