HsaINT0171674 @ hg19
Intron Retention
Gene
ENSG00000056558 | TRAF1
Description
TNF receptor-associated factor 1 [Source:HGNC Symbol;Acc:12031]
Coordinates
chr9:123671508-123673791:-
Coord C1 exon
chr9:123673614-123673791
Coord A exon
chr9:123671657-123673613
Coord C2 exon
chr9:123671508-123671656
Length
1957 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACA
5' ss Score
8.88
3' ss Seq
CTCTGGCTTCTGCGTTTCAGCCT
3' ss Score
6.72
Exon sequences
Seq C1 exon
GTGGTGGAGCTTCAGCAGACCCTGGCCCAGAAAGACCAGGCCCTGGGCAAGCTGGAGCAGAGCTTGCGCCTCATGGAGGAGGCCTCCTTCGATGGCACTTTCCTGTGGAAGATCACCAATGTCACCAGGCGGTGCCATGAGTCGGCCTGTGGCAGGACCGTCAGCCTCTTCTCCCCAG
Seq A exon
GTAACACCTCCCAGGGGCACAGAGACCTGCCTGGGGAAACAGGCCCCACAGGACCCAGGAAGCAAGCAGTGAAAACTGCCAGCTCTGTGACAGACACGCTGTGTCCAGTTTAGGCCAGTGCCCATTCAGGCCACTCACCATGGGCAGGAACCATGCTGGGATCTTCAGGTTGGTGGGTGAACCGTGCTCTGCCCTGTGGCTCTCAGCCACACATAGCGGTGGCCCCAGCTGACTGACATTCAGGCCCTTTCTCCTCCCTGAATGTCAGTCCCATTCTGCAAATAGGAATCAAAACTGTTACCCACTTCATGGGTTTGGGATGTGAAGGAAAGTGTGCTGTGGGCCACAGTATGTGCAGATGAGATGGATGTGGATGATGATTTTCACAAGTGAACACCGTGGCCTCAGAGAGCCGACAGTCTGAAATAAGATTAGAGAACTGAGTAAGACACATGCACTTGTGTATGATTGCAGGTAGCATATGTGAATGAGTGTCTTACTCAGTTCTTACTCATTTCTGGGGCCCCTGGGCTTGGCACAATGTCTTGCATAAAGTAATTACTTGGCAAGTGTTTCTCTTAACTAAATGATATCTGTTAATATAACAGTGCATATATTTGTGCAAAAAATGAGGCAGCAGACTGCGTGCAGTGGCTCATGTCTATAATCCTAACACTTTGGGAGGCTGAGGCAAGAGGATCATTTGAGGCCAGGAGTTCAAGACCAGCCTGGGCAACGTAACAAGATCCCATCTCCACAAAATTTTTTTTAAATTAGCCAGGCATGGTGGCCTGCACCTGTGGTCCTAGCTACTTGAGAGGCTGAGATGGGAGGATGGCTTAAGGAGTTTGAGTCTGCAGTGAGCTATGATGGTGCCACTGAACTCCAGTCCAGGCAACAAAGCAAGACCCTCTCAAAAAACAATTTTTTTTTAACGAGGCAGCGGAGTGTGTCACAATCCCAGAGCAGGGCTGGGACTCCTTTCCTGCAGGAGTAGCGCTCATCCCACTGTGTTGGGACAGCTCTCTTCATGGGGTGGCCTCGAGCCCTACTTGTAGACCTTTTTCCCTCAATTCTTTTCAAAGAGGGAAAAAGCAAGCAGTACCTCGTGCTTCCTGTTCTACCAAAACGTAATGGGCAAAGATGAGTCAGACTGCCAGCCTGTCCCTCCTCCACCCTCTTCCTGCCTGCCCCCAATTCATGTCCCCAGTCAGCCTCTCCCAGAAGGGCGCTCTGCCAGAGGACATGCTCTCATGGGATGGCCCCTTTAGCTGCCCAGGGGGTTTCTGTGCATGTTCACCAGGTATGATTCAGCCCTCAAAGGGTTTTGCCACCTGAGAATGGCTGGCAGAACTGCGAGTCACCCCATGTACCCCCAGCCTCCAGGGGACCCCAGCCAGTTGGCATAGGGCAGAACTGTGAGTCACCCCATGTACCCTCAGCCTCCAGGGGACCCCAGCCAGTTGGCATAGGGCAGCAGAAAGAAACTGCTGCTGGGAGGCAGGAAGCCTGGCCCCTCATTCTTGCTGGGTCCCCAACATACCGTGAGATGGTGACCAGCCACTTTGTTTTTCTCAGCTTGGTTTCCAGACTGTAAAACATAGGTTGGTTAGATCAGTGGTTCTCAGAGTGTGGTCCTAGGACCAGTGGCATTGGCAACCCCTGCAAACTTGCTGGAAGTGCCAACTCTCAGTTCTCACCCCAGGGTCACTGAGTGAGAAACTCTGAGGGTGGGGCCCGGCAGTGTATGACTTGGATGGCCAGCTGACAAACACTAAGCTAGATGACCCCCAAGAGCCCATTCCTGTCTGACACCCTACTCGAGAAGAATGCTGGGTTCTAACCCCATCTTTCATGGTTTTGAGCCGCTGACCTTGGGCATGCCTGACCACTGGATCCCAGTCCCACATCTGCAAAGTCCAGCACTTCCCAACTGCCTCTGGCTTCTGCGTTTCAG
Seq C2 exon
CCTTCTACACTGCCAAGTATGGCTACAAGTTGTGCCTGCGGCTGTACCTGAATGGAGATGGCACTGGAAAGAGAACCCATCTGTCGCTCTTCATCGTGATCATGAGAGGGGAGTATGATGCGCTGCTGCCGTGGCCCTTCCGGAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000056558-TRAF1:NM_001190945:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0091721=MATH=PU(15.5=36.7)
A:
NA
C2:
PF0091721=MATH=FE(34.5=100)
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:
GTGGTGGAGCTTCAGCAGAC
R:
ACGGCAGCAGCGCATCATA
Band lengths:
310-2267
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)