MmuINT0090900 @ mm9
Intron Retention
Gene
ENSMUSG00000026468 | Lhx4
Description
LIM homeobox protein 4 [Source:MGI Symbol;Acc:MGI:101776]
Coordinates
chr1:157548824-157552002:-
Coord C1 exon
chr1:157551831-157552002
Coord A exon
chr1:157549747-157551830
Coord C2 exon
chr1:157548824-157549746
Length
2084 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CTCCGTTCTTTTGTCCACAGAAG
3' ss Score
10.27
Exon sequences
Seq C1 exon
GTTTGGTTTCAGAACAGAAGAGCCAAGGAGAAAAGGCTAAAGAAGGACGCGGGGCGCCATCGCTGGGGCCAGTTCTACAAGAGTGTCAAGAGGAGCCGGGGAGGCAGCAAGCAGGAGAAGGAGAGCTCAGCAGAGGACTGTGGGGTTAGTGACAGTGAGCTGAGCTTCCGAG
Seq A exon
GTGAGCAGGGCTGGAGGGGTGAGGCCGAGGCCCTAGGTGAGACCCTGGGGGACACGAATCCTGGCCCGCAGGAGGGATCTTTCTGATGATAACCTCTTGGCCCAGGATTTTCCGAGGCTTTCAGTAAAGGGTGGGAAGGGTGTTAGTGGCCCTTCCAAAAGGGGTGAGGAGTAGAGTACAAGAGAACAGTTGCTGGGATACGGAGGGCTTGGGGTCCTAGGGACCCAGCCTAGCCCGGGCCTGGCCCAGAGGCCCCTCCCACTTTCCTACTGTCGAAGATGCCCTCAGCATCCCACACAGTTATGAGCAGATGGCCCTCTCAGTCTTTGGCCCAGCCCTCCTGCACCTCTCCCTTTGCAGGGATACTGAGCCCCTCCCACGGGCCCCTAGAGTAAGCTGGTCCTCCAATCCTGGTTGCAGGAGGACATGCTCAACAGGCCTTTTCCTGGGAAATCAATAATGTGAGTGCATGATGGGGAACTGGCTGCGTTTCTGAGACCCCCCTCCCCCCACTACTCACTCCATCTGCCCTCTGCACACAAGCTTTGCAGCATGCGCTACGTTCAAATCTGTGCATCAGCAAAATTGCAAATTATCGCATGAGTGGATCCTCAGGTTGTTTACAAATAACCACGAGTGTTCTTGGTCACCGAGCCCTCAAATACAGAAGATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATAGTAGGGAGGCCAGAGTCCTGAACCAAGGATCAGAAACCCAATTTCTAGTGTAGCTCTGTCAAGGCCATCCGTTTCTCCTGCGCCTCAGTCTTTACCTGGGGAAATCTTTACCCATCTCACAGAGCTGTTATGGACATCTGTGGACACAACCAGCTGTGGATGTGTTTATGGAAAGATAAGCACTCCTCTGTACATGATGATAAATGGATGGCATGGCTGTTCCCATAGTAGCCTAGCATAGGGACGGCAGGTACCAGGCGAAGGGCCAACTCAGTCATTTTACAGTGGAGGAGTCTAACCTCCACCTTCTTCCTGCTCCCTTGGAATGACACGTGCTCCCTCTTTTGTAATATTTGTGAGTGGAATGTGGGGCTGAGAGAGACAGAGTGTTGAAGTCTCATCACAGTGTGCCAGGCCAGGTAGACGTGGGAAAGGAGACTGGAGAAAGTTGCTCAAAGCTGTGAAATCTCTGAACACAGCCCAAACTCTTAGGACACAGTGCTTAGGACCCAAGGAGGGCCAAGGAGATTTGTGCCATTGCCAGGCCTTTTGGCAAGATTGGGAAAACAGGTTAATCCCACCTGAGCTGCTCCAATCCATACCTGGAGCACAGAGGAGCACTAACTCTCATTTCTCTTGGGTACAGGCGGGCCTCTGGGTGTAACATGTTCTCTCTGGGTAATACACAATCTTGTAATTCTTAAGACTCAACCTGCTCGCCTCTATTCGAGAGAGAAATTCTTTCAGCAAATTCCATTAGATCCCCTTAATGAAATTCTTCAAGAAACCAGAAGGTCCATTTACCTTAATCCAGTCATTCTTTATCCTCAGTAAGTAGGTTATTGGATATGGAAAGGAACTGAGTTCTTTGATATTGAACCCCATTTTTTGGGTGGATCAGGATTTAACGTACAGGCCTGAGAGTGGCTCCCAGCCATCTTTATCAAATGGGCCTGTTTCTCAACCAGGCCAGACAAGCACTTGGCTTGGTTTGAACGCCTTCGGGGTAAAATGGACCAGCATAGTTTCGATTTGTGAGAGAATGTGGCCCACCAAACCCTGGCAGGCATTCACACTCCTCAGGGTAGCCAGGGCATCTCAGAGCTCCTCCAGACCAACAGGCTCCCCAGCCATGGCACCTGGGGATTTAGATGCAGGCATTCCTTGTTCTCCCTTTGGTCTGGGTTGGTCTTCAGATGTCAGGCTGACATGTTGGTGTCTGACCTGTGCTTGGCAGGGAGACAGCTGCTGCCCGTGGGCATCCCTCCTGGTCGTTGTATTGCTGGTTTTAAAGATCAGGGACTGCAGAGTCCTGGGCACTGACAATAAATCTCCGTTCTTTTGTCCACAG
Seq C2 exon
AAGATCAAATACTCTCAGAGCTTGGCCACACCAATAGGATTTATGGCAACGTGGGGGACGTTACAGGCGGACAGTTAATGAATGGGAGTTTCTCCATGGATGGGACAGGACAATCCTATCAGGACTTGAGGGATGGGAGCCCTTATGGAATCCCCCAGTCTCCGTCCTCCATATCGTCCCTCCCATCCCATGCTCCTTTGCTCAATGGGCTGGATTACACCGTGGACAGTAATCTGGGCATCATTGCGCATGCAGGGCAGGGAGTCAGCCAGACACTGAGAGCCATGGCTGGGGGACCCACCTCTGACCTCTCGACAGGAAGCAGTGTAGGCTACCCTGATTTTCCAACTAGCCCAGCCTCTTGGCTCGATGAGATGGACCATCCTCCTTTTTAGACTTTCCTCGTCACCCTCCTTGTCCTCCTGGTATGAGAGAATGTCTTCAAGGATCAAAAGTACGCCAATGTGAATTTCCATTATTTTCAATGGAAGTCCTCCGCCGATTCCCAGGAGGCGGAGACCACACTAGGATACTGCTTTCTTGGGAAGAGACAGGAGAGCAGCCTCATCTCTACCACAGCACAGGGGTGGACAGCCTAGAACTCTAAGGATGCTGGCTTGTTGGCTCCCTCCCCTCCCGCCCTGCTTAGAGGCTTTGGCTGCTCAGTGCTTGGACAGCACAAGGTGACTGTGACAGGCCACCTTGGCCTTTGGGGACTCTGCTCCAGCTGGTGCATCTCACACTTGGTCTCCCAAATCATCCCTCTCACCAGAACCAGGATTCCCGTGGGGGAGGCACCATGGTGCCCCCCCCCCCCAGAATAATAAAATAGTTTCTGGACCACCTTGATTACACACTAATTTTCAAAATAAAGTCAGTTCTAAAGGCTAGTAAAATACTGATGCCCACAGTTTGATATTAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026468-Lhx4:NM_010712:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.626
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=19.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: