HsaINT0018488 @ hg19
Intron Retention
Gene
ENSG00000169925 | BRD3
Description
bromodomain containing 3 [Source:HGNC Symbol;Acc:1104]
Coordinates
chr9:136895446-136899951:-
Coord C1 exon
chr9:136899823-136899951
Coord A exon
chr9:136898828-136899822
Coord C2 exon
chr9:136895446-136898827
Length
995 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCG
5' ss Score
9.67
3' ss Seq
CCCTGCCCATGTCTCCACAGAGA
3' ss Score
11.13
Exon sequences
Seq C1 exon
CAGCAAGCGGGAAGAAACAGGCAGCCAAGTCGAAAGAGGAGCTAGCTCAGGAAAAGAAGAAGGAGCTGGAAAAGCGTCTGCAGGATGTCAGCGGGCAGCTGAGCAGCAGCAAGAAGCCCGCCCGGAAAG
Seq A exon
GTACCGCTGGCGGCCGCTGTGCCACCCCTCTTTAGGGGGGTGGGGGGTGTCAGCAGTAGGGGTTTGAGCATCGAGCAGGCCCACGTCTGAGTGTGGCTTACCTCCTGATGAGCTCCATGTTCTTAGACGAGCTCTTGAGCTCCTGAAACCTCCATTTCCTGGTCTGTCACTGGGGGTCATACCCCAACCCTGCAGGGAGGTGTGCACATGTCAAGTGTGTGTGAACACAGCCCATTCCAGGGCACCACAGACAGAGGACCCCCCAGGAGAGGGCTCTTGTGGGGCTGGACTGGGCAGCCCAGCCAGTGAGCTGGGCTCACCGTGAGCTTTCTGACTGTTCCCTGGCAGTGGCATCAGTTCCATGGCAGGCCGAGGTAGCAGAGGCGGGAGGCCCAGCCCCATGCCCTGCGCTTTGCCAGGTCCTTTGCTCAGGGGAGCCAGCATTTGAGCCCTTGCCTCCTTTTTCTGGACCCTGTTAGAGCACACATCTCTTTTCCTGGCTTCCAGGACACACATATGGGGGGGACAGTAGGGTCCTATCTGGACTGGAGCATGTTCTAGCTGGGGGCCATGGCCTTGCGACATGGTTTGCCCAGTGTCGAGACAGGGCCCATGACCCTGCCCGCTGAAGGGGTCTGTCTCCTGTAGTCACTCTTTGGACGCCCCAGGCAGAGTAAGCGCTCCAGAAACGCCAGCAGCTGGTGTTCCTGTCGCTGCTGGTGGCCATGTGACTGGTGGATGTTTTTGATGGGCAGCCTTTCTCGCATCCATCATTTCCTGTTAGTAGTCTGCATTCATTTTTTTCCTGTCTCAAGTATATTCAGATAGTCTTGTTGACCTGATTAATTTCAATAAATACTTATTAAACGACTGGGTCAGGAAGTGGGTGGGTCGTGGCACCCAGTGTGATGGTGTCACGCTGGCATGGACGACATGCCGCCAAGCGGGTCAAGAAGCGGGTGTGCGAGCGCATCTCCCTGCCCATGTCTCCACAG
Seq C2 exon
AGAAGCCCGGCTCAGCACCCTCAGGGGGCCCGTCCAGGCTCAGCAGCAGCAGCTCCTCCGAGTCTGGGAGCAGCAGCTCCAGCGGGTCCAGCTCTGACAGCAGTGACTCAGAATGAACTGGCTTCGGACAGAACAGGACAGATGGATGTCGCACACGCCGAGACTCTGCCGTACCCCTCTGTGGTTCATATTACTACTTCTGTTCCATGGTGTGCAGGTCTGCTTCTTAATTCAGTGTTATGATATCTTCCAGTTTTTGCTTTCATAGGTCAGAGATCTATCTTGTGTGTGCGTTAGACTTGATGAGAAGGTGTGAACTCTGCAGAAAGTCTCTTCTTCATCACTGAATTCAGTCACTTGGAGATGACAACTTCAAATGCTAACCCGATGACCCCAGAAAACCGTGTGAGATTCGTACCGAAGAACCTTGTGGAATCCCTTTGCTTAGGCCCAACCTGGTCGATAGCTCGAGAAAGAATTTTTTCCAAGGAAATGTCTCGGATATGGGTACTGTATTTGAAAGCTGTTAGCTTTGTCAACACGCATTGTCCTTGTCATTTGGGCCCCGAGCTCTGACCCTCGTGTCTGACGCGGCCACCTCTTTCTGGAGGGGCTGAGGACAGATGTGCCTGCTTGTGGAGACCAGGCTGGGCCTAAGCGAAGGGTCATCGCAGCCCCAGCCCGGAGCGTGGAGCCCTTGGGGGGTGGTCGGGTGGGATGTGCGTTCTCCGCTCGTGGTGATGTCAGGAGCTCCTCGGAGGGAACAGAGCGGCTGTGTATGCAGCCTGCAGGTTTCCATACACTGAAGCTTTTACCTCAACTTTAAAAAAAAAAAAAGAAGAAAAGATTTAAAAAAAAAAAAAAAGGAGACTTTTTTTGTAAGGTTCGGCAATTTTCTACGGAAGTCCAGCCCGCTGTGAGTCCCCGCCTGGCTAGCGCTGCCCCTGCTGCTGCTGCCGCGCCACCCTTGGGAACCACTTCCCGAGCTTATGTGTATATAAATAGTTATTTATTAACATCATTGGTCATTTTTAAAAAAAAGAAAATAAGAAAAAACCGCAGAAGAAATGCATTCACACAGTCGCAGAGATGCAGGCCTTGCCAGTGGTGTGCCGGGCGCGGGTCCTGTCTGGCGGCGGCCTGTCGTCTCCAGGTGCTAACTCCTGCCACCGCGCGGTGCTCACCCACGTCTGTTCGCGCGCTCGCCCCTGGGTTTGTTGGGTTTTTTGGTTTTTTTCTTTGTGGTTTTTTTTTTTTTTTTTTTTTGTATGAAACTTGGAGGCTTACAGGTATAGACAGCTTTCAGCTACAGCACATTCTAATTTTTTATTTTGTTTAGTTCTTTTGTATTCACTTCTGGTCTCTTTAAGACTGTTTTAAAAGAAATCAATTTAGGGAACCCCAGTTATATAATATAAACTTTGTAATCTGAGAGAAAAAATGTATAGTAAATCTAAGTCTTGATTTTTAACTTTCTATTGTAAAAAATAATAATATACAGAGTTTAATAGAAGGTGATGTTTTGGTTTTGTTTTCCCAGAGGCTGCCATATGGTCTTTGAGTACGGGGATGTCCCAAACTGGCCCACCAATGAGCATGGCGGCTCCGGCCAGGAATGCCAGAGTTAGCCTCCCAGGCTTGCGGGTGGACATGCCTGCTCCCTGCCAGCCTCCAGTGGCCTGGCCAGGCCCTCCCGAGCCTGTCTGCCCTCCCCAGGGGTGGAGGAGTCTCTGGGCCCCAGGAGGATTCCCTCCCGGAGACTCGCACGGTGCTCCCTGCTCACGCGTTGTCACAGTTAGTCCGGAAATGACTGAAACCAGGCATTCTCCCGGACCTCAGCGTGGGGGAGCCTCCAGGCAGACGCTGGGTATGGAGCTGTGGTGTGGTCTGTCCTGTATGGTGGCCAGTGCTTTCTGCCAGCATTTCTGGATGGATATAGGGACTATCATTAGTATCCTAATACACGGTGATTTTAAAACAACCATAAAATTGATTCAGAGTCCACTGACCCTTACAGATGTAGGTATACCCTTACTGGAGAGGGAACTCTGATGAGGAGATGCTGGTAAATTATCATTTTTTAAATTGCTGGTGAGTCTGACACTTGGTGAGTTTTCAGCCAGTTTGTTAAACTTTTAATTAAGTTTTGTTTATAATAAAAATATAAATGGATTTGAAAGTTTCCATTTTTTAAAGTTACCCTCGTTTTCAAAGGTATTTTCTAAACAGATCTTTAATGGACTATTTAAACCGAATTTAAGGAATTCACACACGACAGTTGACAGGTCTTCACGCAGGCTGGTTGGTAACGTGCTGCCAGCACAGGGCTGGGTGATACGTACACCCTAAGCCGGGGGTGCCTGGGGCTGGGGGGCGCTCCTTGCAATGCCCCTCCAGCCACAGGGCAGTGAGGTGCTGCCTGTGTGAGCCGTCGGGGGAGCGGCCGGCTGTGGGGGCAGCGCAGCAGGAGCATCGTGGGGCCTTTCCTTCTCGGCTGGTTCTCTGTGACGGTGGCGTCGGCTCGCCTCTGCTCCTTTCATCTAGAAAGAAGCCACTGACCCTGACAGCCCACGGCGGGTACACTGAGCAGCTGCATTGGTGCTGTCACTTTTTTAAGGCTTTCTGTCCAGACTTCAACACTGGTTTCTTTTCAGAGTTTCGAAGGATTAATGACTTCCTCAGCGCCCTTGCTGGCGGGCTGAGGGTGACAGTCACGTCCGTTTCTTCTGTATTAGAAGGCTGCGGTGATTCAATTAGATTGTCCCACTGCTGAGACCTGTAGGGCAGCTTCTAACATGCTTTTTTCAAGGGGAGAGGAGTAGTGACAAGTCGTGTGTCGGAATTGGATTTGAGAACACTCTGAATGACCCCTGGAGGCCGAGGGGGCAGGCTTCGGGCGTGAACTGAACTCCAGACCCCTCTTTGTGTTGGGCAGTGTCATCTTGCTTACAAACTGTAAGACACATTTTTTTGTGTGTTTGTTTTTGTTGTTGTTCTTTTGCAGCACTCACGCCTCTGACAGTCTTTTGGGAAAGAGTAACACCCACATACAGAATTTGTCACATCCAGAGTAGCACTGTTCCTTAATACTGGCATAATGCTTCCAGGAAGTTTTTCTTTTTTATATTTAAAATGTTACTTTTCTGTATGATGTGCATGCAAGTTTACCGTAACTTTTCTTAAACTTTTTAGTGCCGTTTCTAGTATATTCCTGTAAATGTCAGTTACTGAAAATGAGTCCAATGTAAGTAGTTTAGCTTGTTTATTGCAATGCTGGCCTCAACACAACAGAATAAAAATGGTAGAAAGTACTCTTTGATGTTTCTGGTAATCATGGACCCTTCTCCTGGGGCATTTGTTTTGTTTTCATAATAAAAAGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169925-BRD3:NM_007371:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF084185=Pol_alpha_B_N=FE(37.4=100)
A:
NA
C2:
PF084185=Pol_alpha_B_N=PD(32.2=94.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAAGAAACAGGCAGCCAAGT
R:
CAGACCTGCACACCATGGAAC
Band lengths:
342-1337
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)