BtaEX0037213 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000000575 | TNC
Description
tenascin C [Source:HGNC Symbol;Acc:HGNC:5318]
Coordinates
chr8:105989551-106013095:-
Coord C1 exon
chr8:106012823-106013095
Coord A exon
chr8:106011988-106012260
Coord C2 exon
chr8:105989551-105989673
Length
273 bp
Sequences
Splice sites
3' ss Seq
AGTTCTTTGTCCTTCTCCAGGAG
3' ss Score
9.43
5' ss Seq
CAGGTACTC
5' ss Score
7.04
Exon sequences
Seq C1 exon
ACCACACCCCTGAACTGGGAAACCTCACCGTGACCAAGGCTGGCTGGGATGGCCTCAGACTCAACTGGACCGCCGCTGACCAGGCCTACGAGCATTTTGTCATTCAGGTGCAGGAGGCCAACGGGGTGGAGGCGGCTCAGAACCTCACGGTGCCCGGGAACCTGCGGGCTGTGGACGTCCCGGGCCTGAAGGCCGCCACTCCTTACAGAGTCACCATCCACGGGGTGATCCGGGGCTATAGGACCCCAGTGCTGTCTGCTGAGGCCTCCACAG
Seq A exon
GAGACACTCCCCACTTGGGAGAGGTCACGGTGTCCGAGGTGGGCTGGGAGGCCCTCAAACTCAACTGGACGGCTCCAGAAGGGGTCTACGAGCAGTTTCTCATTCAGGTGCAGGAGCCTGGCAAGGAGGAGGCAGCCCAGAACCTCACTGTCCCGGGAGGGCTGAGGTCCGTGGACCTGCCTGGGCTCAAGGCAGCCACTCACTATAGCATCACCATCCGTGGGGTCACTCGGGACTTCAGCACAGCCCCTCACTCTGTTGAAGCCTTAACAG
Seq C2 exon
CCATGGGCTCCCCGAAGGAAATCATTTTCTCAGACATCACTGAAAACGCAGCCAGTGTCAGCTGGATGGCACCCACTACCCAGGTGGAGAGCTTCCGGGTCACCTATGTGCCCATTGCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000575_MULTIEX1-3/10=2-C2
Average complexity
C3
Mappability confidence:
84%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.228 A=0.255 C2=0.000
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=87.0)
A:
PF0004116=fn3=WD(100=88.0)
C2:
PF0004116=fn3=PU(48.8=92.9)

Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGGCCTACGAGCATTTTGT
R:
ATAGGTGACCCGGAAGCTCTC
Band lengths:
301-574
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]
SPECIAL DATASETS
- Pre-implantation embryo development