Special

HsaALTD1017566-2/3 @ hg38

Alternative 5'ss

Gene
Description
TNF receptor associated factor 2 [Source:HGNC Symbol;Acc:HGNC:12032]
Coordinates
chr9:136898713-136899672:+
Coord C1 exon
chr9:136898713-136898895
Coord A exon
chr9:136898896-136898928
Coord C2 exon
chr9:136899594-136899672
Length
33 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCAT
5' ss Score
4.89
3' ss Seq
TTGCCTTTTTTCCCCACTAGCTC
3' ss Score
8.31
Exon sequences
Seq C1 exon
GGCTTTGTTCGCGGGGGTCACAGCTCTCATGGCTGCAGCTAGCGTGACCCCCCCTGGCTCCCTGGAGTTGCTACAGCCCGGCTTCTCCAAGACCCTCCTGGGGACCAAGCTGGAAGCCAAGTACCTGTGCTCCGCCTGCAGAAACGTCCTCCGCAGGCCCTTCCAGGCGCAGTGTGGCCACCG
Seq A exon
GTACTGCTCCTTCTGCCTGGCCAGCATCCTCAG
Seq C2 exon
CTCTGGGCCTCAGAACTGTGCTGCCTGTGTTCACGAGGGCATATATGAAGAAGGCATTTCTATTTTAGAAAGCAGTTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000127191-24-44,25-44,26-44-2/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact

Protein isoform when splice site is used (Ref)

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

C1:
PF0009720=zf-C3HC4=PU(74.4=46.0)
A:
NA
C2:
PF0009720=zf-C3HC4=PD(23.1=33.3)


Main Inclusion Isoform:


Main Skipping Isoform:
NA


Other Inclusion Isoforms:


Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCAAGCTGGAAGCCAAGTAC
R:
GAACACAGGCAGCACAGTTCT
Band lengths:
112-145
Functional annotations
There are 2 annotated functions for this event
PMID: 9461607
This event
The authors describe here the identification and characterization of tumor necrosis factor receptor (TNFR)-associated factor 2A (TRAF2A), a splice variant of the TRAF2 molecule utilized for signal transduction by members of the TNFR family. TRAF2A and TRAF2 cDNAs are identical in sequence with the exception of an extra 21 base pairs of sequence encoding a 7-amino acid insert (via use of HsaALTD1017566-2/2) within the TRAF2A RING finger domain (TRAF2 uses HsaALTD1017566-1/2 instead). TRAF2A protein is capable of binding to the cytoplasmic domain of TNFR2 (p75) and is detectable in T-lymphoma cells stably transfected with the TRAF2A cDNA. Unlike TRAF2, TRAF2A has a short half-life ( approximately 100 min) in these cells and is expressed at only low levels in transiently transfected COS-7 cells. However, TRAF2A levels in transiently transfected COS-7 cells approach those of TRAF2 upon coexpression with TRAF1 and/or TRAF2, indicating that TRAF2A stability is regulated by the binding of other TRAF family proteins. Also in contrast to TRAF2, TRAF2A is unable to stimulate NF-kappaB activity when overexpressed in 293 cells and acts as a dominant inhibitor of TNFR2-dependent NF-kappaB activation.
PMID: 9733779
This event
TRAF 2A, a TRAF 2 splice variant with an altered ring finger (contains 7 additional amino acids (due to use of alternative splice site donor, HsaALTD1017566-2/2), is a specific activator of JNK, whereas TRAF2 (uses HsaALTD1017566-1/2) activates both NFkappa B and JNK pathways.


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Autistic and control brains