HsaINT0091740 @ hg19
Intron Retention
Gene
ENSG00000106852 | LHX6
Description
LIM homeobox 6 [Source:HGNC Symbol;Acc:21735]
Coordinates
chr9:124975885-124976348:-
Coord C1 exon
chr9:124976253-124976348
Coord A exon
chr9:124976060-124976252
Coord C2 exon
chr9:124975885-124976059
Length
193 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
TGCCGAGGCTGTCGTTCCAGGTG
3' ss Score
5.71
Exon sequences
Seq C1 exon
GTTATGCAGGCGCAGTTCGCGCAGGACAACAACCCCGACGCTCAGACGCTGCAGAAGCTGGCGGACATGACGGGCCTCAGCCGGAGAGTCATCCAG
Seq A exon
GTGGGACGGGGGTGGGCGGGGCCTGGGGACCGCGGGCACGCCCCGGAGCTCGTAGCTGGGCTCGGCGCGGAGGGTGGTGCGTGCACGTGGCCATCCTTCTCCAGGAGGCGACGAGGCAGTCCCGCCTGGGGTCTCCCGGCGGCGCGTCCGACTCTTTTCCTCGAGGCTGAGGCTGCCGAGGCTGTCGTTCCAG
Seq C2 exon
GTGTGGTTTCAAAACTGCCGGGCGCGTCATAAAAAGCACACGCCGCAACACCCAGTGCCGCCCTCGGGGGCGCCCCCGTCCCGCCTTCCCTCCGCCCTGTCCGACGACATCCACTACACCCCGTTCAGCAGCCCCGAGCGGGCGCGCATGGTCACCCTGCACGGCTACATTGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000106852-LHX6:NM_014368:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.594 A=NA C2=0.619
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(54.4=100)
A:
NA
C2:
PF0004624=Homeobox=PD(19.3=18.6)
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGTTCGCGCAGGACAACAA
R:
CTCAATGTAGCCGTGCAGGG
Band lengths:
258-451
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)