DreINT0167132 @ danRer10
Intron Retention
Gene
ENSDARG00000022000 | traf3
Description
TNF receptor-associated factor 3 [Source:ZFIN;Acc:ZDB-GENE-040801-257]
Coordinates
chr17:29218960-29219263:-
Coord C1 exon
chr17:29219212-29219263
Coord A exon
chr17:29219065-29219211
Coord C2 exon
chr17:29218960-29219064
Length
147 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TTTGCTTTTTTCCATGCAAGATA
3' ss Score
5.43
Exon sequences
Seq C1 exon
TAAGCCTAACCCAGTGTGTCCAGCTGATCTACTACCACTTTTTGAAGATAAG
Seq A exon
GTAAGAAAGTGAAGCCAAACGCTGCAAGGACACACCCACTCCGTTACATATTAAATCACACTCACACAGCTCCAAGTGAAAGTAATGAGGGCTGGATAACAGGCAGCACACAAAACAATCTTGTTTTTTTGCTTTTTTCCATGCAAG
Seq C2 exon
ATATTCCGGGATGTTTGCTGCAATAGGGAAATCATGGCTCTTAAGGTCTACTGCCGAAGTGAGAAAAATGGATGTAAAGAACAAATGTGTTTACAGCAGGTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000022000:ENSDART00000031458:3
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:
PF0009720=zf-C3HC4=PD(21.1=44.4)
A:
NA
C2:
NO
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:
AAGCCTAACCCAGTGTGTCCA
R:
TGACCTGCTGTAAACACATTTGT
Band lengths:
154-301
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]