Special

RnoEX0092215 @ rn6

Exon Skipping

Description
tenascin C [Source:RGD Symbol;Acc:621057]
Coordinates
chr5:79824318-79829716:-
Coord C1 exon
chr5:79829444-79829716
Coord A exon
chr5:79828660-79828932
Coord C2 exon
chr5:79824318-79824590
Length
273 bp
Sequences
Splice sites
3' ss Seq
CATTCTTTGTCCTTCTCTAGGGA
3' ss Score
11.07
5' ss Seq
CAGGTATTT
5' ss Score
7.51
Exon sequences
Seq C1 exon
AAGAAGTACCTTCTCTGGAAAATCTCACCGTGACCGAGGCCGGCTGGGATGGCCTCAGACTCAACTGGACTGCAGATGACCTGGCCTATGAGTACTTTGTTATTCAGGTACAGGAAGCCAACAAGGTGGAGACTGCTCACAACTTCACAGTACTTGGTAACCTCCGGACTGCAGACATCCCGGGCCTCAAGGCTGCCACTCCTTATAGAGTCTCCATTTATGGGGTAGCTCGGGGCTATAAAACACCCGTGCTCTCTGCTGAGACCTTCACAG
Seq A exon
GGAAAACTCCCAGTTTGGGAGAGGTGACTGTGGCTGAGGTGGGCTGGGATGCCCTCAAGCTCAACTGGACTGCTCCAGAAGGAGCCTATACGAACTTTTTCATTCAGGTGCTAGAGGCTGACATGACCCAGACTGTCCAGAACCTCACAGTCCCAGGGGGACTGAGGTCAGTGGACCTACCTGGGCTCAAAGCAGCCACCCGCTATTACATCACCGTTCGAGGGGTCACCCAGGACTTCAGCACAGCCCCTCTCTCTGTTGAGGTCTTGACAG
Seq C2 exon
AGGAGATCCCTCAACTGGGAGGCTTGTCCGTGACTGAGGTCAGCTGGGACAGCCTTACACTCAACTGGACCACAGATGATCTGGCCTATAAACACTTTATCATTCAGGTGCAGGAGGCCAACAATGTAGAGGCTGCTCAGAACCTCACAGTATCTGGTAGCCTCAGAGTTGTGGACATCCCAGGCCTCAAGGCTGATACCCCTTATAGAGTCTCCATCTATGGGGTGATCCAGGGCTATAGAACACCAATGCTCTCTGCTGATGTCTCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058645-'16-31,'16-27,17-31
Average complexity
C1
Mappability confidence:
100%=100=100%
Protein Impact

Alternative protein isoforms (Ref)

No structure available
Features
Disorder rate (Iupred):
  C1=0.043 A=0.000 C2=0.011
Domain overlap (PFAM):

C1:
PF0004116=fn3=WD(100=87.0)
A:
PF0004116=fn3=WD(100=89.1)
C2:
PF0004116=fn3=WD(100=88.0)


Main Inclusion Isoform:


Main Skipping Isoform:
NA


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Conservation
Chicken
(galGal4)
ALTERNATIVE
(TNC)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
ALTERNATIVE
(tnc)
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAACAAGGTGGAGACTGCTC
R:
AGCAGCCTCTACATTGTTGGC
Band lengths:
293-566
Functional annotations
There are 1 annotated functions for this event
PMID: 11714809
[Likely mapping: domain TnFnIII A2; PMID:25482829]. 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]