GgaINT0054797 @ galGal3
Intron Retention
Gene
ENSGALG00000011389 | TRAF3
Description
NA
Coordinates
chr5:52382413-52384281:+
Coord C1 exon
chr5:52382413-52382587
Coord A exon
chr5:52382588-52383750
Coord C2 exon
chr5:52383751-52384281
Length
1163 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
TTCTCTCCATTTTCTAACAGGCA
3' ss Score
9.9
Exon sequences
Seq C1 exon
CGAGTGATAGACAGTCAAGCAGAGAAACTGAAAGAACTGGACAAAGAAATCCGTCCCTTCCGACAGAACTGGGAGGAGGCTGACAGCATGAAGAGCAGTGTGGAATCCCTCCAGAACAGAGTGACTGAGCTGGAAAGTGTTGACAAAACTGCGGGGCAAGGAGCTCGAAATACAA
Seq A exon
GTAAGTGTAAGCACAATGGACCGAAGTACTCGGTAGTGCTGTGAAAGGAAAAAGGATATCCACTGAATGCCAGTTTCATTATCATTCTCCTGTGAAAGCATCAATAATTCTGATTCTTCTGATTCATGCATAGGAAATGATGCAGTCGCTTCAACGCTGTGGCACTGATTCCAAGCTGTTTCTGAGACTTAATTCTTTTATTTTGTTTTCTTGACCAGTGTCTTGATTACAATATTATAATTCATTATAAACACTTCTTTAGCTGATCTTTGAAAGCCAGTAGCTTTCAGCATCTTCTTTAAATGCATTCTCAGTGTACTAAGAGGTCATTTTCTATTATTTGTTCTCATCCATGAGTAGATTAACATTAGTATTATCCAGCTGAAATTATCTGCTCTGCTATCTGTTACAGAATTGTATTTGATCCAAAGAATTACTGTGAGATGTGCTTGAGTATTAAGGTTGTTGTCATACTTGCTGAATAGTATACATCATATGTAAGGGTTTAAATAATAAGGCCAAAGAACTTAACATTTAAATAGATGTGTATAAAACAAACCTGCTTCTCAGTGTTGTACGTTGATCAATTTTGTCAGTGTGTAAAGAGTAGAACATTACTTCTCATGCAAGGGAAAAGGGACAGCCTTCCCTCCCAAGTAAGTGACCATATAAAGCAGTGCTAAGCTTGAATTTTCCGTTCTATTATCATGTACTTTAGACAAGGTAACTACTACACTTCTCAGACAAGTGGTGTGTGAGAAGAATATTTTGAGTAATTGGTGGGCAAAATTCCCTTTGAATTTCAGAGGGATTATGTAGGAACTATGAGTCCATCCAAGGCTAATAAGCTACAGATTATGCTACCAAGTATGTTCTCAAAATACTGAAGCTTCTGTTGCTTGCTGGCCAGACAAAATTTTAGATGATTTGAATAGTTGACTCATACTGAATGCATCATTAACACCCACAAATGTAAAAATCCTAATTAACCTAGTTTCTAGCTGGCAAACTATTGGCAGTGGAAGTTGTTTCAAAGGTGACCAAATGTGGTTTGGTTCTTGGAGAAATGTTTGCGTATCCACTAACAGTATTGATGATCAATTGTTACGGTCTTTAGAAAAAAGCCTATTTTCTTACCCCCTATTCTCTCCATTTTCTAACAG
Seq C2 exon
GCATGCTAGAGACACAGCTCAGCAGGCACGATCAGATGCTGAGCGTTCATGATATTCGGCTGGCTGACATGGACCTCCGATTCCAAGTTTTAGAAACTGCTAGTTACAATGGAGTGTTAATTTGGAAAATTCGAGATTATAAACGTCGGAAGCAAGAGGCAGTCATGGGGAAGACTCTGTCCTTGTACAGCCAACCCTTTTACACTGGATACTTTGGCTACAAGATGTGTGCCAGAGTTTACCTTAATGGAGATGGCATGGGAAAGGGGACGCACTTGTCGCTGTTTTTTGTCATAATGCGTGGAGAATATGATGCATTGCTTCCTTGGCCATTTAAACAGAAAGTGACTCTCATGCTAATGGATCAGGGTCCGTCTCGGCGCCACTTAGGAGATGCTTTCAAGCCAGATCCAAACAGCAGCAGTTTCAAGAAGCCAACTGGAGAAATGAACATTGCGTCTGGCTGCCCAGTCTTTGTGGCTCAAACTGTTCTAGAGAATGGAACGTATATTAAAGATGATACTATTTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011389:ENSGALT00000018576:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.455 A=NA C2=0.068
Domain overlap (PFAM):
C1:
PF127182=Tropomyosin_1=FE(40.3=100),PF0205011=FliJ=PD(46.0=78.0),PF101744=Cast=FE(36.5=100)
A:
NA
C2:
PF127182=Tropomyosin_1=PD(16.7=12.6),PF101744=Cast=PD(12.6=10.5),PF0091721=MATH=WD(100=74.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCCGACAGAACTGGGAGGAG
R:
TCTGGCACACATCTTGTAGCC
Band lengths:
354-1517
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]