HsaINT0171669 @ hg19
Intron Retention
Gene
ENSG00000056558 | TRAF1
Description
TNF receptor-associated factor 1 [Source:HGNC Symbol;Acc:12031]
Coordinates
chr9:123688214-123688966:-
Coord C1 exon
chr9:123688828-123688966
Coord A exon
chr9:123688580-123688827
Coord C2 exon
chr9:123688214-123688579
Length
248 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
ATGACTGGACACTCCTAAAGCCT
3' ss Score
-0.56
Exon sequences
Seq C1 exon
ATGGAGTCATCAGAACCCACTGTGAGGAAGTGACTTCTCCTTGAGGTCACCCAGACACTCCAAACAGAGCAGAGCAAAAGCGCCTAGAACTTGAAATTTTGGACCTGTCTCCAACACCCTGGGGATTTCCACCAGGAAG
Seq A exon
GTGAGCACCCCCACTGAGAATTCCAGGCTGCTCAGAGGTGCCAGGGAACACAGACCAGGGACCAGCTGTGGCCCCCTCCTCCGATGTGCCCAGGGAAGTGGGGGAAGCCAGCGGCAGCCTGCGATTCTCAACCAGGGGAACTCTCACTGTGCTTTCTGAGAGTCTGTGACACGGGTCATTTTCTCTGACTTGCTCTCTTGCTTTTTCTCACTCTAAAAAAAAAAAAAAATGACTGGACACTCCTAAAG
Seq C2 exon
CCTTCAGTCACCATCCAGGGGATTTTTATCGCCACAAAGGGTAATTCCTGCTCCATCCCTGCTGTGACTCAGCTGTGACGTTGAACCACACAAGCCAGAGAGAAGAAGATAAAGTCATCAGAGCTCCTACTCACCAGAGAGTGAGGCCCAGGCCAGGACTCCACAAGGCTGGTCCCCTGCCCTGGAGCAACTTAAACAGGCCCTCTGGCCAGCCTGGAACCCTGAGATGGCCTCCAGCTCAGGCAGCAGTCCTCGCCCGGCCCCTGATGAGAATGAGTTTCCCTTTGGGTGCCCTCCCACCGTCTGCCAGGACCCAAAGGAGCCCAGGGCTCTCTGCTGTGCAGGCTGTCTCTCTGAGAACCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000056558-TRAF1:NM_001190945:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.362
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCAGACACTCCAAACAGAGC
R:
GGGCCTGTTTAAGTTGCTCCA
Band lengths:
293-541
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)