BtaINT0026725 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010582 | BRD3
Description
Bos taurus bromodomain containing 3 (BRD3), mRNA. [Source:RefSeq mRNA;Acc:NM_001076873]
Coordinates
chr11:104878541-104880077:-
Coord C1 exon
chr11:104879741-104880077
Coord A exon
chr11:104878679-104879740
Coord C2 exon
chr11:104878541-104878678
Length
1062 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
CCTGACTGTCTTTTTCCTAGGAT
3' ss Score
9.67
Exon sequences
Seq C1 exon
CCGCCCTGCAGGTGCTGACCGGTTGGGCCCGGACATGGAATGTCGCGCCTCGGCAGGAAGCACAGAGGAAGCCAGGGCCTCCCTGAGCCGCTGCTGTGACGGCCAGTGAGCGAGCAACTGGAGGATGTCCACCGCGACGCCGGTCGCCCCCACGGGGATCCCGGCGGCCCCGGGCCCGGTGAACCCGCCCCCGCCGGAGGTCTCCAACCCCGCCAAGCCCGGCCGCAAGACCAACCAGCTGCAGTACATGCAGAACGTTGTGGTGAAGACGCTCTGGAAACACCAGTTCGCCTGGCCCTTCTACCAGCCCGTGGACGCCATTAAGCTGAACCTGCCC
Seq A exon
GTGAGTGCCCTGCCCGCCGCCCCAGCCCCTCCGGGGCCCCGACTCCTGCCTGACGGTCCTGCCCGCCGCCCCTCCCGGGCCCCAACTCCTGCCTGTGAGGGTCCTGCCCGCCGCCCCTCCGGGGCCCCAACTCCTGCCTGTGAGGGTCCTGCCCGCCGCCCCTCCGGGGCCCCGACTCCTGCCTGTGAGGGTCCTGCCCGCTGCCCCTCCGGGGCCCCGACTCCTGCCTGTGAGGGTCCTGCCCGCCGCCCCTCCGGGGCCCCAACTCCTGCCTGTGAGGGTCCTGCCCACTGCCCCTCCGGGTCCCCCTGTCCTGGGAGGACAGCCCCTGTGGCCTTGGCTGCAGGTGCTAGGAGGGCGGGCCCAGCCCAGAATCTGTGATGATGGAAGAGCAGAGGGGACACGCAGGCCTGGGGGCGGGGAGGGCAGCTGCCCCAGGTGCAGGGAGTGGGAGGCCGTGGCCTCGTGGGTGGACGAGGCGGACCAGCCCTGGCGCAGAGGCGCACTGAGGCTCAGCCCGCACCAGCCCCGTCCCGCCGAGTGATGCGTCTGCACACACAGCCTTGTGCTTACGTGGGGGCGGCCGGCCTTCCCGGGGATGGCGCCCTAGCTGCATGCCTGGGGCCCACCTGACTGTCTGACGGCTTTCTCCTCTGGGCCTGAGCGGAGAACCCCAGAGTCCTGCAAGGGCAGCCCTGGGCCAGCACTTGGCAGCCTGGCTCCTGAGCCAGCTTGGCCGTCAGGCATGTACAGGCCCTAGAGTGAAGTTTGGGACCCAGAGAGGGGGCCTAGCCCCTCGTCCGGCTCCTAGACCCACTCTGCAGTCCTCTGTCCACACAGACTCCCATCAGACCAGAGAGTCTTGGCAGGGTCCGTGCTGGCCCAGGGCTCCCCCAGACCTGGCGCCAGCCCCGCCCCGCCATCAGCTGGACAGAAACTTAGGTCCAGCCCCAGTGCTGAGGTGCTGGACAAGACCGCCTCGTGCGCGATCTCGGCCCTTGGGAATCAGGAAAACCGTCTTATTGAACCCAACAGTAACGCCCCTGACTGTCTTTTTCCTAG
Seq C2 exon
GATTATCACAAGATAATAAAAAACCCCATGGACATGGGAACCATTAAGAAGAGACTAGAAAATAATTATTATTGGAGCGCAAGTGAATGTATGCAGGACTTCAACACCATGTTTACAAATTGTTACATTTATAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010582:ENSBTAT00000013992:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.465 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043920=Bromodomain=PU(33.3=40.8)
A:
NA
C2:
PF0043920=Bromodomain=FE(51.7=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:
CAGTGAGCGAGCAACTGGAG
R:
ACATGGTGTTGAAGTCCTGCA
Band lengths:
346-1408
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development