HsaINT0018501 @ hg19
Intron Retention
Gene
ENSG00000141867 | BRD4
Description
bromodomain containing 4 [Source:HGNC Symbol;Acc:13575]
Coordinates
chr19:15378227-15379853:-
Coord C1 exon
chr19:15379716-15379853
Coord A exon
chr19:15378363-15379715
Coord C2 exon
chr19:15378227-15378362
Length
1353 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CCCTGTGTCTCCTTATCCAGCCT
3' ss Score
7.7
Exon sequences
Seq C1 exon
GATTACTATAAGATCATTAAAACGCCTATGGATATGGGAACAATAAAGAAGCGCTTGGAAAACAACTATTACTGGAATGCTCAGGAATGTATCCAGGACTTCAACACTATGTTTACAAATTGTTACATCTACAACAAG
Seq A exon
GTGAGATGTAGGGGTGGGTGTCCAGCTGCCCTGGGGAGAGAGGAGGGGAGGCGACGGCAGTGGGCATGTCAGGAGCCCGTGGGCAGGGGTGTTGGGTGTGGCTGGGCTTGGAGTCTGGCAAGAGGAGACCCTTGGAGGTAGAGGTAATGAGACCTGTGGTTGTTCCTGTGACTGGGTGTGGGCTTTTTTGCTGGGAGGAGGGTGCTGGCCATGTTGAACTTGCAAGCTGTCCTTGTTAGCCTGAAGCATGTGCTTCTGGTGCCCTTGGGATTTTGGTTCCTGAGCATGTCTAGTAGAGAAGGTGTGAGGAGAATAGTGGCGACTCATGACAAAGTCCATTTGGGTGATGTAAATTGTTAGGAAAGAGCCTGCTAAAATGTAGTTGTGCAGAGGTGTGCCCAAACAGAGACCTCCACGTGAGAGAGGGTGTGATGGGGCCGGCGCAGAGCTCAGTTGCTCTGTGGGTGATGGTCTGCTGGAACTGTGGACATGACTGTCAATAACTCTTGGCCATAGATGAAGTGTCCCCCCGATCCTACATGTAGACCTGAAGGTCACTTCCTAACCCCGTAGCCAAACCTTTCGGCTCGGCTGTGCCATGAAGCCAGATCATTTGTTTACAGTTCAGACCACAGATGTGATTAAAATCAACCCTTTCAAATAGAACGACTCTGGAGGGAGACACTATACAGAACTCAGCTTTTGACCTCTGCTGGTGTAGTGGGTAAAAATGCCCAGAAGAGATGGGTAGGTGAGTTTCTTGAAGTTTACTGTGTTTTTTAAAGTCTCAGCTCTCACCACTTAGGTTTGAGCAAAATGTGCAGACCAGGCTCTCAGTTTAGAACTGAGTGGGAACAGCATGTTATAGATGAGGTGACAGAGTGGGACCCCTCAACTAGTGTGAGATGTGCAGTGCCCAGAGTCCTGGTGAGCTGCCATGGGGGTACGTTGGGGAGCATTGCTGGGGCCCTGCTAATGTATCATGGCAAGAAATCCTGTGTCATTCACGTATTTCTGGTGAAATTGAATTGTGTCAAAGGAGGGCCCCTTTCAGTGATTGGCTGAGCTTGGTAGATGCTTAAGGCATTAGGATGGCTTCTCAGATAGGCCAGAGCTTAAAAGATGAGGGAGGTGCAGGTAGACAAGTGTAGGCTCAGCACACCTGTGGGAACACAAGCCTCTGTGATACCTGGTAGTGTAGCCATTGTGGCTCCTTTGGGTGCAGATCGGGGAAGGACCCGGAATACGACGCTTCATGTTTTGGGGGCAGGGGGTGGGTGGCATGGGGTGCCCTGTCTACAGAGGTGGGGAGGGGAGGGCCCTCTGACTCTACCCCTGTGTCTCCTTATCCAG
Seq C2 exon
CCTGGAGATGACATAGTCTTAATGGCAGAAGCTCTGGAAAAGCTCTTCTTGCAAAAAATAAATGAGCTACCCACAGAAGAAACCGAGATCATGATAGTCCAGGCAAAAGGAAGAGGACGTGGGAGGAAAGAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000141867-BRD4:NM_014299:3
Average complexity
IR-S
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(52.3=100)
A:
NA
C2:
PF0043920=Bromodomain=PD(11.6=21.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCATTAAAACGCCTATGGATATGGG
R:
CTGTTTCTTTCCTCCCACGTCC
Band lengths:
262-1615
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)