GgaEX0017152 @ galGal3
Exon Skipping
Gene
ENSGALG00000011389 | TRAF3
Description
NA
Coordinates
chr5:52368808-52373642:+
Coord C1 exon
chr5:52368808-52368888
Coord A exon
chr5:52371657-52371731
Coord C2 exon
chr5:52373550-52373642
Length
75 bp
Sequences
Splice sites
3' ss Seq
ACATTTTTTTCCTATTGCAGTTG
3' ss Score
10
5' ss Seq
CAGGTCAGT
5' ss Score
8.94
Exon sequences
Seq C1 exon
AAACATGAAGATACAGACTGCCCGTGTGTCATGGTTTCATGTCCTCATAAATGCAGTGTTAAAACACTCATGAGGAGTGAG
Seq A exon
TTGAATGCACATTTGTCAGAATGTATTAATGCCCCAAGTACCTGTAGTTTTAAGCGTTATGGCTGCACTTTTCAG
Seq C2 exon
GGAACAAACCAACAAATTAAAGCACATGAAGCCAGCTCAGCAGTGCAGCATGTTAACTTATTGAAAGAGTGGAGCAATGCTCTAGAAAATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011389-'12-16,'12-15,13-16
Average complexity
C2
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
PF0217613=zf-TRAF=PD(1.8=3.7),PF0314511=Sina=PU(17.5=40.7),PF041569=IncA=PU(8.8=55.6)
A:
PF0314511=Sina=FE(38.1=100),PF041569=IncA=FE(14.1=100),PF101744=Cast=PU(0.7=4.0)
C2:
PF0314511=Sina=PD(39.7=80.6),PF041569=IncA=FE(17.6=100),PF0205011=FliJ=PU(5.0=16.1),PF101744=Cast=FE(21.9=100)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATGAAGATACAGACTGCCCGT
R:
AGCATTGCTCCACTCTTTCAA
Band lengths:
159-234
Functional annotations
There are 1 annotated functions for this event
PMID: 24671418
The noncanonical nuclear factor _B (ncNF_B) pathway regulates the expression of chemokines required for secondary lymphoid organ formation and thus plays a pivotal role in adaptive immunity. Whereas ncNF_B signaling has been well described in stromal cells and B cells, its role and regulation in T cells remain largely unexplored. ncNF_B activity critically depends on the upstream NF_B-inducing kinase (NIK). NIK expression is negatively regulated by the full-length isoform of TNF receptor-associated factor 3 (Traf3) as formation of a NIK-Traf3-Traf2 complex targets NIK for degradation. The authors show that T cell-specific and activation-dependent alternative splicing generates a Traf3 isoform lacking exon 8 (Traf3DE8) (HsaEX0066805) that, in contrast to the full-length protein, activates ncNF_B signaling. Traf3DE8 disrupts the NIK-Traf3-Traf2 complex and allows accumulation of NIK to initiate ncNF_B signaling in activated T cells.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]