DreINT0167114 @ danRer10
Intron Retention
Gene
ENSDARG00000069482 | traf1
Description
TNF receptor-associated factor 1 [Source:ZFIN;Acc:ZDB-GENE-071120-4]
Coordinates
chr8:12385321-12386893:-
Coord C1 exon
chr8:12386825-12386893
Coord A exon
chr8:12385744-12386824
Coord C2 exon
chr8:12385321-12385743
Length
1081 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGT
5' ss Score
8.46
3' ss Seq
TATGAATTGTTTTAATTCAGGGC
3' ss Score
6.89
Exon sequences
Seq C1 exon
AATAATCAGCCGGCCAACTCAAAAAAGAAAGAACCATGCATTTTCTCAGACGTTGGTTGTCCTTTTAAG
Seq A exon
GTTGGTTTTGTTGATAATGCCACTATTTTTCATAATGTTGTGCTATATATCATTTTTGGAACAAAGTTCTATATAGAGGAGGTAATTTGGACCATTATTATGCCATTATATATATTTATATCTATATATATAGCCCCCCATTTTTGCCCATTAGGCCTACCTTGGGTTTATTTTTGCTAATTTAAGCCATTTTTCAAAAGATAAATATATTGTATAAAACTAAACATTATTTATATTACTATCATTCATAGTTCCTATACACCTAATAAGCTCTTTATATTAATAGACAATACACAGATATTGATGTTTCATAATGTTTTACACTACATTATTTGAATCTACCAAGTTAGTTTACAATGTTTACATTGCTCTACTTACAATAAATCTAAATCCCAAATATCAGAAATGACAACAGATTGTTAAGATTTAATTAATGTCAGTTTTATTGCTATTGATTTATGCATTTACTTAACAAATTTCATTCAATCATTTTCCTTCTGCCTTTTCCCTAGTTTATCACAGTGGAATGAACCGCCACTTACTTGACATATTTATATATTTTTACTTTTAGCTGGTTTTTGTAACGTGTTTTAAGTTAAAATAATTTCTAATCGCATCTTTAGTGATTTTCAACTAATTACACTGTCTTGTCTTAATAGGCGGATTTAGCGTTTTTTGCAAAAAAAGCACAAGTGGACTTAGCTGGTTTTGATGCAAAATAAAATTTACCTTTTTAAAAACCAAAGAAATGTCTAAAGTGACATTTATTTTAAAAAGTTATTTCATTTACTAGCTAATAAAATGAAACTTCTGAACCTAATTAGCAGAGCCTGATAGAAAATGCTCATTTACAAGAAAAGAAGTCTGATGGATTTAGAGGGTTTTGCATCTGAACTCTCATATATATACATACACACTCACCGGCCACTTTATTAGGTACTCTAAAAAACCCTCATAATTTTTATGGTGTAAAAAAAATCAAACATTTTTTTTTTTTTTTAAATAAACCAAATCTGACCTCACCTTGACTTTATGTTCTTTTCCCTTTAACTTTTACAATATATGAATTGTTTTAATTCAG
Seq C2 exon
GGCAACCCAGACAAAGTAAAAGAACATGAGTCTTGCAGTCATGCGGGTCACCTGCAGCTTCTACTGGACGTGACCAGGGCTCTTCAGCGAACACTGAACTCAGCAACTGAGCGAGTCTACCAGGACAGCCCTGTTTTTCTTGAGCCTGGACCAAATGGCTCTTCACTCGCTCCTCAGGCTGATGGTGACATAGAAACGGATGGAGGAGATCCGGGAGTGAGTGACAAGGCCTTCAGCCTCCACGATGATCAGGTTGAGCTCGCCGCCGGCCAGCAGCTGGACGCCCTGCAGCAAAAAGTGCAGGTCATAGAGAACATCATTTCCGCTCTGAACCGAGAGGTAGAGAAGACACAGATCAGTGTGGTGGCAATGAATAGAGACCATTGCAACAGCCAGCAGATCATTCAGCATTTGGAAGCTACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069482:ENSDART00000101174:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.400 A=NA C2=0.370
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF078897=DUF1664=PU(88.6=44.0),PF0101715=STAT_alpha=PU(81.5=37.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTCAGACGTTGGTTGTCCTT
R:
TCAGAGCGGAAATGATGTTCTCT
Band lengths:
357-1438
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]