Special

RnoEX0092217 @ rn6

Exon Skipping

Description
tenascin C [Source:RGD Symbol;Acc:621057]
Coordinates
chr5:79811667-79824590:-
Coord C1 exon
chr5:79824318-79824590
Coord A exon
chr5:79821804-79822076
Coord C2 exon
chr5:79811667-79811939
Length
273 bp
Sequences
Splice sites
3' ss Seq
CCTTTCCTCTCATCTTTCAGCCA
3' ss Score
10.69
5' ss Seq
CAGGTACAT
5' ss Score
7.79
Exon sequences
Seq C1 exon
AGGAGATCCCTCAACTGGGAGGCTTGTCCGTGACTGAGGTCAGCTGGGACAGCCTTACACTCAACTGGACCACAGATGATCTGGCCTATAAACACTTTATCATTCAGGTGCAGGAGGCCAACAATGTAGAGGCTGCTCAGAACCTCACAGTATCTGGTAGCCTCAGAGTTGTGGACATCCCAGGCCTCAAGGCTGATACCCCTTATAGAGTCTCCATCTATGGGGTGATCCAGGGCTATAGAACACCAATGCTCTCTGCTGATGTCTCCACAG
Seq A exon
CCAAAGAACCTGAAATTGGAAACTTAAATATTTCTGATGTAACTCCTGAGAGCTTCAATCTCTCCTGGACAGCTACCGACGGGATCTTCGACATGTTTACTATCGAAATTATTGATTCTAATAGGTTGCTGCAGACAGCAGAACATAATATATCTGGTGCTGAACGAACTGCCCACATCTCGGGCCTTCCACCTAGTACTGATTTCATTGTCTACCTCTCTGGAATTGCTCCCAGCATCCGTACCAAAACCATCAGTACCACAGCCACCACAG
Seq C2 exon
AAGCTGAACCGGAAGTTGACAACCTTCTAGTTTCAGATGCTACTCCAGACGGTTTCCGTCTGTCCTGGACTGCTGATGAAGGGATATTCGACAGTTTTGTTATCAGGATCAGAGATACCAAAAAGCAATCTGAACCACAAGAAATAACCCTCCCTTCCCCCGACCGTACCAGGGACATAACAGGTCTCAGAGAGGCCACTGAGTACGAAATTGAACTCTATGGAATAAGCCGTGGAAGGCGATCCCAGCCAGTCAGTGCCATAGCAACAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058645-'19-37,'19-32,21-37
Average complexity
C2
Mappability confidence:
100%=100=100%
Protein Impact

Alternative protein isoforms (Ref)

No structure available
Features
Disorder rate (Iupred):
  C1=0.011 A=0.185 C2=0.373
Domain overlap (PFAM):

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


Main Inclusion Isoform:


Main Skipping Isoform:
NA


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Conservation
Mouse
(mm9)
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:
ATCTATGGGGTGATCCAGGGC
R:
GCCTTCCACGGCTTATTCCAT
Band lengths:
298-571
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]