DreINT0038148 @ danRer10
Intron Retention
Gene
ENSDARG00000078904 | brd4
Description
bromodomain containing 4 [Source:ZFIN;Acc:ZDB-GENE-030131-267]
Coordinates
chr3:52941785-52942147:+
Coord C1 exon
chr3:52941785-52941922
Coord A exon
chr3:52941923-52942011
Coord C2 exon
chr3:52942012-52942147
Length
89 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAG
5' ss Score
6.38
3' ss Seq
GTATGTGTCGCCCTCTGCAGCCT
3' ss Score
8.06
Exon sequences
Seq C1 exon
GACTATTACAAGATAATCAAAAACCCTATGGACATGGGAACAATCAAGAAACGCCTAGAGAGCGCATTCTACACCAGTGCCCAAGAATGTATTCAAGACTTCAACACCATGTTTACCAACTGCTACATTTACAATAAG
Seq A exon
GTAGAGCTCAATGTTTCTGCTGCCATCATTGGTGATGGATTGGAGGGAATTTTGGGTGTGTGGTTAATGGTATGTGTCGCCCTCTGCAG
Seq C2 exon
CCTGGGGATGACATAGTCTTAATGGCCGAAGCACTGGAGAAGGTGTTCCTTACCAAGATTTCAGAGATGCCCCAGCAGGAGGTTGAAATATCCACCACGGCCGGCAAAGGTCGTGGCCGGGGCAGGAGGGATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000078904:ENSDART00000115117:4
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=0.435
Domain overlap (PFAM):
C1:
PF0043920=Bromodomain=FE(52.3=100)
A:
NA
C2:
PF0043920=Bromodomain=PD(11.6=21.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCATTCTACACCAGTGCCCAA
R:
CGGCCGTGGTGGATATTTCAA
Band lengths:
178-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]