GgaINT0125449 @ galGal3
Intron Retention
Gene
ENSGALG00000009014 | TRAF2
Description
NA
Coordinates
chr17:928388-929118:-
Coord C1 exon
chr17:928895-929118
Coord A exon
chr17:928467-928894
Coord C2 exon
chr17:928388-928466
Length
428 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACT
5' ss Score
9.01
3' ss Seq
ATTGTTTTTGTGTCTGCTAGTTC
3' ss Score
8.11
Exon sequences
Seq C1 exon
CAGGCTCTGCGCGTACAGCCGGAATTTTTTGTTCCCATGGCAGCAGCAAACTCGACTCCGCCCGGCTCTCTGGACCTGAGCCAGCCCGGGTTTGCGAAGGAGATCCTGGGAACTAAGCTGGAGGTGAAGTACCTCTGCTCGGACTGCAGGAACATATTGAGGCGGCCCTTCCAGGCACAGTGCGGGCATCGCTACTGCTCCTATTGCTTGAAGAAAATCATAAG
Seq A exon
GTAACTCTCGTGCCTTCACCCTTGTGATGAATGCTTAGAAGCGAGCAGCAGAGATGAAGGAGCTGGAGGACCGTTGTGCTGTCTGAGGGAAGGAGCGGTGTGTAACCTCTGAGGGGTGTGTGATGTCTTTATTCTTCTGTGGGTTCCCTCAGCTCTCTCCTGGACTGATGGGTGCCCATTATGCCTACACGTGAGGCACACGGCTCGGAGGAGTTCACTTCTGTTCCCTCTCACTGTTGCCTTTGAGTGGAGCAGGGAACAGTGACTCGTAATAAGCCCCTAATAGCAGAAATGGGTATCCATACTACACCTGAGCAAAGGCTCGGTGGATTGTTTAAAGGATAAGAAATTCCTCTCATTGTATTACGTTATTAGAAGCCAATTATATCATAAATTGGGTGTTTGATTATTGTTTTTGTGTCTGCTAG
Seq C2 exon
TTCTGGACCTCAGAAGTGTGCGAGCTGCATTCAGGAAGGAATATACGAAGAAGGAATTTCTATTTTGGAAACGAGCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009014:ENSGALT00000014665:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.063 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009720=zf-C3HC4=PU(74.4=46.0),PF131921=Thioredoxin_3=PU(16.9=20.6)
A:
NA
C2:
PF0009720=zf-C3HC4=PD(23.1=33.3),PF131921=Thioredoxin_3=FE(33.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGCTCTGCGCGTACAG
R:
GAGCTCGTTTCCAAAATAGAAATTCC
Band lengths:
302-730
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]