Special

MmuEX0048239 @ mm10

Exon Skipping

Description
tenascin C [Source:MGI Symbol;Acc:MGI:101922]
Coordinates
chr4:63976446-64006509:-
Coord C1 exon
chr4:64006246-64006509
Coord A exon
chr4:63995541-63995813
Coord C2 exon
chr4:63976446-63976568
Length
273 bp
Sequences
Splice sites
3' ss Seq
AAATTCTCTGCCTTCTTCAGAGG
3' ss Score
7.06
5' ss Seq
CAGGTATCA
5' ss Score
7.33
Exon sequences
Seq C1 exon
AAATTGATGCACCCAAGGACTTACGGGTGTCTGAAACCACACAAGACAGTCTGACGTTTTTCTGGACGACACCCCTGGCCAAGTTTGATCGTTACCGCCTCAACTACAGCCTCCCCACAGGCCAGTCGATGGAAGTCCAGCTGCCAAAGGATGCCACCTCCCATGTCCTGACAGACCTGGAGCCAGGGCAAGAATACACTGTTCTCCTCATTGCTGAGAAGGGCAGACACAAGAGCAAGCCTGCACGTGTGAAGGCATCCACGG
Seq A exon
AGGATCTCCCTCAGCTGGGAGGCTTGTCTGTGACTGAGGTCAGCTGGGACGGCCTCACACTCAACTGGACCACAGATGACCTGGCCTATAAGCACTTTGTCGTTCAGGTGCAGGAGGCCAACAATGTGGAGGCCGCTCAGAACCTCACGGTACCCGGCAGCCTCAGAGCTGTGGACATCCCAGGCCTCAAGGCCGACACCCCTTATAGAGTCTCCATCTACGGGGTCATCCAGGGCTATAGAACACCGATGCTCTCTACTGACGTCTCCACAG
Seq C2 exon
CCATGGGTTCTCCGAAGGAAATCATGTTCTCAGACATCACTGAAAATGCAGCCACAGTCAGCTGGAGGGCACCTACTGCTCAGGTGGAGAGTTTCCGGATCACTTATGTACCTATGACAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028364_MULTIEX1-3/6=C1-C2
Average complexity
C3
Mappability confidence:
100%=100=100%
Protein Impact

Alternative protein isoforms (Ref)

No structure available
Features
Disorder rate (Iupred):
  C1=0.404 A=0.040 C2=0.048
Domain overlap (PFAM):

C1:
PF0004116=fn3=WD(100=89.9)
A:
PF0004116=fn3=WD(100=88.0)
C2:
PF0004116=fn3=PU(48.8=92.9)


Main Inclusion Isoform:


Main Skipping Isoform:
NA


Other Inclusion Isoforms:


Other Skipping Isoforms:
NA
Other assemblies
Conservation
Chicken
(galGal4)
ALTERNATIVE
(TNC)
Chicken
(galGal3)
ALTERNATIVE
(TNC)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGGTGTCTGAAACCACACAA
R:
AGCTGACTGTGGCTGCATTTT
Band lengths:
304-577
Functional annotations
There are 1 annotated functions for this event
PMID: 11714809
This event
(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]


SPECIAL DATASETS

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