DreINT0038117 @ danRer10
Intron Retention
Gene
ENSDARG00000006527 | brd3a
Description
bromodomain containing 3a [Source:ZFIN;Acc:ZDB-GENE-030131-6141]
Coordinates
chr21:18235967-18236923:-
Coord C1 exon
chr21:18236568-18236923
Coord A exon
chr21:18236105-18236567
Coord C2 exon
chr21:18235967-18236104
Length
463 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
ACTTTACTTTTTATGTCTAGGAT
3' ss Score
8.62
Exon sequences
Seq C1 exon
AGGTTGAAGGTTGGGTCCTGCAATGGGATATGGTCCCTCTCAGATGACTGAAGAGCTAAAAAAACAGAAAAGCATAAAAAAGGCACTCTGAAAATAAGTCTTTTGCAGAATAAAAAAACCTTTCCCATTAAGCAGTTTTTCCCCTCTTCACCAAAATGTCAGCTGTCACTTCCGCAACCCCAGAACCTCCTGCAGCCGCAAACCCTCCTCCTCCAGAGGTGATCAACCCTACCAAACCTGGCCGCAAGACTAACCAATTGCAGTACATGCAAAATGTTGTTGTCAAGACGCTGTGGAAGCACCAGTTTGCATGGCCATTTTACCAGCCAGTTGATGCTGTTAAGCTTGGCCTTCCG
Seq A exon
GTAAGTAAATGTGTGTTAGACATAATATAATTGTTTTAGCATCCATCATTTTCCATATTTAAACTAGCTTTTTTATCATGGAAGCCTGTATTTTGCGGTTGAAAAAATTAGGTTATTCTGGCTTTTTTAACTTAACAGTTATCAAACTCTCACAATTGCAAATGCACATCTCACAGTTTGTATTTATCTTGTCAGAACATAACATTTCTAAATTTTCAATTGCAAGTTAGCATCTGTTGTATCTTGCAATTTGAGATTATATGTTGCAAGTTTCAGTAAATTATTGCTTGCAATTGCATGTGTTTTTTTTTTTTTTGCTTTTTAAATTATTGTTTAATTTTTTAATAACCCCTCATCAGAGTTGTGATATGAGGAAGAAGGTCAGCTAGATGAACCCTATGGTTAGTTTTGTTGTTTGTGAGGATGAAACTTTTTGTTGAAAAACTTTACTTTTTATGTCTAG
Seq C2 exon
GATTATCACAAGATCATAAAGAACCCAATGGATATGGGCACCATCAAGAAAAGACTGGAGAGCGTTTACTACTACAGTGCAAGCGAGTGTATGCAGGATTTCAACACAATGTTCACAAACTGTTATATTTACAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000006527:ENSDART00000135239:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.448 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043920=Bromodomain=PU(33.3=43.3)
A:
NA
C2:
PF0043920=Bromodomain=FE(51.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGTTTTTCCCCTCTTCACCA
R:
TGTGAACATTGTGTTGAAATCCTGC
Band lengths:
342-805
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]