DreINT0038118 @ danRer10
Intron Retention
Gene
ENSDARG00000006527 | brd3a
Description
bromodomain containing 3a [Source:ZFIN;Acc:ZDB-GENE-030131-6141]
Coordinates
chr21:18235741-18236104:-
Coord C1 exon
chr21:18235967-18236104
Coord A exon
chr21:18235877-18235966
Coord C2 exon
chr21:18235741-18235876
Length
90 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
ATTTTTATTTGTTTTCTTAGCCA
3' ss Score
6.45
Exon sequences
Seq C1 exon
GATTATCACAAGATCATAAAGAACCCAATGGATATGGGCACCATCAAGAAAAGACTGGAGAGCGTTTACTACTACAGTGCAAGCGAGTGTATGCAGGATTTCAACACAATGTTCACAAACTGTTATATTTACAACAAG
Seq A exon
GTATGACTTGGCACAGACTAGTTTAAAACACAGTTTTGAGACAGAGGAAGCTTAGACAATTAATGTATATATTTTTATTTGTTTTCTTAG
Seq C2 exon
CCAACGGATGATATTGTGTTGATGGCACAAGCGTTAGAGAAGATCTTCCTTCAGAAAGTGGCCCTCATGCCCCAGGAAGAGGTTGAGCTGCTTCCACCTGCCCCGAAGGGCAAAGGGCGCAAACCAGCAGGGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000006527:ENSDART00000135239:3
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=0.413
Domain overlap (PFAM):
C1:
PF0043920=Bromodomain=FE(51.7=100)
A:
NA
C2:
PF0043920=Bromodomain=PD(11.5=21.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACCCAATGGATATGGGCACC
R:
GGGCCACTTTCTGAAGGAAGA
Band lengths:
181-271
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]