HsaINT0016648 @ hg19
Intron Retention
Gene
ENSG00000143032 | BARHL2
Description
BarH-like homeobox 2 [Source:HGNC Symbol;Acc:954]
Coordinates
chr1:91177579-91180313:-
Coord C1 exon
chr1:91180088-91180313
Coord A exon
chr1:91178182-91180087
Coord C2 exon
chr1:91177579-91178181
Length
1906 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
GCACACCCGCTTTCTTTCAGGAC
3' ss Score
8.3
Exon sequences
Seq C1 exon
GGACAAAGGAGGAAGGAGACCGGGAGATTACGAGTAGCCGTGAGAGTCCCCCTGTGAGAGCCAAGAAGCCTCGAAAAGCAAGGACAGCTTTTTCCGACCACCAGCTCAATCAACTGGAGCGTAGCTTTGAGCGGCAGAAGTACCTGAGCGTGCAGGATCGCATGGACCTGGCTGCAGCGCTCAACCTCACTGACACCCAAGTCAAGACCTGGTACCAGAACCGCAG
Seq A exon
GTAAGGGAGGCACTTTGGGGGAGCAAAGGTGTCTGGCCATTTAAGTCATGATCATTATACCAATCTTCTTCCCTCCTGGCCTCCAGAGACTCTAAGGACTGAGAGTGACCCTGGAGTGGGCACTTGGGTGCTTTAAGGATGGGGCAGGGATGAGCCACACCCCCAAGGTGAGAGAGACCAAAGGGCAGCTGGAATTTGGACAATTTTGCAATTCTATGTGCTTTAACAGGTGCTACTTTTCCTCTGAAACCCGAGCCGCTGGAATTCCCCCCACTTCATCCCCAAATCAATGAAGCCACACCTTCTCAAATTGAGACATCTGTGCAGCTGACACTTAGGTCCAGAGAGCCTGCGCGGTGCACCCCTTGGGCCCACCCCAGGCTGGTTCCAAAGGTTTGTAGCCAACAACACGGCCCGGCCCAGCTATTGCTATTCCCACAGAGCTGTCCCACCAGCCTCGGCGTAAATGTCCTTGCTTTGGCCTGTGAGGCGGCTGGGAGAAGCAGGATCCAAGCCTTGGTCAGTGTAGCTGCAGAGACTAGGAGAGCCCAGCTGGGTTAGAGTAGGTTTGGCAGCCGCAGCCTGGAGAATCGGCGGCTGGCCAAGCATCCGGACAGGGAGAAGGAAGGAGTGTGGGTCTGTCCCCTGTACTGGCTGCCTCTGCTGTCTCAACATGGAGCTAGAGTGCTGCAGAGCCTGCCTGGCACTGCTCCTTCTCTAGAAGGGAAATTAAGAAAGCAAAAGTGACTGCCAGTGCTCGCAGGGCCACGAAGTGTAGAGTGGAACCTGGGCAATCTGAGGCAGAGGTTTTGCTGTGTTTTCAAGCCTGGCACTCATCTCCTTGTCTCGATTTTCTCTACCCCTCCTTTTCTCCCGTTTGTGTTCTAATCGTCCATAAGTGCGGTTGGAAATGCCCATCCACTTGTCATCTTTACCATAATTTTCTGTCTCATTACATACGGTTTCAGCCACCCTAATTCTGTCGGAAAACATTAGTGTCATTTGTAGCCAATTTAAAATGGGCGACATGTTTATTAATTTGGCTGGAGCTGCCGGGTATGGATGGCCCACCAGCCCTGCGTTCCTTCATAAGGTATTTGAGCAAACGCCCGCTCTCTTCTTCCTAGCAGGGTGTGCAGCGGGGGAGGGAGGAGACTGAGAAAAGCTGATCACAGGTTTTAATTGTTACTTTATCTCTGAGGAGGAAATACCTTGAAATGCATTCACCCCCACCTCAGAATGGCCAGGAGGTACTTTGCCCTTGGGAGAACCCTCCCTCAAATGAATTCCATTTTGAGACCTTGTTGCCATCCTCCCCTTAAGCCCCCTGCCCACTGTAAGGTCCTGTCAGGCTTATGAGAGAAATATGTCTCCCAGCCCTGGGGACTGAGAGGGGCTGGGGTCCCTGGCTTAGGAGTCTCTGCATCCCTTTGTTTACGGTTTCTTCTCTCACAGCCTGGCGGGGAAGGAAGAGGGGCTGAGAGCAGACTCTTTGGGATTGTTGGGAGTTGGGAGATGTGGAAGGGGAACTAAGGAAGGAGGAAAGTGACTGCTTGTGGAAGTCTCCTTTGGCCCTAAGGAAAGTTTCCAGAAGTAGCCAAACTACAAGGGGGGCGACAGCAGAGCAGAGGTTTAGGAAAAGGAAGCAAGGCCTGTAGGATTTCATTTGTGAGGGTCTCAGCCACTGAAGGTGTAATTTACAAAACTGGCTTTGGGTTTGGGTCTTTCTGGGAGCAAGGCTGGGGCAGGAGATGTGGTGCATTGCCAGTTTGAAGAGGTCTCTGAGTCTTCCTGCCACCCAGGGAGAATGAAGGAGGAGGCAGGAAGGGGCCAGAGAAGGGGCCGGGTCTTGGTGCCTGGACCATGCCCACAGCTGCTGGGTGCCTGCACACCCGCTTTCTTTCAG
Seq C2 exon
GACCAAGTGGAAGCGGCAGACAGCGGTGGGCCTGGAGTTGCTGGCCGAGGCAGGGAACTACTCGGCGCTGCAGAGGATGTTTCCATCGCCTTATTTCTATCACCCAAGCCTGCTGGGCAGCATGGACAGCACTACGGCGGCGGCGGCTGCCGCTGCCATGTACAGCAGCATGTACCGGACTCCTCCAGCACCCCATCCCCAGCTGCAGCGGCCCCTGGTGCCCCGTGTGCTCATCCACGGCCTAGGGCCTGGGGGACAGCCAGCCCTTAATCCATTGTCCAGCCCCATCCCAGGCACCCCACACCCCCGGTGAAAACATTGCAGCGAAGGCACTGCAATCCCTTCCCCATATCCCTGCCCAACCCGGACTGCTGCCCGTCCTCTCCCTGCTCCAGGCCACTAGGCCTCCCTTGCAGCCAACTCTGGAAGGCAGAGGAGTAAGAGAGGAAGATGCTTACCAGTGGGCAGGGGACCCCCAAAGAGGAGCCAGCCCTCTGCTCTCCATCTCCCCACCCCTAGAAACAGGGCTGGAAATCTCCCCCACAGCAGTGTGACTGGTGAAAATGCTGACCCCACACAGAGTGCAACCAGTAAGTGAAAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143032-BARHL2:NM_020063:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.566 A=NA C2=0.365
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(89.5=67.1)
A:
NA
C2:
PF0004624=Homeobox=PD(8.8=4.8)
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:
CTGTGAGAGCCAAGAAGCCTC
R:
GTCCGGTACATGCTGCTGTAC
Band lengths:
355-2261
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)