RnoEX0092216 @ rn6
Exon Skipping
Gene
ENSRNOG00000058645 | Tnc
Description
tenascin C [Source:RGD Symbol;Acc:621057]
Coordinates
chr5:79821804-79828932:-
Coord C1 exon
chr5:79828660-79828932
Coord A exon
chr5:79824318-79824590
Coord C2 exon
chr5:79821804-79822076
Length
273 bp
Sequences
Splice sites
3' ss Seq
AAGTTCTCTGCCTTCTTCAGAGG
3' ss Score
6.23
5' ss Seq
CAGGTATCA
5' ss Score
7.33
Exon sequences
Seq C1 exon
GGAAAACTCCCAGTTTGGGAGAGGTGACTGTGGCTGAGGTGGGCTGGGATGCCCTCAAGCTCAACTGGACTGCTCCAGAAGGAGCCTATACGAACTTTTTCATTCAGGTGCTAGAGGCTGACATGACCCAGACTGTCCAGAACCTCACAGTCCCAGGGGGACTGAGGTCAGTGGACCTACCTGGGCTCAAAGCAGCCACCCGCTATTACATCACCGTTCGAGGGGTCACCCAGGACTTCAGCACAGCCCCTCTCTCTGTTGAGGTCTTGACAG
Seq A exon
AGGAGATCCCTCAACTGGGAGGCTTGTCCGTGACTGAGGTCAGCTGGGACAGCCTTACACTCAACTGGACCACAGATGATCTGGCCTATAAACACTTTATCATTCAGGTGCAGGAGGCCAACAATGTAGAGGCTGCTCAGAACCTCACAGTATCTGGTAGCCTCAGAGTTGTGGACATCCCAGGCCTCAAGGCTGATACCCCTTATAGAGTCTCCATCTATGGGGTGATCCAGGGCTATAGAACACCAATGCTCTCTGCTGATGTCTCCACAG
Seq C2 exon
CCAAAGAACCTGAAATTGGAAACTTAAATATTTCTGATGTAACTCCTGAGAGCTTCAATCTCTCCTGGACAGCTACCGACGGGATCTTCGACATGTTTACTATCGAAATTATTGATTCTAATAGGTTGCTGCAGACAGCAGAACATAATATATCTGGTGCTGAACGAACTGCCCACATCTCGGGCCTTCCACCTAGTACTGATTTCATTGTCTACCTCTCTGGAATTGCTCCCAGCATCCGTACCAAAACCATCAGTACCACAGCCACCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058645-'17-32,'17-31,19-32
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.011 C2=0.185
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=89.1)
A:
PF0004116=fn3=WD(100=88.0)
C2:
PF0004116=fn3=WD(100=79.3)

Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGCCCCTCTCTCTGTTGAG
R:
GTGGTGGCTGTGGTACTGATG
Band lengths:
302-575
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]