DreINT0167130 @ danRer10
Intron Retention
Gene
ENSDARG00000022000 | traf3
Description
TNF receptor-associated factor 3 [Source:ZFIN;Acc:ZDB-GENE-040801-257]
Coordinates
chr17:29210539-29213332:-
Coord C1 exon
chr17:29213149-29213332
Coord A exon
chr17:29211594-29213148
Coord C2 exon
chr17:29210539-29211593
Length
1555 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGA
5' ss Score
8.91
3' ss Seq
TTTGTCAACCCTGTCTTCAGCCT
3' ss Score
5.58
Exon sequences
Seq C1 exon
ATGTTGATGAGCTCTCACTCAGAGAAGCTGCTGGAGGTGGAGATGGAGCTGCGGGAGCTCCGTCCACTGCGGGCCATGAGGGAGGAGGTGGAGACTCTCAGGGGCTCTGTGGAGAGCATGCGCTCGATGGTCTCTTCTCTTGACTCAAGCTGTGTCAATTCTGCTTCTGGTTCTCATACCCTGG
Seq A exon
GTAAGAAAATTTTATAAATATTAGAGGTATAACTCTACATATATTTGTATAAAAATGTCAGTCTTTCAGTTTGGTATGCATATGAACTGAATAAATACATTGTTTTTTTATATATATATATCTTACTGTCTTTTAGTCAATGCTGTGCCAGATGATGCTTGCAAAAATCTTTACTAGGCATTAAATAGTTCATCTTCTGTCTAATAATTGCAAGATGCTTTGTGCTTAATCTTATAAGGGACAGTCTTATCCTTTAATTTCTATTTTATTAGGAAATACAGTACAACAAAACAATAATAGGCAATTGAATGCTCAGTTCAAATGCAATAATTTCTTCCTCTTTTCAACTGGTTATAGCACAAAATTAACATGGATAAAGATCTTGTCTCATTTAATCACTTGGGTAAAAAAGGTCAATAAAACAGCTTCACACTTTGTTATAGATTCCTTATATTTTACTTAAACTATCAGTGATGTCTTAATTATTTAATGAACATCAATCTGTTATGAAACGCATTAAAATACAGTGTATAAATTGCAGTTTCAGAAATGAATTAGATTTTATCATTTAGACATTAATACAATGGCTCCACTTGTATCTATGCATTTTTTTATTCAATTATTGGTCCTATTTGATATTAAGTGGCCTTAAATACTAGGTTCTTACAGCACATCAAAAAAATAAATATAATCCTGTGTTCATAATGTGTTGCAGAACACAACTGGTGTTCTTAAGGTGGGATTTAGGTGAGGTTAGGTACAGGTTTTGGGGTATGGGTAGGTTTAACTATGGATTAAGGTGAAATAGATGGTCAACAGTGTTCAATCAATCATAAGTACAATGTATAAACATGCATTCACACTATAAGTACATTGTAATAGATTAATAATTTCAGTTTAAGTATGTATTAGTTAAGGACACTTAATATAATATGGGACCCAATTATTGATTATTACTAATAAATAATAAATGTAAGAGACTTCCGCACCTTCTTCACAGTTCCTAGAACTATTGTGTGGACCATGTTTTTTCCTGCCAGAAAAATGGTACCAGAAATATGATCCAGGGCAAATGAGTTCTCTGTGAATTGGGCCTGGTGGCTAGCTTTGTTGAGTTTTTTTAACTACCTAGTGTGAAAATGATCGTAATCTGCAAGTAATGGCTCTATAGATGACAGCATTAGCAAAGACAACTTTTAAATCTTTTATAACATTGCCTATAGCCTTGTGGGCAACATATAGCGCCATTGTGCATTGGGTGACTCAAGTTCAAGTCCCAACTTGCAGACCTTTCCTGATCCCGTATCCCCTTTCTCTCTCCAACTTTGCTTTCTGTCCAGCTACTGTACTATCATAATAAAGGCAAAAAGCTATAATATGGTTTAGCAAACCACTGTTAAATTAAACAAAAATAAACATACCAAACTGTGACTTCAAATCTTTGTACTCAATCATCAACTTTGTGTACTGATTCATCCCTAATATACACCAATACAAGTACTGATGTGTGACCCTAACACTGATTATTTTTAACATTTGTCAACCCTGTCTTCAG
Seq C2 exon
CCTCCTTAGAGCAGCAGCTCACACGCCATGATGACCTGATGAGCGTTCACGACGTGCGGCTGGCAGAGATGGATCTGAAGCTGCAGGTGCTGGAGACGGCCAGCTTCAATGGTACTCTCATTTGGAAGATTCGGGATTACAAAAGGCGGAAACAGGAAGCTGTGGTCTCCAAAACCCTTTCGCTCTACAGCCAGCCCTTTTACACAGGGTATTTCGGCTATAAGATGTGCGCCCGCGTCTATCTCAATGGAGATGGGATGGGCAAAGGCACACATCTCTCGCTCTTCTTCGTGGTCATGCGTGGTGAATATGATGCCTTGCTACAATGGCCGTTTAAACAGAAAGTAACATTAATGCTAATGGACCAGGGGCCGGCAAGAAAACACTTAGGCGATGCCTTTAAACCGGACCCCAGTAGCAGTAGCTTTCGCCGGCCCACTGGCGAAATGAACATCGCATCAGGCTGTCCGCTTTTTGTGGCTCAGACTGTGCTAGAAAATGGAACCTATATCAAAGACGACACCATCTTTATAAAAGTGACTGTAGACACTTCAGACCTCCCTGACCCTTGAGTTCAACTTCAGCGGGTCCAACTAAAATCAAGAGTCACGCAGAGCCCCTTCCAGCCAAGACTTCAGAGGGCGATGCTGAACAAGGAGCATCCCACAAGTGTGGGGTTCTAACAGACCAAATCAGGAGTTTGGGCTCGTGTGATGGCGTGCTCTTCTGGAAACAACAGTGCCTTGCTGGGCTAGATGGTTACAGCCTTTAAGAGGAGCACAGAGTAGACGAAATCTCCCAAGTCAACCACATCTCAAATGCAGCGAAGAGTAAGACGTCAACTCTAATCCAAGAGACATTCTCGAGGAAAAACAAAAGTGAATGGTTACTAGATCAGATTCCCAACCTCGTTCCTGGAGGCACACCGACAGTACACATTTTAAACTTGTCTGGCTCTTAATCTAATCCGGAAATGTAAGGAAGATGGTGTACTTTTAAGTGTGTGTCCAGTAAAATGGTTGGCACGGTTGATTAACATCCAGCCCAAAGTGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000022000:ENSDART00000031458:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.053
Domain overlap (PFAM):
C1:
PF073947=DUF1501=FE(22.9=100),PF041569=IncA=FE(33.3=100),PF086146=ATG16=PD(30.5=74.2),PF130941=CENP-Q=FE(37.2=100),PF061607=EzrA=PD(35.4=72.6),PF041027=SlyX=PD(17.2=17.7),PF153721=DUF4600=PD(67.1=88.7)
A:
NA
C2:
PF073947=DUF1501=PD(12.0=16.8),PF041569=IncA=PD(8.2=7.9),PF130941=CENP-Q=PD(7.3=6.3),PF0091721=MATH=WD(100=73.8)
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:
TCACTCAGAGAAGCTGCTGGA
R:
GCGAAAGGGTTTTGGAGACCA
Band lengths:
353-1908
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]