BtaINT0152126 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003012 | TRAF1
Description
TNF receptor-associated factor 1 [Source:HGNC Symbol;Acc:HGNC:12031]
Coordinates
chr8:112202339-112203323:-
Coord C1 exon
chr8:112203258-112203323
Coord A exon
chr8:112202750-112203257
Coord C2 exon
chr8:112202339-112202749
Length
508 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
CAGCCCCACTCTTTCGGCAGGGA
3' ss Score
6.66
Exon sequences
Seq C1 exon
GATCACCCCGAGGTGGCTGAGGCTGGAGTTGGGTGCCCCTTTGCAGGTGTCGGCTGCTCCTTCAAG
Seq A exon
GTAAGTATCTAGGTGTGAGAAAGGAGGTCTGTACACTGCAGTCTCAGACCTCCTTGCTCAGCCCCTCGGGTTTTCCCCCAACATCCAGCTGCTGCTCTGGATGTACCTTACGTGGCTCACAAGCCAAAAAATCACTAGTAAATCATCTTTGTATTCAGGGGAGTTCTTCTTAAAGTCTCACCTGAGCATTGTAGTAGCATCACAACAATGACCCTCCCCTCCCCACTACCCCCAACCCCTGTGCCTCTCTCCATGGTCCTGAATCATCACTGTGCTGAGGGCAGGACAGAACGGCTGCTCTGGAAGCTGGAGTGCACACGGCTCAGCACGGGCGTGTCTAACGCCAGGGCCCTTCTCCACGTCCCTCTCGCTGTGTACTTCCCGTTGCTGGATGAATGGATATGACATCCCTTGGTAACCTGTGATGGCAGGACTCTCCTTGGCTCCTTGGTGCTCCCTCCTCCTCCTCCTCCTCTGTTTTCACTGATCAGCCCCACTCTTTCGGCAG
Seq C2 exon
GGAAGCCCAAAGTTCATGGAGGAGCATGAGGTCACCTCCCAGGCCGCCCACCTGAACCTGCTGTTGGGGTTCATGAAGCAGTGGAAGGCCCAGCTGGGCTCTGGCCTGGGGTACGGGCCCATGGCCCTGGAACGGAACCTGTCAGACCTGCAGCTGCAGGGGGCCGTGGAGGTGGCCGGGGACCTGGAGGTGGACTGCTACCGGGCCCCCTGCTCCGAGAGCCAGGACGAGCTGGCCCTGCATCACTTCATGAAGGAGAAGCTCCTGAACGAGCTGGAAGGGAAGCTGTGTGTGTTCGAGAACATTGTCGCTGTCCTCAACAAGGAGGTGGAGGCCTCCCACCTGGCCCTGGCCGCCTCCATTCACCAGAGCCAGCTGGACCGCGAACACATCCTGAGCCTGGAGCAGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003012:ENSBTAT00000043659:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.136 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GTGTCGGCTGCTCCTTCAAG
R:
TGTTGAGGACAGCGACAATGT
Band lengths:
342-850
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]