Special

MmuEX0048240 @ mm9

Exon Skipping

Description
tenascin C [Source:MGI Symbol;Acc:MGI:101922]
Coordinates
chr4:63637480-63667543:-
Coord C1 exon
chr4:63667280-63667543
Coord A exon
chr4:63654061-63654333
Coord C2 exon
chr4:63637480-63637602
Length
273 bp
Sequences
Splice sites
3' ss Seq
CCTTCCCTCTCATCTTTCAGCCA
3' ss Score
10.91
5' ss Seq
CAGGTACAT
5' ss Score
7.79
Exon sequences
Seq C1 exon
AAATTGATGCACCCAAGGACTTACGGGTGTCTGAAACCACACAAGACAGTCTGACGTTTTTCTGGACGACACCCCTGGCCAAGTTTGATCGTTACCGCCTCAACTACAGCCTCCCCACAGGCCAGTCGATGGAAGTCCAGCTGCCAAAGGATGCCACCTCCCATGTCCTGACAGACCTGGAGCCAGGGCAAGAATACACTGTTCTCCTCATTGCTGAGAAGGGCAGACACAAGAGCAAGCCTGCACGTGTGAAGGCATCCACGG
Seq A exon
CCAGAGAACCTGAAATTGGAAACTTAAATGTTTCTGATGTAACTCCTAAGAGCTTCAATCTCTCCTGGACAGCTACCGACGGGATCTTCGACATGTTTACTATTGAAATTATTGATTCTAATAGGTTGCTGCAAACAGCAGAACATAATATATCTGGTGCTGAACGGACTGCCCACATCTCAGGGCTTCCACCTAGTACTGATTTCATTGTCTACCTCTCTGGAATTGCTCCCAGCATCCGTACCAAAACCATCAGTACCACGGCTACCACAG
Seq C2 exon
CCATGGGTTCTCCGAAGGAAATCATGTTCTCAGACATCACTGAAAATGCAGCCACAGTCAGCTGGAGGGCACCTACTGCTCAGGTGGAGAGTTTCCGGATCACTTATGTACCTATGACAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028364_MULTIEX1-4/6=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=0.168 C2=0.031
Domain overlap (PFAM):

C1:
PF0004116=fn3=WD(100=89.9)
A:
PF0004116=fn3=WD(100=79.3)
C2:
PF0004116=fn3=PU(48.8=92.9)


Main Inclusion Isoform:


Main Skipping Isoform:


Other Inclusion Isoforms:


Other Skipping Isoforms:
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
ALTERNATIVE
(TNC)
Chicken
(galGal3)
ALTERNATIVE
(TNC)
Zebrafish
(danRer10)
ALTERNATIVE
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
(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
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types