BtaINT0152128 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003012 | TRAF1
Description
TNF receptor-associated factor 1 [Source:HGNC Symbol;Acc:HGNC:12031]
Coordinates
chr8:112198398-112200679:-
Coord C1 exon
chr8:112200502-112200679
Coord A exon
chr8:112198547-112200501
Coord C2 exon
chr8:112198398-112198546
Length
1955 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACT
5' ss Score
8.63
3' ss Seq
CTCTGGCTTCCGCATTTCAGCTT
3' ss Score
7.54
Exon sequences
Seq C1 exon
GTGTTGGAGTTGCAGCAGACCCTGGCCCAGAAGGACCAGGCCTTGGGCAAGCTGGAGCAGAGCCTGCGCCTCGTGGAGGAGGCCTCCTACGACGGCACCTTCCTCTGGAAGATCACCAACGTCACCCGCCGATGCCATGAGTCGGCCTGTGGCAGGACCGTCAGCCTCTTCTCCCCAG
Seq A exon
GTAACTCCTCCCGGAAGGCAAGCGCGGGGCGGCCGGTACCGGCACCTGCAGAGGAGGCAGGCCCCACGGGGCCCAGGAGACAAGCCGGGGGTAGGGGGTGGTCCGCTCTGACAGCCGTGCTGCATACGGTTAGGCCTGCGGCCGTTCAGAGGCCCGGCCCTGCCAGGCCCGTGGAGGTGGTGGGCTCCTCCCCACCCCGCCGTGTGGAGCAGGGGCTGTGGGCACCAGGCTGGCCTTCTGCCTCCCTGAACACCGGTTACATTCTGCAACTAGGAATAAGTCACCTCAGTCATTTGTGTGGATACCGGTTTTGAAAGGGAGTGCACTGTGAACCCGAGTCTGTGCAGACTTGAGGGGAGTGGAGGATGGCTTTCACAGGTGCCCCAGCCCTCCGAGACCCAGTGACCTGAAATCAGACAAGGGGAGATCTAGGTAAAACCACAGGCATCTGTGTACAATTGTGGGGAGCATGTGAGCGAGTATTGTGTAAATCAGGGCAGTTCTTACTCATTCCCGGGATCCCGGGGCCTGGCACTTCATCTTGCGTAAAGCAGGCAGTTACTCGGTCGGTGCTGCTCTTCCTCAGCTGAGACCTGCTTATGTGACGCTGTGTGTGTCTGTGCTCAGACCTTGTGCTTTCCCCCTTGCCTCCCTCGTGTGTGTCTAAGGAAAATGGGTGGGTTGTTAAGGAGGATTTCTGCTGAAGGCAGTGTTAACCCCCACTCACGTCTGCTCCAACCTCATGCCTTTCCAGTCCGTCAGCTCCTCTGACTCACCCAAGCCCAACAGCGCTAGGATTAAGAGGGGGCGTGGGAGTCTGCCCCACCCCACAGGGCAGGTGGGCCCCCAAGCCAGGCGCCTTGCCTCAGGAACCGGGGCAGCTCCTTCGTGGGGTGGCCTTGCCCTCTACACGTAAGCTTTTTGTCCTGGCTGCTTTCCAAAGAGGGAAAAAGCAAGCAGTGTCTCTGGCTTCCTGTTCTACCAAAGCACAGAGGGCAGAGATGAGTCAGACCGTCAGCCTGTCCCCGCTCCACGCCTTCCCGCCCTGCACAAGCTGTGCCCGCTCTGCCCCTCCCAGACGGGCCCTCATGGGGACAGCTGCTGGAACCCACACTCAGATGGCTCTTTCAGCTGCCCAGGAGAGAGCCCACAGGCCCTATACCTAATCACCAGGGGATGATTCATCCCAGGGGCCTGTGCCGAGGCAGGTTGTGAGTCTCCCCACTCCCTCCCAGCCCCCAGGAGACCCCAGCCGCTTAGCCTGGGGCTGCAGAAAGAGCTGCGTGTTGGGACGTACGAGGCCGGGCCCCTCACTCTGGCCCTGACCCCAGCTCGCTGTGACTTTGTGGGCCGGTCACTTCCCCTTGCTGGGCTCCAGCTCCTGACTACGAAGTGCACGTCGGTTAAATCGGGAGTGTGGTGGGGCCAGCAGCGCCTCTGTGCCCTGGCAGAAACATAAAGTTTCTCAGTCCTCACCCTGCACTGCTGAGTCAGAAACTCCAGGCCTGGGTCCTGGCAGTCTGCGATTCTGGTGGCCCTTGACATCCAGCGGTTCAGGTGGTCTCCAAGATTTAATGCTCTATGTTTTTGTTTATTGTTGAGTCGCTAAGTCATGTTCAACTCTTTTGCGACCCCATGGACTGTAGCCCGCCAGGCTCCTCTGTCTGTGGGATTTCCCAGGCAAGAACACTGGAGAGGGTTGCCATTTCCTTCTCCAGGGGATCTTCCTGACCCAGGGTTTGAAGCCACGTCTCCAGCCTTCCAGGCAGATTCTTTACCGCTGAGCCACCGGGGAAGCCCCCTGGTGCTCTTTGGTGGAGAAGCGGCTCCAATCCCAGATGTCACAGTCTGGGGCCATGACCTGGGCTTGCCTAACTGCCAGCCCCAGTTTCCTCATCTGCAAAGTCTAGCACTTGCCAGCTGCCCTGGCAATGACTCTGGCTTCCGCATTTCAG
Seq C2 exon
CTTTCTACACCGCCAAGTACGGATACAAGCTGTGCCTGCGGCTCTACCTGAATGGGGATGGGACGGGGAAGAGGACCCACCTGTCCCTCTTCATCGTGATCATGAGAGGGGAGTATGATGCTCTGCTGCCATGGCCTTTCAGGAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003012:ENSBTAT00000043659:5
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:
PF0091721=MATH=PU(15.5=36.7)
A:
NA
C2:
PF0091721=MATH=FE(34.5=100)
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:
GTGTTGGAGTTGCAGCAGACC
R:
TTGTTCCTGAAAGGCCATGGC
Band lengths:
326-2281
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]