HsaINT0091739 @ hg19
Intron Retention
Gene
ENSG00000106852 | LHX6
Description
LIM homeobox 6 [Source:HGNC Symbol;Acc:21735]
Coordinates
chr9:124976253-124976662:-
Coord C1 exon
chr9:124976562-124976662
Coord A exon
chr9:124976349-124976561
Coord C2 exon
chr9:124976253-124976348
Length
213 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCG
5' ss Score
10.05
3' ss Seq
CCGCCCTCCCCGCCCCGCAGGTT
3' ss Score
10.98
Exon sequences
Seq C1 exon
GGAACGGCCTCACGTTGGAGGGGGCAGTGCCCTCGGAACAGGACAGTCAACCCAAGCCGGCCAAGCGCGCGCGGACGTCCTTCACCGCGGAACAGCTGCAG
Seq A exon
GTACCGCTGCAAGCAGTGGGCGGCGGGGGCGGGGGCCGGGCCGAAAGTGGGCGGGGCCGACAATGTCTCCTGGCTCCGCCCCTCGGGCCGGACCCGGGTGGCGGGGCGGGGCCGCAGCTGCCTGGGGCGTGGCCTGTGGACTGGCGCCGCTGATTGGGCCGGGGTCTCGGAGTCTCTGCGTGCGAGCGCCTCACCGCCCTCCCCGCCCCGCAG
Seq C2 exon
GTTATGCAGGCGCAGTTCGCGCAGGACAACAACCCCGACGCTCAGACGCTGCAGAAGCTGGCGGACATGACGGGCCTCAGCCGGAGAGTCATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000106852-LHX6:NM_014368:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.824 A=NA C2=0.594
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(21.1=35.3)
A:
NA
C2:
PF0004624=Homeobox=FE(54.4=100)
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:
CTCACGTTGGAGGGGGCAG
R:
CTGGATGACTCTCCGGCTGAG
Band lengths:
189-402
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)