MmuALTA0010034-2/2 @ mm10
Alternative 3'ss
Gene
ENSMUSG00000026890 | Lhx6
Description
LIM homeobox protein 6 [Source:MGI Symbol;Acc:MGI:1306803]
Coordinates
chr2:36091606-36094433:-
Coord C1 exon
chr2:36094213-36094433
Coord A exon
chr2:36091707-36091760
Coord C2 exon
chr2:36091606-36091706
Length
54 bp
Sequences
Splice sites
5' ss Seq
ACGGTACCC
5' ss Score
6.32
3' ss Seq
CCCCACCCCGTCCTTTCCAGGCT
3' ss Score
8.83
Exon sequences
Seq C1 exon
CCGATTTGGAACCAAGTGCGCCCGGTGCGGCAGACAAATCTATGCCAGTGACTGGGTGCGGCGCGCACGCGGCAATGCCTACCACCTGGCATGTTTCGCCTGCTTTTCCTGCAAGCGCCAGCTATCCACCGGTGAGGAATTCGGCCTCGTTGAGGAGAAGGTGCTTTGCCGCATCCATTACGACACCATGATCGAGAACCTCAAGAGGGCCGCCGAGAACG
Seq A exon
GCTGCCACTAGAAGAGATGGGGACGCGTGGTCAGCCGCTTCTGTCGCCCCCCAG
Seq C2 exon
GGAACGGTCTCACGCTGGAGGGGGCAGTGCCCTCGGAACAGGACAGTCAGCCCAAGCCAGCCAAGCGCGCGCGGACGTCCTTCACCGCAGAGCAATTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026890-10-11,10-10-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.006 A=NA C2=0.835
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.4=2.7),PF0041217=LIM=WD(100=77.3)
A:
NA
C2:
PF0004624=Homeobox=PU(21.1=35.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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:
GAGGAATTCGGCCTCGTTGAG
R:
CTTGGGCTGACTGTCCTGTTC
Band lengths:
144-198
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types