Special

HsaEX6062710 @ hg19

Exon Skipping

Gene
Description
tenascin C [Source:HGNC Symbol;Acc:5318]
Coordinates
chr9:117825196-117827198:-
Coord C1 exon
chr9:117826926-117827198
Coord A exon
chr9:117826075-117826347
Coord C2 exon
chr9:117825196-117825468
Length
273 bp
Sequences
Splice sites
3' ss Seq
AGTTCTTTGTCCTTCTCCAGGGG
3' ss Score
9.34
5' ss Seq
CAGGTATTC
5' ss Score
6.49
Exon sequences
Seq C1 exon
AACAAGCCCCTGAGCTGGAAAACCTCACCGTGACTGAGGTTGGCTGGGATGGCCTCAGACTCAACTGGACCGCAGCTGACCAGGCCTATGAGCACTTTATCATTCAGGTGCAGGAGGCCAACAAGGTGGAGGCAGCTCGGAACCTCACCGTGCCTGGCAGCCTTCGGGCTGTGGACATACCGGGCCTCAAGGCTGCTACGCCTTATACAGTCTCCATCTATGGGGTGATCCAGGGCTATAGAACACCAGTGCTCTCTGCTGAGGCCTCCACAG
Seq A exon
GGGAAACTCCCAATTTGGGAGAGGTCGTGGTGGCCGAGGTGGGCTGGGATGCCCTCAAACTCAACTGGACTGCTCCAGAAGGGGCCTATGAGTACTTTTTCATTCAGGTGCAGGAGGCTGACACAGTAGAGGCAGCCCAGAACCTCACCGTCCCAGGAGGACTGAGGTCCACAGACCTGCCTGGGCTCAAAGCAGCCACTCATTATACCATCACCATCCGCGGGGTCACTCAGGACTTCAGCACAACCCCTCTCTCTGTTGAAGTCTTGACAG
Seq C2 exon
AGGAGGTTCCAGATATGGGAAACCTCACAGTGACCGAGGTTAGCTGGGATGCTCTCAGACTGAACTGGACCACGCCAGATGGAACCTATGACCAGTTTACTATTCAGGTCCAGGAGGCTGACCAGGTGGAAGAGGCTCACAATCTCACGGTTCCTGGCAGCCTGCGTTCCATGGAAATCCCAGGCCTCAGGGCTGGCACTCCTTACACAGTCACCCTGCACGGCGAGGTCAGGGGCCACAGCACTCGACCCCTTGCTGTAGAGGTCGTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000041982-'14-16,'14-15,15-16=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact

Alternative protein isoforms (Ref)

No structure available
Features
Disorder rate (Iupred):
  C1=0.109 A=0.098 C2=0.207
Domain overlap (PFAM):

C1:
PF0004116=fn3=WD(100=88.0)
A:
PF0004116=fn3=WD(100=90.2)
C2:
PF0004116=fn3=WD(100=88.0)


Main Inclusion Isoform:


Main Skipping Isoform:


Other Inclusion Isoforms:


Other Skipping Isoforms:
NA
Other assemblies
Conservation
Chicken
(galGal4)
ALTERNATIVE
(TNC)
Chicken
(galGal3)
Zebrafish
(danRer10)
ALTERNATIVE
(tnc)
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGAGCTGGAAAACCTCACC
R:
ACCTCGGTCACTGTGAGGTTT
Band lengths:
305-578
Functional annotations
There are 1 annotated functions for this event
PMID: 11714809
This event
[Likely mapping: domain TnFnIII A2; PMID:25482829]. 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.


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Autistic and control brains