MmuEX0026398 @ mm9
Exon Skipping
Gene
ENSMUSG00000026890 | Lhx6
Description
LIM homeobox protein 6 [Source:MGI Symbol;Acc:MGI:1306803]
Coordinates
chr2:35937470-35946656:-
Coord C1 exon
chr2:35946482-35946656
Coord A exon
chr2:35942888-35942991
Coord C2 exon
chr2:35937470-35939595
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
GTGTGGTTTCAAAACTGCCGAGCGCGTCATAAAAAGCATACACCGCAGCACCCAGTGCCGCCCTCTGGGGCACCCCCGACCCGCCTCCCTTCTGCCCTGTCCGACGACATCCACTACTCTCCGTTCAGCAGCCCAGAGAGGGCGCGCATGGTCACCTTGCACGGCTACATTGAGA
Seq A exon
GTCAGGTACAGTGCGGGCAGGTGCACTGCCGACTGCCTTACACCGCGCCCCCTGTCCACCTCAAAGCTGATTTGGACGGCCCGCTCTCCAGCCGGGGTGAGAAG
Seq C2 exon
GTCATCCTTTTTCAGTACTAACGCTGCCGGCGCTTGCACATCTGTCCATGGGCACCACACAGCTGCCCCTCAGCCGCTGAGATCCAGCATCCAGCTGTGGCCAGGGATCCACCACCTCTGTGTACACCCTCACCCGCTGCTGTCCTGCCCTCTGCCAGTGGCCCCATCAACCCAGGCCTGGTCTTTCCCTCTCCTGCTGAGAACCAGAACCCACCAGGAGCAGCAGAGTCCCTCTCTGGGAAGGCAGGCTCCCTGAAATGTGGCATCAGCATGAAAACAAGCAGCCTGTCTTTCCTCATTAACTGGGAGTCCCACTTACCTACTGTCAGCTGATCACAGCAGCAATGGCTAATTCAGTCCGAGTCAACAACAGCCTCCTACTTCACAGGTTCTCTTCTCCCCCACATTGGCCTTTATTTACTACTTCCTTGGAACCATCTCCAAATTCCAAATAGCCAACAACCCCCAACATTATATACTCTGCTGCTTTTGTCTGGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026890-'10-14,'10-13,12-14
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=0.585 A=0.143 C2=0.137
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:
ACCTTGCACGGCTACATTGAG
R:
CTCCTGGTGGGTTCTGGTTCT
Band lengths:
242-346
Functional annotations
There are 1 annotated functions for this event
PMID: 10393337
[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
- Pre-implantation embryo development
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types