Special

DreEX0008936 @ danRer10

Exon Skipping

Gene
ENSDARG00000078362 | TNC (2 of 2)
Description
tenascin C [Source:HGNC Symbol;Acc:HGNC:5318]
Coordinates
chr5:5244294-5286422:-
Coord C1 exon
chr5:5286159-5286422
Coord A exon
chr5:5256131-5256403
Coord C2 exon
chr5:5244294-5244416
Length
273 bp
Sequences
Splice sites
3' ss Seq
ATAACAGTTTCTCCCTTTAGATA
3' ss Score
8.58
5' ss Seq
CAGGTAACT
5' ss Score
8.63
Exon sequences
Seq C1 exon
ATCTGGATCCTCCTCGAGACTTGGAAGTTCAGAGCTCCACTGAAACCAGCGTGGATCTGGTCTGGAAGAGGCCGAGGGCCAAGATCTCCACCTACAGGCTGGCGTATGTGTCTGTGGAAGGGCGGCGGGAGGAAATTGAGCTGCCAGCCAGTGCGAGCACCTCCACACTGAGCGGCCTGATGCCTGGCATGAGCTACACAGTGACCCTGGTGGCTGAACGTGGACACAGAAGAAGCGCTCCTGCTACCGTCACCGCATCCACAG
Seq A exon
ATAGAGCTCCAGCGATGGGCAATCTGTATGTGTCTAATGTAACATCACAGAGCTTCTTCGTTTCATGGAATGACACGAAAGGAGAAATTGAGCGGTTTGTCCTGGAGATTATAGACTCCAGCTGGCAGCAGGAGCCGATTGAGTATAATCTGTCTCAGAGCGTTCAGTCGTATGAGATCACTGGGCTAAGGCCGACTACTGACTATATAGCTTACGTCACTGGAGTGATGAAGGGAAGGAGAACAGACTCGGTCAGTGCTGTCGCCTCCACAG
Seq C2 exon
GCCTCGGAGCTCTACGAGATCTTCATTTCTCTGATATCACGGACACGTCAGCTGTGGTTTACTGGACTTTACCTCGTGCTCAACCTGACTCTTACAGAATCACCCTCATCCCAATACAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000078362_MULTIEX1-2/6=C1-C2
Average complexity
C3
Mappability confidence:
100%=100=100%
Protein Impact

Alternative protein isoforms (No Ref)

No structure available
Features
Disorder rate (Iupred):
  C1=0.427 A=NA C2=0.000
Domain overlap (PFAM):

C1:
PF0004116=fn3=WD(100=88.8)
A:
PF0004116=fn3=WD(100=85.9)
C2:
PF0004116=fn3=PU(48.8=92.9)


Main Inclusion Isoform:
ENSDART00000112856fB786


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
ALTERNATIVE
(TNC)
Chicken
(galGal3)
ALTERNATIVE
(TNC)
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGATCTGGTCTGGAAGAGGC
R:
AGTCAGGTTGAGCACGAGGTA
Band lengths:
303-576
Functional annotations
There are 1 annotated functions for this event
PMID: 11714809
(for the Human Region). 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]