GgaINT1028427 @ galGal4
Intron Retention
Gene
ENSGALG00000009014 | TRAF2
Description
TRAF2 protein [Source:UniProtKB/TrEMBL;Acc:E1BTY1]
Coordinates
chr17:547100-547794:-
Coord C1 exon
chr17:547607-547794
Coord A exon
chr17:547179-547606
Coord C2 exon
chr17:547100-547178
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
ATGGCAGCAGCAAACTCGACTCCGCCCGGCTCTCTGGACCTGAGCCAGCCCGGGTTTGCGAAGGAGATCCTGGGAACTAAGCTGGAGGTGAAGTACCTCTGCTCGGACTGCAGGAACATATTGAGGCGGCCCTTCCAGGCACAGTGCGGGCATCGCTACTGCTCCTATTGCTTGAAGAAAATCATAAG
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
ORF disruption upon sequence inclusion (1st CDS intron)
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)
A:
NA
C2:
PF0009720=zf-C3HC4=PD(23.1=33.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGGCAGCAGCAAACTCGAC
R:
AGCTCGTTTCCAAAATAGAAATTCCT
Band lengths:
265-693
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]