MmuINT0090911 @ mm10
Intron Retention
Gene
ENSMUSG00000026890 | Lhx6
Description
LIM homeobox protein 6 [Source:MGI Symbol;Acc:MGI:1306803]
Coordinates
chr2:36090962-36091415:-
Coord C1 exon
chr2:36091320-36091415
Coord A exon
chr2:36091137-36091319
Coord C2 exon
chr2:36090962-36091136
Length
183 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGG
5' ss Score
6.92
3' ss Seq
TGCAGAGGCTGTCGTTCCAGGTG
3' ss Score
3.81
Exon sequences
Seq C1 exon
GTTATGCAGGCGCAGTTCGCGCAGGACAACAACCCGGACGCGCAGACGCTGCAGAAGCTAGCGGACATGACGGGCCTCAGTCGCAGGGTCATCCAG
Seq A exon
GTGGGGCTCCGGGGTCTCGGCCTTCAGGTCTAGGGTGAACCTTAGGGAAGCGCTGAAGCTCGTAGTGGTACGGATGGTCGCGCGTGCACGTGGCCGCCCCTCTCCAGTGTGGCCTAAGGACCCCAGTCGGCACGGGTTGACCCTTTTCCTTGATTACTGAGAGTGCAGAGGCTGTCGTTCCAG
Seq C2 exon
GTGTGGTTTCAAAACTGCCGAGCGCGTCATAAAAAGCATACACCGCAGCACCCAGTGCCGCCCTCTGGGGCACCCCCGACCCGCCTCCCTTCTGCCCTGTCCGACGACATCCACTACTCTCCGTTCAGCAGCCCAGAGAGGGCGCGCATGGTCACCTTGCACGGCTACATTGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026890:ENSMUST00000112961:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.551 A=NA C2=0.591
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(54.4=100)
A:
NA
C2:
PF0004624=Homeobox=PD(19.3=18.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGTTCGCGCAGGACAACAA
R:
CTCAATGTAGCCGTGCAAGGT
Band lengths:
258-441
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