DreINT0167134 @ danRer10
Intron Retention
Gene
ENSDARG00000022000 | traf3
Description
TNF receptor-associated factor 3 [Source:ZFIN;Acc:ZDB-GENE-040801-257]
Coordinates
chr17:29218105-29218774:-
Coord C1 exon
chr17:29218610-29218774
Coord A exon
chr17:29218186-29218609
Coord C2 exon
chr17:29218105-29218185
Length
424 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCA
5' ss Score
7.88
3' ss Seq
TTTGTCGTCTCTCTTTGCAGAAA
3' ss Score
12.66
Exon sequences
Seq C1 exon
GAGCATTTGGTAATTTGTCCATATTTCGAGGTGCCGTGTCCTTTGGGAAAGTGTAAGGAGAAGATGATGAGGAAAGATATGCCCGAGCACCTAAGCCGCAAATGCAAACACCGAGAGGTCACCTGTGAATTCTGCAGTCTCAAAATGGCCCTCACTGAATTACAG
Seq A exon
GTACCACACTTTGCCCAAAACCCCCCAGTTCCTATAAAAAGGACCTGAAATCTCATGGAAAGTACTTAGAAATTCAAGCAAGCTTTTTTTTTTTTTTAGATATCATTGAGTTTTTTTTTTTCCTTGATTGGAATTAGTGGACGTCTCGGTTCCTCTATGAGAAGTATTCCCCTTGTGTGCTGTCATTAATGTCCCATGACCTTTAAGTTTCACATTTGTACAAGGAACTTAGGGGAATCTCCCGTTATGCAGACTGTCATTTAGAGAATGATCGATGTGTGTTTTCACTTCAGTAATGCTTTGTTTTTCCGCCTGGTTAATCCTGTCATTATTACTCTAGACACTAACAGTTTTTTTGGTTTGGTTAAGCGTGAGCATCTTGAAACATGTCAGAATGCCGTGTTTTTGTCGTCTCTCTTTGCAG
Seq C2 exon
AAACACAAAGAAACCGTCTGTCCTGCATTTCCTGTAGCATGTCCTAATCATTGCTCGTTTTCTTCTATTCTAAGAAGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000022000:ENSDART00000031458:5
Average complexity
IR
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:
PF0217613=zf-TRAF=PU(94.6=96.4),PF073947=DUF1501=PU(15.4=74.5)
A:
NA
C2:
PF0217613=zf-TRAF=PD(1.8=3.7),PF073947=DUF1501=FE(9.8=100),PF041569=IncA=PU(1.1=7.4),PF086146=ATG16=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCATTTGGTAATTTGTCCATATTTCG
R:
TTCTTAGAATAGAAGAAAACGAGCAA
Band lengths:
239-663
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]