MmuINT0090892 @ mm10
Intron Retention
Gene
ENSMUSG00000026934 | Lhx3
Description
LIM homeobox protein 3 [Source:MGI Symbol;Acc:MGI:102673]
Coordinates
chr2:26202974-26204121:-
Coord C1 exon
chr2:26203950-26204121
Coord A exon
chr2:26203177-26203949
Coord C2 exon
chr2:26202974-26203176
Length
773 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGC
5' ss Score
5.66
3' ss Seq
GCACCCTGTGCATCCTGCAGGCG
3' ss Score
7.29
Exon sequences
Seq C1 exon
AGATCCCGATGTGTGCAGGCTGTGACCAGCACATCTTGGACCGTTTCATCCTTAAGGCTCTGGACCGACATTGGCACAGCAAGTGTCTCAAGTGCAGTGACTGCCACGTCCCTCTGGCTGAGCGCTGCTTCAGCCGCGGGGAGAGCGTCTACTGCAAAGACGACTTCTTTAA
Seq A exon
GTAAGCTGGCTGGGCTGCCGAATTGCTTTCACAGTTGGGGAAGAGTAGAAGAGGGCAGGGTTGGCAGAAAACAGGCTGCGGGTGAGCGCCATACCTAGGTCCCTACCCAAATAGGGCACCCTGAAGTCTGGCCAAGCTCAGGTTTGGGTTTCCCGTGACATCTTTAAAAATATTTTTTTATTTTATGTGTATATATGTGAGTGGCTACATATTCATACTGTGCACCGCATACATTCCCGGTGTCCTCAGAAGATTGAAAGGGCATCGGATTCCCCGCAACTGGAATTACAAATGACTGTGAGTGCTAGGAATGGAGCTCAGACCCTCTGGAAGAGCAGTCAGTGTTCTTAACCACCCAGCCCAGCCGAATCTGCAGCCCCAACATTATTACTTTTTACAGTAGTTTGTTTTATAATCCATAAAAGCAGTTGTTAGGTTAAAACAAAATTAACCCAAATTTGTAGAATTGTATGAGACTTACTCTCCCTCTTAAAATGTGTTTTTGTTCCTTAAATGTCTGGGATGTGGGAAGCTCAGGTTCTTGGAGCTGAGGGAACTGACTCAGGTAAAGTCGTGGCCCTCTAGACCCATCTTTCCCAACATCAAGAAGCAGATTTTGCTACCCAAGGTACTGTGGCTCTGCGGAGGCTGCAGGACAGACGGGGCTGATGGAGTCTTCCTGACCGCACCTCGGGCGCTGGGAGCTGGCTGCTTTGAGACCCGCTCCAGGCGAAGGAGCCCCTCCGCTGAGCCGCACCCTGTGCATCCTGCAG
Seq C2 exon
GCGCTTCGGGACCAAGTGCGCCGCATGCCAGCTGGGCATCCCGCCCACGCAGGTGGTGCGCCGCGCCCAGGACTTCGTGTACCACCTGCATTGCTTCGCCTGCGTGGTCTGCAAGCGGCAGCTGGCCACGGGCGACGAGTTCTACCTCATGGAAGACAGCCGGCTGGTGTGCAAGGCGGACTACGAAACAGCCAAGCAGCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026934:ENSMUST00000028302:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.014
Domain overlap (PFAM):
C1:
PF0041217=LIM=PU(94.6=91.4)
A:
NA
C2:
PF0041217=LIM=PD(3.6=2.9),PF0041217=LIM=WD(100=87.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGCACATCTTGGACCGTTT
R:
TGCTTGGCTGTTTCGTAGTCC
Band lengths:
345-1118
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