HsaEX0035746 @ hg19
Exon Skipping
Gene
ENSG00000106852 | LHX6
Description
LIM homeobox 6 [Source:HGNC Symbol;Acc:21735]
Coordinates
chr9:124964856-124976059:-
Coord C1 exon
chr9:124975885-124976059
Coord A exon
chr9:124971893-124971996
Coord C2 exon
chr9:124964856-124967059
Length
104 bp
Sequences
Splice sites
3' ss Seq
AGGCATCCTCTCGTCCACAGGTC
3' ss Score
9.64
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
Exon sequences
Seq C1 exon
GTGTGGTTTCAAAACTGCCGGGCGCGTCATAAAAAGCACACGCCGCAACACCCAGTGCCGCCCTCGGGGGCGCCCCCGTCCCGCCTTCCCTCCGCCCTGTCCGACGACATCCACTACACCCCGTTCAGCAGCCCCGAGCGGGCGCGCATGGTCACCCTGCACGGCTACATTGAGA
Seq A exon
GTCAGGTACAGTGCGGGCAGGTGCACTGCCGGCTGCCTTACACCGCACCCCCCGTCCACCTCAAAGCCGATATGGATGGGCCGCTCTCCAACCGGGGTGAGAAG
Seq C2 exon
GTCATCCTTTTTCAGTACTAACGCTGCCGGCACTTCCGCATCTGCCCGTGGGCGCCCCACAGCTGCCCCTCAGCCGCTGAGATCCAGTGTCCAAGCTGCGGCCAGGAGTCCACCCACCTCCGCATCCACCCCCGTCCGCCATCCTGCCCACCACCAGGTCGGTTCCCGAGGCCTGGCCTTTCCCTCTCCTGCTGAGAACCAGAACCCACCAGGAGCACCACAGAGTCCTCCTCTTGGAAGGCAGAACTCCCTGAAATCTGGAATCAGGGTGGAAACAGCCTGTTTTTCCCATTTAAACAGGAGTCCTCTTCAACTTCAGCTGATTACAATAACAAAAGGCGGAATTGAATTGTGCGATGCCAACGGCCTTCTCATTTACAGGTTTTTTTCCCCCACATTGGCCTTTATTTACTACTTCCTTGGAACCATCTCTGAATTCTGAATAGCTGACAACCCCCAATGTTATCCACTCTGTTGCTTTTGTCTGGAAAACTCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000106852_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (No Ref, Alt. Stop)
Show structural model
Features
Disorder rate (Iupred):
C1=0.619 A=0.200 C2=0.250
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=18.6)
A:
NO
C2:
NO
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTCATAAAAAGCACACGCCG
R:
GCAGCTTGGACACTGGATCTC
Band lengths:
250-354
Functional annotations
There are 1 annotated functions for this event
PMID: 10393337
This event
[Negative results]. LHX6 splice variant with/without cassette exon HsaEX0035746 interacts with Ldb1 in co-IP assay performed on lysate from transfected COS7 cells.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- 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)