MmuINT0090910 @ mm10
Intron Retention
Gene
ENSMUSG00000026890 | Lhx6
Description
LIM homeobox protein 6 [Source:MGI Symbol;Acc:MGI:1306803]
Coordinates
chr2:36091320-36091706:-
Coord C1 exon
chr2:36091606-36091706
Coord A exon
chr2:36091416-36091605
Coord C2 exon
chr2:36091320-36091415
Length
190 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCC
5' ss Score
8.63
3' ss Seq
GGCCCTTCTGCGCCCCACAGGTT
3' ss Score
9.04
Exon sequences
Seq C1 exon
GGAACGGTCTCACGCTGGAGGGGGCAGTGCCCTCGGAACAGGACAGTCAGCCCAAGCCAGCCAAGCGCGCGCGGACGTCCTTCACCGCAGAGCAATTGCAG
Seq A exon
GTACCCCGGGCAAGCCCCGAAGCGTGTGGGCGGGGCTTCGGAGTGGGCGTGGTTGTTCGGGACTTGTGACTCCGCCCCTTGTGCGGGGACCCGCGTGAGGCCGCTCCAAGGATGAAGCTGCCTGGGGCGTGGCCTCGGACCCTGAGCCTCTGATTGGGCGGAGGTCTCAGGGCCCTTCTGCGCCCCACAG
Seq C2 exon
GTTATGCAGGCGCAGTTCGCGCAGGACAACAACCCGGACGCGCAGACGCTGCAGAAGCTAGCGGACATGACGGGCCTCAGTCGCAGGGTCATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026890:ENSMUST00000112961:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.835 A=NA C2=0.551
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(21.1=35.3)
A:
NA
C2:
PF0004624=Homeobox=FE(54.4=100)
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:
GAACGGTCTCACGCTGGAG
R:
CTGGATGACCCTGCGACTGAG
Band lengths:
196-386
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