MmuINT0090895 @ mm9
Intron Retention
Gene
ENSMUSG00000026934 | Lhx3
Description
LIM homeobox protein 3 [Source:MGI Symbol;Acc:MGI:102673]
Coordinates
chr2:26055732-26057782:-
Coord C1 exon
chr2:26057614-26057782
Coord A exon
chr2:26057032-26057613
Coord C2 exon
chr2:26055732-26057031
Length
582 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
TTGTTTTTGTTTTATTGCAGATG
3' ss Score
11.57
Exon sequences
Seq C1 exon
GTGTGGTTCCAGAATCGCCGGGCTAAGGAAAAGAGACTGAAGAAAGACGCTGGCCGGCAGCGCTGGGGACAGTATTTCCGCAATATGAAGCGCTCCCGCGGCAGTTCCAAGTCCGACAAGGACAGCATCCAGGAGGGACAAGACAGCGACGCCGAAGTCTCCTTCACTG
Seq A exon
GTAAGTTGGCCGCGTTAACTCGGGCTGGCCTCTGGCCTGATTCCTCTGGCTGCCTCTCTGGGGATGATCCACTCAGGCTCCCTGTTCCTGAGGCGACCGACCCGCTGCAACTCTGGAATTGTACAATACAAAGCGTCCTGAAGGCAGAGAAGATACTTCCATCCTCCTCTGAGGGACCCAACTCTTTTTCCACACCAGGAACGCCGCTCACATCCCTTAATACCCACTTCTGTTTGGGGCTGTATTGTCACCTCGGTTACTAGCACAGCCCCTGGGCCCTTAAATTTTCTCATCTAAAAAATGATTCCCTCCCATGCCCCCCTCCTCCAGGCTTGCCCCATCCTGGGCTCTGGCTGGGGTAGCAAGCCTCCTTGGAGGTGCAGCTGAAGGGGCTGTGGGTAGTGGAGTGAGGGGGGCAGGCAGAAAGCAGGGCTAAGTTCTGAGAGTGCTGAAGAGACTGTCCCTGACCCACTTGTTCCTGTTTATAAGACTGTCTCCTCTATTCAGTCAGGGTTCTGATGGAGGGGTGAGCTTCTCAGCCAAGCTCTCTGTTTTTTTGTTTTTGTTTTTGTTTTATTGCAG
Seq C2 exon
ATGAGCCGTCCATGGCTGACATGGGGCCTGCTAATGGCCTGTACAGCAGCCTGGGAGAGCCTGCCCCTGCGTTGGGCCGGCCCGTAGGAGGCCTGGGCAGCTTTACCCTGGATCACGGAGGCTTGACGGGTCCAGAGCAGTACCGAGAGCTACGCCCAGGCAGCCCCTATGGCATCCCCCCATCTCCTGCAGCCCCCCAGAGCCTTCCTGGCCCCCAGCCTCTCCTCTCCAGCCTGGTATACCCAGACACCAACTTGAGCCTTGTCCCTTCAGGGCCCCCAGGTGGACCCCCACCCATGAGGGTGCTGGCTGGAAATGGGCCCAGCTCCGACCTGTCCACAGAGAGCAGTTCTGGCTACCCAGACTTTCCTGCTAGCCCTGCTTCCTGGCTGGATGAAGTAGACCATGCTCAGTTCTGACCGAGGCCTCTGCTTCCCCTGGCTCTAACTCAGGGGTCTTGGTGCTGCCTCTGGGTGGATGGCTAGCCCCATCCCATGCTGTCCATTCCAAGGACCTCTGAGGGAAGGACAGGGTTCCCAAGTGAGAGAATAGGGACTGTCCCACTTCCAGGCTCTCTGGCAGCTCCCTGGGGCTGAGGGACTCCAAAGTCCTTCCTTGGACACAAGGGTGGCCTGCCTGGTGGCTGTCCACAAGCCAGTGACCATTTCTTGTAAGCATTTCTCTTTCTTTACTGGCCAGTTAACCCTTGCTGCTATTTCCGACAGGGCAGGAGGCTAGGCCTACCTAATGTCCTGGCAGAAAACAACAGTAACGCCTTGCTTCATCGCTTCTGATGGGGCTTGGTAGGAGACTGTGCTTGTGTCCTTCCTGGCCACTGACAAAACCTGGGAGCACACCTCTCCTCCTTACTGCTGCCAGCTCTCCCTCCCCGGAGTCTCCAGATCATTCTGTTCTGGAATGCCGTGTGTTGGGGGAGTAGAGCTTTCTGGAGCCCCTTCTCCAAGGCGTAGCCTCTAAATGCGAGAACAATTCCCCTTCGGAGGCACAGCCTCCCTCGGGTGCAAAGCAGAATTGTGCACCGTGAACAGACACCTTTGCCAAACAGACTGTGGTCCCGAGCAGGGTCGGGGGGTGGTTCCACTGGAGGAGGCTGGGCTGGGGGTCCTCCCAACCCAATCTGTCTCAGACACAAAGCTTGACCACGTGAAAGTTAAGATCATTCCTGAAAACAGGATCTTGGCTACCTGTTGGTTCTGTAAACACCCTGTAACTTTTATTTATTCCCTGGTGATCCGCTCTTTCCAAGACTTCAATAAATTTGTCAGTTTCAGTGCTAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026934-Lhx3:NM_001039653:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.684 A=NA C2=0.971
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=19.3)
A:
NA
C2:
NO
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:
GCAGTTCCAAGTCCGACAAGG
R:
CCTGAAGGGACAAGGCTCAAG
Band lengths:
343-925
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: