MmuINT0090898 @ mm10
Intron Retention
Gene
ENSMUSG00000026468 | Lhx4
Description
LIM homeobox protein 4 [Source:MGI Symbol;Acc:MGI:101776]
Coordinates
chr1:155705172-155710315:-
Coord C1 exon
chr1:155710113-155710315
Coord A exon
chr1:155705327-155710112
Coord C2 exon
chr1:155705172-155705326
Length
4786 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGC
5' ss Score
9.89
3' ss Seq
TACGGTGGTTTTCGCTACAGATG
3' ss Score
8.21
Exon sequences
Seq C1 exon
ACGCTTTGGCACAAAATGCACAGCCTGCCAGCAGGGCATCCCCCCGACCCAGGTGGTCCGCAAGGCTCAGGACTTTGTCTACCACCTGCACTGCTTTGCCTGCATCATCTGCAACCGGCAGCTGGCCACGGGGGACGAGTTCTACCTTATGGAGGATGGCCGGCTAGTGTGCAAAGAAGACTATGAGACAGCCAAGCAAAACG
Seq A exon
GTAAGCAGAGCTGGCCATGCTCATGCTCCGGTGCCTGCCTCTCTCCGTCCCTCTTGCCCAGCCCTCGGGACACTGCGGATGCTCAGCCTAGTCCAAGAATTGTCACCAGAGCTCCGCTCAGTTCTGAGCAATCTCCAAACCCTCAGACCTTGCTGGCTTTGTGAAGCATTAATAGAGCTGTAGTTATTGAGAGTTGCTAAGGTCCTTATGAAGTTGTGAACTCGGTGGTCTCCTGGCCTGGAGCACAGCTGGTGGGCTGAGGGGTGGCTGGGAGCTTGCTGTGGGAGTGTGTGGGGGGAGTATATTTGGGGTACATACCTCCCTTGTCATTTCATTCCTCACAGGATGCAGCCAACGAGAGCTAAAGGACTTGCAGGGTTGGCTTGTTTTCAGTTGTCTCCTTCTTCTCCTCAGACTGTGGCTCAGGGGAACTGACTCTTGAGTGCCTGAAGCCCTGAAGTTTGAGCGAGTGTGTCAGTCAGTCAGTCAGAGAAGTCACTGAGAGGAGCCATGTTTAGGGAGACTCAACAGTATGATGGCCTCTACCTCACCTCAAAGCCACAGCCCACACTGCAATGGAAACTTGCAGCTCAGTATAGGTTGAGGTCACCCCTCAGTGTTTCCCAGACACCCCTGGGAACCTGGCCTTAGCTGGACAGCCTGAGAATCTGCTGTGCTTGTCCTCTTTGTCATAGCCTCAGAGAGCAGAGGCCTTCACTGTCTGAACAGGGCTCAGACCCGTGCATGCCCCGTACTCTCCCCAGGAAGGTCAGTCCTGACTCTCACTTTCCTGAAAGCACCCCTGACTCTCGGCTTCTCCGTAACAGCTCTGCCAGTATCATGTCCTGCATCTTAATCTAGAATTGAACCAAACCCAATCTAGGCTTCTTAAGCCATGACTCCCAGAACCTCAGGGTCCTTTGCCCTTGACTACATTTTTATCAACTCAGGTATGTCTGTGGAAGGCAGCTCTGTGGATGGTCTGGGTGTGATGGAAGCAAACCACCAACCAACCAACCAACCAACCAACCAACCAACCAATTCCATTATTTCTTTCTAGCTCTTTTCTGGGCTCAGTTACCCATATTGTCTGGGTCTGATACTACATGGAGAAGTTAGATTTTTGTGGTGGGGAGCAGGCTGAGGTAATTCTTCAGGGCCCTGTGGTGAGTCAGCGAGGCCAACTTTGGTTTTGGCAGGATGGGACAGGAACCTCCTTTCTCTTGGGGACTCCTAGCTCTGGCCTCTCTTGGTGGATTGAAGACATTGGTCTTCTTCCTCCAGGACCAGAGACCTCTATAGATCCCACCCAAACCTCTGCCTTGATGTGCTCATTCACTCTGGTTCAGTGGTTCTGAACCTTCCCAATGCTATGAACTTCTAATACAGTTCCTCATGCTGTAGTGACTTCCAACCATGAAATTATTTTTGTTGCTACTTTGGAACTGTAATTTTACTACTGTAAAATGATTCATACTATACATATCTGTGTTTTCCAGTTGTCTTAGGTGACCCCCAAAAGGATTGAAACCCATAAGTTTCTCTAGCTCCTTAAAGCTCTGTGATGCTGCTTTGTAATCCACCAGGATGTCACAGAGGGTGTCAACACAGAGCTAGCAAGGCAATCTAGAACTCTGATGACCTCTATCAGACCTTCACAGAAGCAGTGCCTCTCCTGGGCCTGTCCTGGCTTGCATTGTCAAAGACCTCATGTTGACCTTGTGTTTTCTCAGCCCACAACCTCCTGGTGCTGTGGATGATCCCAGCGAGGAGGGAGACTGTCACAGGGGAGGCAAGAATGTCATCACAGACATTGTCATCTTATGGAAGGAGTTTGTCCCACTGTAGCCTTCTGTAGGACACTGCAGTAGGGTGACAGTATCATGTCCTGCATCTTTTTTGTTTTGTTTTGCTTTTGTTTTTGAAGACAGGGTTTCTCTGTATAGCTCTGGCTGTCCTGGAACTCACTTTGTAGGCCAGGCTGGCCTCGAACTCGGAAATCTGCTTGCCTCTGCCTCCTGAGTGCTGGGATTAAAGGCGTGCGCCACCACACCCAGCTCATGCCCTGCATCTTAATTCAGAATTTGGCCAAACCCAATCTAGGCTTCTTAAACCACCACTCCCAGAACCTCAGGGTCCTTTGCCCTTGACTAGCATTCCTAGGAGAAGAAGACCAATGGCCTCTGAGAGGCCAAAGCTAGGAGTCCCCAAGAGAGAGGAGGCCACAAGCCAAAGCCAAGGTTGGCCCCGCTGGCTCACCACAGGGCCCTGGAGAGTTGCCTCAGCCTGCTCCCCAACACAGAAATCTACTGGTCTTGGCACCCAAGGCTGGGTGGGCAGCTTACAGGCTTGGAGCTTCTCTGCCAAGTTGTATAACTGGCTAAGTCTCAGCCTTGTCACACTGGGGTGTCTCCTGGGGCTAACTAGGCAGTGGCTTATAAAGGGGGATACAAAATAAGAGCAAGGGCCTAGCAGAGAGAAATGTAGACAGGAAGTGAAGTACACTATAAGACTAAAAGCAGCCGAAGGTCCGGGTTCGTATTTCCCAGGTGTCCCTTGCCTCCAGCTGTCAGACAGGCTAGGACCCTCCCTCGTGTGCAGGGACCTTGACGTGGTAGGGGATGTTTGGCTGTTTTTAGTTGTCATTCCTTTCTGTTTTTCTAACCTCATTCCAGGCTCATAATTCCCTCCCTTGTGCTAAACAAAGGGTCTCCTATCAGCGATTTGCATAGGAGTAGGAATGGCTTTGTTCATTCATCTCATCTCCTTCGATATTTACATTTTCAATATAATGACCCTGCATTTTATGCCAGGGACAAGTTTTAGGAGACACTGCATAATTCAAAGTGAACATATGTTAAGGCTAATTTTCCACGGGAATTAATGCTATAAGTGTGTGTTGCTGGGGTGTATTCTGCAGTCACACCGATCTATAACCAAACTGTATTTTGCTTTAATGCTACTTTTTATTTTCTCAGCATTATCTCCAGTACCTTGCTGAATGCTCTCTCCTAAATTAACAGCCCGGGGTGTCATGGTCTTGCTTGGCCTTCTTCATCGTGTTTTTATCACATTTAACTTCCGCACCAAAGTTATTGATTTTTGGGTACATTTTTCAGCATGAGCACTGCCACCACCACTTAATGAATACTTGGATGACATTGTTATAGGATATAAAAAAGATTTTAAATTATAATAACAGCGAATGTTAAAATAACAGCATAATAGTTCCCATAATCACATGAAGAAAGTCCTGTGGATGTGGGCAGGGCTGCTGTACCAACCAGCCCCCACCATGGGGAAGGGCACGGACACGGGCTGTGAGAAAATGTGTTCTAATTCACTTGGCCAACCTGCTCTGAAACTAAATGACTCTCAGGAATTGGGTCCCCTCCCCTGCCACACATACATACACTGCCACACCACACACATACACCCTGCCATGTACATACATACACATACATCCTCCTATGCACACACACACACACACACACACACACACACACACACACCCTGACACACAATACCCTGACATAAAAACAGACACACCTTGACACACACACAAACACACAAACACACACACACCCCACACACTGTTTCTTTTGAGGAAGGGATTTTCGTGTTGGCCAGGCTGGCCTCCAACTCGTGGGATCTGGGACCATAGGCTTATACCTTTTGTTGTTGTTGTTGTTTCATGATTTGGAAGTTTTTACTTGAAGGTCATCTGCATATTTTGAAAGCACATCACCTCATTTATATAATTTAGACTTATATCATCAAACAGTGCTCTGATGTGAGCTCTATAAACCTGGTGGAAAGGGCTGAGCGGTGAGCTGACTCCCAGAATGTCCTAGAACTAGGGACTGAATGCATGTAAGTTTCATAGCAAACTTGTACACAGTAGGCACTTAATATATGTTGGCCATTATTGTTCCTAAATAAGAGCTTTTTTAAATGGAAAGGGAGAGGGGAAAAGGTGGGGAGAAAGGCAAGGTCACTTGTGAGGGCTCTGAGAACTGGGGGTGGGGGTGGGGGTCGCTTTTTTTTTCTTGCCGATCCTATTTTTAGCTTTCCCCCAGGCATGCTGGGCAAAGCCTAGTCTAAGGGCTGGCAGACAGACAAACTACACCTCGTTGTGAATCACTGATCCCAGGATGTCACTCTGTGACCAAATGTGACAACCCAGCTTTAACAAGAACTTGAGGCTGACTACTAGAAACCCACTGAAGACTTTTGCTGACCAGTGTGTTGCCCTAAACTAGTCCTTAACTAGTGCTTTTCAGAAAATCCGACTGTGACCCACAGCTTGAACCGCATTTGACTTTTCAATTAAGTGCCTGTCTATGCTGTGAAAGTTAAGCATATTTCATGGACCAGTGTGTGTTTTATTCAATTCGTCCTATGAGTTTTGAGAATTAAGCTGACTTCATGACTCCAGGGATAGGGGCAAACATGGATGAGGTGGAGGCTCCCCTCAGTTATGAGACCAGCTAGGCTGGCCGAGTCAACAAGACCTCGATGGGCCGACGGAGCAGGATGCCCTGAAGAGGTGAGGGCACAGGTTTCCTGAAGTAGATCAGAACAGACTATATCTTGGCTCCTTCCTTTGACAGCCTGAGAGGGTGTCTGAGCAGAGTATTCCCCAGGACAGTGTCCCTGCGTGGGGTGTACTCCCCCACGACACTGCCCATTCTTCCACCGAGGTTGTGTGGAGGAAGGAAGTGGGGCAGAGGATGCTCAGGCTACTTCTCCTCAGCTGACTGCATTACGGTGGTTTTCGCTACAG
Seq C2 exon
ATGACTCGGAGGCTGGGGCTAAGCGACCTCGGACCACCATCACAGCAAAGCAGCTGGAGACACTAAAGAACGCATACAAGAACTCCCCAAAGCCTGCCCGGCATGTGAGAGAGCAGCTCTCCTCCGAGACAGGCCTGGACATGAGAGTAGTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026468:ENSMUST00000027740:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.712
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.6=2.9),PF0041217=LIM=WD(100=87.0)
A:
NA
C2:
PF0004624=Homeobox=PU(77.2=84.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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