HsaINT0016646 @ hg19
Intron Retention
Gene
ENSG00000125492 | BARHL1
Description
BarH-like homeobox 1 [Source:HGNC Symbol;Acc:953]
Coordinates
chr9:135462716-135465640:+
Coord C1 exon
chr9:135462716-135462938
Coord A exon
chr9:135462939-135464614
Coord C2 exon
chr9:135464615-135465640
Length
1676 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
GCGTTTATTTCGGCCCCCAGGAC
3' ss Score
9.1
Exon sequences
Seq C1 exon
TGAAGGAGGAGGGCGACCGCGAGATCTCCAGCTCCAGGGACAGTCCCCCGGTGCGCCTGAAAAAGCCACGCAAGGCGCGCACGGCCTTCACCGACCATCAGCTGGCGCAGCTGGAGCGCAGCTTCGAGCGGCAGAAGTACCTGAGCGTGCAGGACCGCATGGAGCTCGCCGCCTCGCTCAACCTCACCGACACGCAGGTCAAGACCTGGTACCAGAACCGCAG
Seq A exon
GTGAGGCCTGGCTGCGGGGGTAGAGGCAGAAAGGGAACTTCCCCTTTCCTCACAGCTCCTGGAGGGGACCAGGAGTCTACAGGTTGGTGCTAAGGGAGGGCCCCAGAGCCTCCCCCATTCTGTAAAAGTGGGAAACTGAGTCCCTAAGGGGACAAGGCCTTGCCCAAAGTCCCCACAGCGAGGGACAGAGATGAGACTAGACTTGGTGTCCAGCGTCCAGTCAGCCCTCCCCCGGATGGGTGGACAGACACATAGGCCACTGAAAATCCAAGTCCTGCCCCAGCTCAGCCGGAGTGGGGGGAGGTCTGCCTGGAGCCCCCACCTGAGCCAGCGTGGGTCTTGGAAGCCCCAGGCCCTTGGAGGGGTGACAGTCTTGATGCCCAGGAAGCCTGTGAAGAGGACGGCCAGGCAGTGGCCCTTGGGGTGTTGAAGCCTGGCCCAGACCGGGCAGCTGCCGCAGGGGCCTCAGAGTTTCTGTGAGGCTCTTCAGGCCTCCCCAGCCTTTCTGGTCCCAAAACCCGAGGGGGGAACTGGCCAAGCCCTTGTTCCTTGGGGACAGGGTGACTGGGAAGTGGGTGTTGGGGCACCGGACTTGAACTCGTTTCCTAATTTCCCTCCCGAACACACTCACCAGACGTAGATGCAAATGTACAAACACAGAGGCATCCACACACTCAACCCAAATAGCCACACACCGACACACACATCAATACAACTTGCAGTCACACACGCACGCACGCTCAGCCCCACAGTCACTCGCACGCTCTTAGCAGAGGCAGGAATGGTGCTTTTCATAAACAAGCCTCAGAACACATCGCCCCATTAATAATAAATACTGATTACTGCTCCGGGCATCAATAATTAAGGCCTGTTACAGTAATTACACAATTATGATGATGATGAATAATTCAGGGAGGGAAACAGGGCTGGTGTGGCTGAGCCCACCTTAGTGGGACCCTGGCTGGTCCGCCTAGCCTCACCTGCAGGTGAGCCTAGGGTCCAGGCCTGACTTCTCCAAACCCCAGGCCGTTGGCTGGCCAAGGCCTCTGGACTTTGGGGCCAGACAGTGCGCAGGGCTCGCAGTGCGAGCCCTGGAGGATGGCAGGTGCAGCCTGCTCCAGCCGGCAGGGCGTGCGAGCCGGGAGCGGGTCCTCTCCGGTTGCCATTTCAGGCCTGCTCGCTTCTGCTAGCTTGCAGCCCGGCCAGCCTGCAGAGGAATCAATCGCATTCCCTTCCCTGAAGAGCACCCCCCCATCCCCTCAGGCCTCTCCAGGGTGATCCTACCTTCATAAAGAGGCACGCGCAGGGAGGAGCACCCCCTACCCAGCTCCAAGGGTTCGTTCTGCGATCTCCTGGGCAGGGTAAGGCGCAGTTAGAGCCGGGCTTTGGGGTCAGACAGCAGGGCTTAAAACCCAGGCTCCTTTTTGAAAACCGGCCCAGACCTCAGTTTTCCTCTCTGTAAAGTGGGGTAAGAGCCACGGAAGGCCGGTGGAAGATAAAAGGAGAGGATGCACGTAAGGCGTGCGATGGTGCCTGGCACTCGGTTATTTATTAACAAATGAGTACGATCCCTCTTGGCCTCCCTACAGGCTCTCTGGGCCAAGCAGTGGGGAGGGGCTGGGGTCGCTGGATGCCCTAGCCCTGATCCCGCCATACGCGTTTATTTCGGCCCCCAG
Seq C2 exon
GACTAAATGGAAGCGACAGACGGCCGTCGGGTTGGAGCTGCTGGCGGAGGCAGGCAATTACTCAGCGCTCCAGCGGATGTTCCCGTCGCCTTATTTCTACCCGCAGAGTCTGGTTTCCAACCTGGACCCCGGCGCGGCGCTCTACCTGTACCGCGGCCCCAGCGCGCCGCCGCCTGCTCTCCAGAGACCTCTGGTGCCCCGCATCCTCATCCACGGACTCCAGGGCGCCAGCGAGCCGCCCCCGCCGCTGCCCCCCCTGGCCGGCGTCCTCCCACGCGCCGCGCAGCCTCGGTGAGGCGCCCGTCGGCTCCGGGGCCTCCTCCCGCGGGCTCGGCGTGGCCCCTTCCGCCCGCCTTTCTGAGGGCGCAGGTTCGACGCCCTTTCCCGGGAGGGGGCCCTGCCCGGCCCTCCCTGGCGCCCCAGCCCAGTGCCCCCCGAAGGGCCAAATGCCAAGTCCACTGAGGCCCGGACCCCGGACTGCGTCTCCCCAGCCCCCCTCGGCGTCCTCTCTCGCGGCCGCTCTGTCCGGGAGCCATCCCCACCCGCCGGGTGTACATACGCGTCTCTGCCACTCCCCACCCCCAGCCTCTGCCGGCTCCCCTAGGCAACCCCTTTCTCCCCAGGAGCGGGTGCGGCTGATTCCCAGGCTTCGCTCTCTCCCACGCCCCTTCTACGCTCCAGGTGGAGAACAGCCCCTCTCCCCGCGCCCCCGCCAGGGAGAGAAGGGGAGTGCGGAGCCCCGTCTCCCTACCCCTCGAGCACCTGGGCCAGCGGCTGAGCTGTACATACCGTGTGCAAAGTGTATATGAAGTTATTTATTCGTGACCCATGAGCCCGTGACCGTGTCCGTGGATTAGTGAGTCTGTGGCCTGTGCCCTCCCCACTCCCAGGCGGGGCAGGAAGGGGCCAAGGGGGCTTGCCCACCCACCCCGACCCCAGCCCCCAGCCTCAGCCCCGGTCCGGGGGCAGCCAGGCCTCTCGGGTTCTCTCTTTTTTAAATGTCGAAATAAACTTCTTACAAATGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000125492-BARHL1:NM_020064:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.440 A=NA C2=0.194
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(89.5=68.0)
A:
NA
C2:
PF0004624=Homeobox=PD(8.8=5.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTTCACCGACCATCAGCTG
R:
AGTCCGTGGATGAGGATGCG
Band lengths:
358-2034
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)