BtaINT0026727 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010582 | BRD3
Description
Bos taurus bromodomain containing 3 (BRD3), mRNA. [Source:RefSeq mRNA;Acc:NM_001076873]
Coordinates
chr11:104877897-104878678:-
Coord C1 exon
chr11:104878541-104878678
Coord A exon
chr11:104878045-104878540
Coord C2 exon
chr11:104877897-104878044
Length
496 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TGCTTCTCCCGTGTCTTCAGCCC
3' ss Score
7.67
Exon sequences
Seq C1 exon
GATTATCACAAGATAATAAAAAACCCCATGGACATGGGAACCATTAAGAAGAGACTAGAAAATAATTATTATTGGAGCGCAAGTGAATGTATGCAGGACTTCAACACCATGTTTACAAATTGTTACATTTATAACAAG
Seq A exon
GTGAGAAGGTGGCGTGGGCCCCGTCGCTGCTGTGAGTGACCTGGGGGAGCGCCAGTATGGGTTTGGCCGGCGTCCACCAGGCTGGGTGCGTCGCAGCGAGTCTCAGGCCCATTCAGGCCACCTCGGCTCCCGCTCAGCCCTTGTCTGGCTGCGACCCCCGCGCCCTGTGCGTGGGCCCACATGCCCTGCTGGCACGGTGAACATTCGAATAGCCTTTTCAGGGGGAGTCGACACCAGATGCTGTAAAACATCCCCACACCTGGACCTTGTTTCCTCTCCATGATGGGATAAAGCGTGGTTTTTATCCTTTGTGCTTTTTGAGTTCTTGCAAGAGTTTCTGTGTTAAAATGTGTTCCTGTTGCTTCTCTCCCGCCCCGCCAGATCCCTTCACAACTTTTTAAACACATATTTTTCTCGAGCAGCGGTTGCGCGTTTGTCTGCTGCGAGCAGCGCGGCTCCTTTCCAGCGCGTGACCCTGCTTCTCCCGTGTCTTCAG
Seq C2 exon
CCCACAGATGACATCGTGCTCATGGCCCAAGCCTTAGAGAAAATTTTTCTGCAGAAAGTGGCTCAGATGCCCCAGGAGGAAGTTGAGTTACTGCCCCCTGCTCCAAAGGGCAAAGGCCGGAAACCCGCTTCGGGAACGCAGAGCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010582:ENSBTAT00000013992:2
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=0.480
Domain overlap (PFAM):
C1:
PF0043920=Bromodomain=FE(51.7=100)
A:
NA
C2:
PF0043920=Bromodomain=PD(11.5=20.0)
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:
AATAATTATTATTGGAGCGCAAGTGA
R:
GCTCTGCGTTCCCGAAGC
Band lengths:
222-718
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development