HsaINT0171692 @ hg19
Intron Retention
Gene
ENSG00000131323 | TRAF3
Description
TNF receptor-associated factor 3 [Source:HGNC Symbol;Acc:12033]
Coordinates
chr14:103336522-103338305:+
Coord C1 exon
chr14:103336522-103336783
Coord A exon
chr14:103336784-103338253
Coord C2 exon
chr14:103338254-103338305
Length
1470 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGC
5' ss Score
8.99
3' ss Seq
TCACTTGTGTTTCCCTGCAGCTC
3' ss Score
12.28
Exon sequences
Seq C1 exon
AACTCCTCTTTCCTAAAATGGAGTCGAGTAAAAAGATGGACTCTCCTGGCGCGCTGCAGACTAACCCGCCGCTAAAGCTGCACACTGACCGCAGTGCTGGGACGCCAGTTTTTGTCCCTGAACAAGGAGGTTACAAGGAAAAGTTTGTGAAGACCGTGGAGGACAAGTACAAGTGTGAGAAGTGCCACCTGGTGCTGTGCAGCCCGAAGCAGACCGAGTGTGGGCACCGCTTCTGCGAGAGCTGCATGGCGGCCCTGCTGAG
Seq A exon
GTAGGCGCCCTCGCCCGGCCCGTCGCCCGGCCCCTTCTCAGCCCTCGGCCTCACCCTCTCCTTCATTCGTTTCTCTAAAAATAAACCTCTAGAGGTTTAAAGCCCTAAAGAAGTCCATAAAAGCCTCCGGGCCCAGCTTGTGAATCCTTTAGGGAGGTGCAGTGGGATCCCACGTGTGGGTTTACTGAGGCCTCTGCGTGTCTCTGACCTGCCCCGCCCGTGTCTTCCCACTCCGTCTGTAGAGCCTTGGTGCCCCTCATATGTGTTGCTGTATTTTATTGAGGAACCTCACAGTTCCATGGAGGAGATACACCAGGAAATGACAAGCCAGTCATTTAAGGGCACGTGTGCTGGTGTGCAAGGATGCCGCAGAGAGGAGGGAGGATGGGGTCAGCTTAAAGGACTGGACAGGTCCCTACCCGAGCAGAAACCTAGGCCGCATGCTTACTCAGCAGGCGTGTGTGGAACATGCACCGAGCCCATGGCAGCCCTTTGCTGCTGAGTGCCAGTGCTGGTACCGCTGGTGGATCATGAAGGCAGGCTGGAGCTTTACTGCAGAATAGCATCGGCCAGAAGAGCACCTTGATTCACCCTGCAGGCCTCATGTTTTCTGGCATTGTGCTGGGTGCTGGGGTCGCTGCGGGATGCCCTGGTCTTGGCCACTGCCGTCAGGGCATGTCGGCCTGGGAAGGTTGCCAGCTCCTCCTCCCACAGCACTCAAGCCTGGGCTGCACCCGAGCCCCAGCCTGGGCACAGCAGCCAGCCCCCTGCCCTGTCACCTGCCTTCACCCTCCCCCTTCTCCATGCTTCCCTCTGTGGTCTTACCCACTCATCCCAAATAGTCAGCTAACCTTTGCCCACTTGGGGGCAAAATGACACTTGAGCTTAGTGACAGCACAGGAGACACAGAACACCGTGTCTCCTAACACAAGAGCCTGGACTACACCTCTGGGCCCAGGAGAAGCTTCCCGGTGGAGGAGGGGCTGGAGCCCCCATATATGGTGGGCCACAGGGGAGGGAGGCTGGTCCCCCTGTGCAGGTGCCATTGGCCTTCCAATAGACAGTGAAGCCAAATGGCCTGTGGAGAAGGGCTGGCTGCTTTTACAACGCAGGAGCAAGGCTCTCCAAGTAAACAGGTACTCACACTGAAGAGCTGCTCTGCAGACAGCTAGCTTTGGTTTCTGAAATAAAATTTCACTTTTACATTAAGTGGAAGGGGCTTTCCAAGTGGGACTGAACTAAACTGTTCTACTTGGTAACTTCCTTTTGAAAAATCAGCATTTTAAAAAATGTAGCCCTTTTCTCCCATGGCTTCCTATGTAAAGTGAATCACCAGGGCGTCCTGAAGCTCTGCTGGTTGCTGTGAGCCACTGTGCAGACCTGACCATAAAGTGAATGCTCCCAGAATCTCCTGAGTCCTCTCAAGAAAGGGACTTCCACTCTAATGCAGTCACTTGTGTTTCCCTGCAG
Seq C2 exon
CTCTTCAAGTCCAAAATGTACAGCGTGTCAAGAGAGCATCGTTAAAGATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000131323-TRAF3:NM_145725:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.317 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0443811=zf-HIT=WD(100=24.4),PF0009720=zf-C3HC4=PU(74.4=35.4)
A:
NA
C2:
PF0009720=zf-C3HC4=PD(23.1=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACTCCTCTTTCCTAAAATGGAGTCG
R:
TCTTTAACGATGCTCTCTTGACACG
Band lengths:
310-1780
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)