HsaINT0171673 @ hg19
Intron Retention
Gene
ENSG00000056558 | TRAF1
Description
TNF receptor-associated factor 1 [Source:HGNC Symbol;Acc:12031]
Coordinates
chr9:123673614-123676016:-
Coord C1 exon
chr9:123675606-123676016
Coord A exon
chr9:123673792-123675605
Coord C2 exon
chr9:123673614-123673791
Length
1814 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
CTGAACAGTCTTCCCTACAGGTG
3' ss Score
7.61
Exon sequences
Seq C1 exon
GGAAGCCCACAGTCTGTGCAAGAGCATGAGGTCACCTCCCAGACCTCCCACCTAAACCTGCTGTTGGGGTTCATGAAACAGTGGAAGGCCCGGCTGGGCTGTGGCCTGGAGTCTGGGCCCATGGCCCTGGAGCAGAACCTGTCAGACCTGCAGCTGCAGGCAGCCGTGGAAGTGGCGGGGGACCTGGAGGTCGATTGCTACCGGGCACCCTGCTCCGAGAGCCAGGAGGAGCTGGCCCTGCAGCACTTCATGAAGGAGAAGCTTCTGGCTGAGCTGGAGGGGAAGCTGCGTGTGTTTGAGAACATTGTTGCTGTCCTCAACAAGGAGGTGGAGGCCTCCCACCTGGCCCTGGCCACCTCTATCCACCAGAGCCAGCTGGACCGTGAGCGCATCCTGAGCTTGGAGCAGAGG
Seq A exon
GTGAGTGTGGGAGGCAGGTTTGCCTTCAAGCCCGGCTGAGCCCCATCCTGTCTCCAGAGCGGCAGACAGGCTTCCTCCTAATCATTCATCCTGCTTACAGCAGTCACTCCATCAAAACGTATCTCCCCTTTATCCCACACCCTTCCAGGAAGAGCGCTGAGTTAGAAGCTGTAGTCAAGGTCATAACCTCCCATCCAGTGCTTCGGTTCCTTTGCTTGAACTTTTGTGATAAGACACCACCTCCCTGAGCAGCTCATTCCAGTGCAGGACATATTCCACTCTTAGCAAGTTCTTCCTTGTACTAAGCTAAAATCAGCCTGTCTCTTCCCTGCATTGTTCCTGGCCCTGCCCCTCAGAGCCCACAAGACAAATCCACCTTCTAGTCCCCATGACAGCCCTTCAGGGATGGAGGGTCAGATTCTGTCCTACCTGAGTGCTTCCCTTTTCAGGCTAAAAGCCCCAGCGCCTTCACGTCTTCCTCAGAGCATGCTGCTTCACATTGCCATCCTACGCTCTGGCTCAGTCTCCAAAGAATTCTGTACGCTTGGAGTATGGTACCAGGCTGACTCCAGATAATCCACTTGGCCACAGTTCTTGGTCCAACAGGGCTGTCTTCTCCCTTATTCTAGAGCTTATACTTTTCTTTTCTTTCTTTCTTTTTTTTTTTCCTTTGAGACAGAGTATTGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGCAACCTCCACTCCCAGGTTCAAGCGATTCTCCTGCCTCAGCTTCCTGAGTAGCTGGGATTACAGGCGTGTGCCACCACACCCAGCTAAATTTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGTCAGGCTGGTCTCGATCTCCTGACCTCGTGATCCACCTGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCATAAGCCACCGCGCCTGGCCTATACTTTTCTTAATGTAGCCAATGACCATTCTAATGTTGCTTCTTTTGCAGTAACATTACATCATTGTCTCATATTGAGTTAGGCCTGGATTTTAGTTCCTGCTTCACCATTACCATTATCTGCCTCACCATTCGCAATTACCATTACAGCAGGTGATCAGAGCCACCTGCCGTGTGGGTCTGAGCAAGTCACTTTCCCTCTCAGGACCTTCCCCATCAGTAAAATTAACGATTAAATTTTCTTTAAGGATGCTCACTTCCATTCATGGCTTCCCTACCTGAGCACACCCAAGAATAAATTTATATTCTTTCCATTTTATTGGGGAAAGCTATTAGAAGGGCCAGGCGCTGAGTTGGAGTGGCTGAGGCTTTAGCCTTTATTTATGTAACTCTTGCTCCAGTTAAAAGGCAGCCTCCCTGAAAGCCACAATTATACCTTCATTTCACCCACAAACTTCCCAGCTCTACTTTTACATACCAGGTACTATGCAAGGCATGGACACAAAGACACAATGAGCATGGGCCCAGCTTTCGGTGGAGGAGACCATCTGGTAGGGAAGCCAGAAAAATATGTCTCATGAAATCATTGTAAGGGCTCTGTAAGAACATATTGAAAGAGAGCAGCTAAGCTAGGACAGTGGTTGAAGGCTTCCCAGATGAGGGGCCATATGAGCTGGATTCCTGGTGGATAAGGAAAAGGAAGGCCAGGCAGGGGGCAGCACATTCAGATGCAGACGCACACCTGAGTGAGGCGTGGTCAGCAAAACACATCTGGGGCAGATCAATCTCCACATCCCGCCATTCCCATCCCATCCCCAAGCCGGGTTCTGGTGTTCCTGGCTGAACAGTCTTCCCTACAG
Seq C2 exon
GTGGTGGAGCTTCAGCAGACCCTGGCCCAGAAAGACCAGGCCCTGGGCAAGCTGGAGCAGAGCTTGCGCCTCATGGAGGAGGCCTCCTTCGATGGCACTTTCCTGTGGAAGATCACCAATGTCACCAGGCGGTGCCATGAGTCGGCCTGTGGCAGGACCGTCAGCCTCTTCTCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000056558-TRAF1:NM_001190945:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.044 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0091721=MATH=PU(15.5=36.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGCAGCACTTCATGAAGGA
R:
GAGAAGAGGCTGACGGTCCT
Band lengths:
348-2162
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)