GgaEX0010152 @ galGal3
Exon Skipping
Gene
ENSGALG00000007113 | TNC
Description
NA
Coordinates
chr17:3044584-3069122:-
Coord C1 exon
chr17:3068859-3069122
Coord A exon
chr17:3056830-3057102
Coord C2 exon
chr17:3044584-3044706
Length
273 bp
Sequences
Splice sites
3' ss Seq
AATGTTGTTTCCCTCCTCAGGAG
3' ss Score
9.85
5' ss Seq
CAGGTATAT
5' ss Score
7.88
Exon sequences
Seq C1 exon
ATCTTGATAACCCCAAGGACTTGGAAGTCAGTGACCCCACTGAAACCACCCTGTCCCTTCGCTGGAGAAGACCAGTGGCCAAATTTGATCGTTACCGCCTCACTTACGTTAGCCCCTCTGGAAAGAAGAACGAAGTGGAGATCCCTGTGGACAGTACCTCTTTTATCCTGAGAGGATTAGACGCAGGGACGGAGTACACCATCAGTCTAGTGGCAGAGAAGGGCAGACACAAAAGCAAACCCACAACCATCAAGGGTTCGACTG
Seq A exon
GAGCACACCCTGAAGTTGGTGAGCTAACCGTTTCCGACATTACTCCTGAAAGCTTCAACCTTTCTTGGACGACCACCAGCGGGGACTTTGACGCCTTTACTATTGAAATTATTGATTCTAACAGGTTGCTGGAGCCCATGGAGTTCAACATCTCAGGCAATTCAAGAACAGCTCATATCTCAGGGCTTTCCCCCAGCACTGATTTTATTGTCTACCTCTATGGGATCTCTCATGGTTTCCGCACACAGGCAATAAGTGCTGCGGCTACAACAG
Seq C2 exon
TTGTGGGATCTCCCAAGGGAATCTCTTTCTCGGACATCACAGAAAACTCTGCTACAGTCAGCTGGACGCCCCCCCGCAGCCGTGTGGATAGCTACAGGGTCTCCTATGTCCCCATCACAGGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000007113_MULTIEX1-2/3=C1-C2
Average complexity
C3
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.407 A=0.083 C2=0.036
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=89.9)
A:
PF0004116=fn3=WD(100=87.0)
C2:
PF0004116=fn3=PU(48.8=92.9)

Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGAAACCACCCTGTCCCTT
R:
TCCAGCTGACTGTAGCAGAGT
Band lengths:
292-565
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]