MmuINT1022212 @ mm10
Intron Retention
Gene
ENSMUSG00000026934 | Lhx3
Description
LIM homeobox protein 3 [Source:MGI Symbol;Acc:MGI:102673]
Coordinates
chr2:26203950-26206575:-
Coord C1 exon
chr2:26206345-26206575
Coord A exon
chr2:26204122-26206344
Coord C2 exon
chr2:26203950-26204121
Length
2223 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGT
5' ss Score
7.07
3' ss Seq
GCTTATTCTTGTATCCACAGAGA
3' ss Score
8.44
Exon sequences
Seq C1 exon
AGAGGCCTCCCGTGGGCACAGCGCCCAGCAGCGACACGAGTCGCTCCGACGCCAGCTCGGAGTCCCTGCAACGGTGGCCTCGCCAGACCCAGGGGAAGTTCAGGGTCGGAGGGCGGCAGCACCAGGCACCTGGCCCCATGGAAGCTCGCGGGGAGCTGGACCCGTCCCGGGAATCCGCGGGCGGAGACCTGCTGCTGGCGTTGTTGGCGCGAAGGGCTGACCTGCGCCGAG
Seq A exon
GTGGGTGCCCGACGGAGAGGCTGCACTGAACAGGCCCAGATGTCCTCGGCTTTTTCTGGCCCTTGTGCGGAGGCCAGCAGAAGCCAAGGTATCTGGACAAGGGTGTGTCTGAGGGGCTCTGACATGGCTAAGCAAAGGCATCTCAAACCTCCAAAGTGTGTGGCCCTCCTGGTGCTGTGTTGTCCTGGCTTTGGGAGCCCTTGGTGATCCAGGAACGGTTTAGGAGACCTTTTGCAGCTCTGAGCTGGCTGAGGCCCCTGAGCTGGAGGGAGCATGTGAAGATGTTTCAGGACTCAGGAATCAGGGAGCAGGAGTTTCTCCTTAGGAACTGCCTTCACTCAGTTCCTTTCCCCCCATTTTCAGCGAGATCAGGTCTGGGTCATGCTGAACTCATCTCCCCTGAGTCGAGTCTTAGTGTCTGCACCGGCAGTTTACCACTAGGCTGGTGGTCAAGACGCGATTACAGGGAAAAGTGGAACTTGTCCGGGCCCCCAGTTTCTTGATCGTACCAGTCTTTTTGCAGGGCTTTGGTTCTGGGGAATAAAAGCGCTCTCCGTTTTCAAGCTGAGAGTATAACAGGATAGGAAAAGAGGAAGTTAGGCTGGCAGAAGGTCTGTCGAAGCAAGTGGGAAAAGGATTCTATGCAGACTGGGGGTATCGGATATGGCCTACTTGCTTATTTATTTATTTATTTATTTATTTATTTATTTTCCAATGGTTTATGGGATGGGTTACCCGCAGGAGCTGGGAGGAAGAGATGGGAGGGGGGATGAGAAAGGGAGGGAGGAAAGCTTGGTAAGCTAGGCTCCAGAGAGAGTTCTGTGAGGCTTGCTAGAGCACTGTTGGCTCCCGAGGCTCCACTGGGCCCTCCAACTCTGTGTAGGAAACTGTACTGAGACTGGAGTTCACCATGCCACGTAAGCAAGAGGAGATCGAGGGTGGCTTCACTGGGAGGCTTGACGGTGGCGACGGCTTTTGTAGGAAGCGGGTGTCCCCGTGTCCCTGCTGTGGGCTTCTTGGCCGAGGCGCTGTCCGTGCCTGGGTGCTGAATTTGCAGTGTTTGGCCTGTCTAGCCACCTCACTCTCTTCTGGGTATCCTTGTGGCCTTACGACGGCTCTGGTGGTGCTCTGGTACAGCTACAGTCGATCTCCACGTCCACACTTGGAGATGTGGTTTTGCTCAGGGTGGGACAGCATCCATCGCAGGCTTGTGCCCAGTGCTGGAGGGAGGTGGGGCAGTCCTTTTCTAATTCCTCCCACCAGTGGAGGCCAGCCTGAAGCTAGTTGTTTGCAGCTAGAGATGTAAAGACACTTGTGTGGGTATGAAGTGAGTGGGCCCTGGGTGCTGCACATGCATCTCCTTTTTCTAGTAACCTTTCCTAAATGGCGGGGATCTCCTTATCCCATGAACCAGTCTTATCCCACCAGCCCCTAAGACGAGATTACACCTTTAGATTTTTCCCACCCAGTTTCCCTGAGGCCTGCAGTCTTTGGGGGATGAGAACTCAGATGCTAGAAGAATTGGTGGTGTAGAGAGTTGAAGTCATCTACCGTGCACTGCAGTTCACACCTTAACAGCAGATCTCTCACATATACATACATACATACATACATACATACATACATACATACATACATATGAAAGCATATGTGTGTGTTCAAAAAACCATAGCCAATGAACTCATAAATACCTGCTGCCATTCAAGTGAGGACAGCATCCACCTATTCATACCTCAGGCAGGGGCCAGCGCTGGACAGCCTCACTTTGCTGGAACTCTGCAAAGGCGATGAAGTTCCATGTGTGGTCTTTTGCCCTTGCTGATAAGGACATGTCTTTCTTTCTTTCTTTCTTTCTTTCTTCTTTTTTCCCCCGGCTTTCCAGATCACCCCAAGAGTGGGGTTTTCGTTTGAGATGGACATGACCTGTCTGGCACTGGCACTTTGTAGAGCTTACAGGACAGCCCAGTCACTTTCCTGCTGTGGACACCTTTCTATACCTATTTCACTTTCCCTTGGCTGCAGTGCGACTGAGGGATGCTGCAGGATACAGTACCTGAGCACTACTCTCACTGGGGAGCCCGGTGGCCCCAAATGCCTACAGGAGACAGTGGCAGAAAAGCCGATCCTTGCACACCCCTAAGGCCTGCAGGCTGACCAAGCTGATGAAAAGGCCATCGCTCATTGTTTGTGGTCCCATGACCTGGCTTATTCTTGTATCCACAG
Seq C2 exon
AGATCCCGATGTGTGCAGGCTGTGACCAGCACATCTTGGACCGTTTCATCCTTAAGGCTCTGGACCGACATTGGCACAGCAAGTGTCTCAAGTGCAGTGACTGCCACGTCCCTCTGGCTGAGCGCTGCTTCAGCCGCGGGGAGAGCGTCTACTGCAAAGACGACTTCTTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026934:ENSMUST00000028302:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.219 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0041217=LIM=PU(94.6=91.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
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
- 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