BtaINT0152148 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013475 | TRAF3
Description
TNF receptor-associated factor 3 [Source:HGNC Symbol;Acc:HGNC:12033]
Coordinates
chr21:69252729-69254153:+
Coord C1 exon
chr21:69252729-69252903
Coord A exon
chr21:69252904-69253461
Coord C2 exon
chr21:69253462-69254153
Length
558 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CCCGCCGTGTCTCCCGCCAGGCC
3' ss Score
11.1
Exon sequences
Seq C1 exon
CGAGTCATCGACAGCCAAGCAGAGAAACTGAAGGAGCTCGACAAGGAGATCCGGCCCTTCCGGCAGAACTGGGAGGAGGCAGACAGCATGAAGAGCAGCGTGGAGTCCCTCCAGAACCGGGTGACCGAGCTGGAGAGCGTGGACAAGAGCGCGGGGCAGGCAGCGCGCAACACAG
Seq A exon
GTGAGCCCGCGCGTCCCAGGCCGGTACTGGGGCCGGCTGTGCGGGAGAGCGGAGCGCCTGCAGGTGACCGGCTTCCTGCGCCAGGCACAGAGCGCAGGGAGGACGCCGACGGGGCCGGGCCTGCGGGCGGAGATGCGGGGCTGCGCAGGAAGGCCAGGGGACAGAAGGTGACCAGCAGGCGGCAGGGGACCCGGCCAGCCCGGCAGCGTGGCTGATGCCTAGAAGCCGCCTGGGCGTGGAGCGGGGAGGGGGTTGCTGAGCGAGCGTCCTAAAACCGCCTGAGCAGGATTAACCGGGAGGAGCCCGATTACGGGGATGCACGTGGGGCCGGATTAAGCCGGCCAAGGAGCCGAGCAGCTTCGATTCCGGGGGGATCGCCCGGAGCTGGGGAGCCGGGGGCAGCAGGCCGGTGCTCCGGGGTGTCCCTGCCCCGCAGGCTGAGGCTGGGGGTCCGGGGCGTGCGTCTCCGGCCCCCCGTGGGCGCGGGCACCCCCACCCCCCACCCTGCGGGCAGGCCTCCGTGGGTCACGTGCGCGCGCCCGCCGTGTCTCCCGCCAG
Seq C2 exon
GCCTGCTGGAGTCGCAGCTGAGCCGGCACGACCAGATGCTGAGCGTGCACGACATCCGCCTGGCCGACATGGACCTGCGCTTCCAGGTCCTGGAGACCGCCAGCTACAACGGCGTGCTCATCTGGAAGATCCGCGACTACAAGCGGCGGAAGCAGGAGGCCGTGATGGGCAAGACGCTGTCTCTGTACAGCCAGCCCTTCTACACCGGCTACTTCGGCTACAAGATGTGCGCCAGGGTCTACCTGAACGGGGACGGCATGGGCAAGGGCACGCACCTGTCGCTCTTCTTCGTCATCATGCGCGGCGAGTACGACGCGCTGCTGCCCTGGCCCTTCAAGCAGAAAGTGACGCTCATGCTGATGGACCAGGGGTCCTCGCGGCGGCACCTGGGGGATGCGTTCAAGCCGGACCCCAACAGCAGCAGCTTCAAGAAGCCCACTGGGGAGATGAACATCGCCTCCGGGTGCCCCGTCTTTGTGGCCCAGACTGTGCTGGAGAACGGGACGTACATCAAAGACGACACCATTTTTATCAAAGTCATAGTGGATACTTCGGACCTGCCGGACCCCTGACGCGTCCCCGGGGCGGCGGATCGAGCAGAAGGCAACTCCTCCGGGGGGTTTGAACCGGCCGTCTCCACCGAGGTCCTCGCGCTCAGAAAAGGACCTTGGGAGACGGAGGAAGCAGCAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013475:ENSBTAT00000017918:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.034 A=NA C2=0.037
Domain overlap (PFAM):
C1:
PF041569=IncA=FE(26.5=100),PF101744=Cast=FE(37.9=100),PF0205011=FliJ=FE(42.3=100),PF0149614=V_ATPase_I=FE(32.8=100)
A:
NA
C2:
PF041569=IncA=PD(6.8=7.9),PF101744=Cast=PD(9.2=7.3),PF0205011=FliJ=PD(8.0=5.8),PF0149614=V_ATPase_I=PD(35.0=32.5),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:
ACTGAAGGAGCTCGACAAGGA
R:
TGTAGAAGGGCTGGCTGTACA
Band lengths:
353-911
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]