MmuINT0091657 @ mm10
Intron Retention
Gene
ENSMUSG00000038765 | Lmx1b
Description
LIM homeobox transcription factor 1 beta [Source:MGI Symbol;Acc:MGI:1100513]
Coordinates
chr2:33567148-33569282:-
Coord C1 exon
chr2:33569050-33569282
Coord A exon
chr2:33567330-33569049
Coord C2 exon
chr2:33567148-33567329
Length
1720 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
TTGGGTTGTATCCTCCACAGTGA
3' ss Score
6.24
Exon sequences
Seq C1 exon
GCTCTTCGCGGCAAAGTGCAGCGGCTGCATGGAGAAGATCGCCCCTACCGAGTTCGTCATGCGGGCGCTGGAGTGTGTGTACCACTTGGGCTGTTTCTGCTGCTGTGTGTGCGAGAGGCAACTGCGCAAGGGGGACGAGTTCGTGCTCAAGGAGGGCCAGCTGCTGTGCAAGGGTGACTATGAGAAGGAGAAAGACCTGCTCAGCTCCGTGAGCCCGGACGAGTCTGACTCTG
Seq A exon
GTGAGCCGAGGCTGGGATGGCTGCAGGACGTGGCACAGCGGGGTGCTGGAGCGCAGAGGGCGGGGCTTCTGAGATCCACAGACCCGCATGTCCGTGCATGGCCAGCCAGCATCAAGGTGTCACATCCAATGTCACATCCACCCTATCACTTATCTGGGTGCCAGCCCTGAGGTACACACAACTGTGTATCACACACATACCCAGGGTCGTAAAGACACTACCTCGTGTGCTTGTACTTAAAGTCATGTACTTACACACCCAAACACGCAAAGCTCCTCCTATGCACACACACATACATGTATATTCTTCATGCATCTGCACCTGACCAGCACACCCATGGGACACACACGCATGACTATATACACACGCACATGTGCTATACCCATGCATATGCTTGCTCTCTAGCAAGATCCTGAAGATTTGTCACTCCTGAGACTTGGACAGGGAACATGTCAAGATGGCTGGCCTGTCTCTGGAGGTACCCTAGGCCCACAGGCATGTCCTCTGTCCACGTGGGGAGTGTCTGAAATTGCCAGGGCTCCAATGTTTGGGCTTCAGTGTGACAGAGTCCTTGTGTATCTGCTGCTGGTCAGCCCTAGGCTAGACCCTGTAATAGCATCCCTGTGGCCACCTGCACTCCCATGGAAGGGAAGGCCACTGGCCCAGCTTACAGACATTGTAAGGCCACAGTCCTCCATGGGGCTAACCTCCAAAGAAGGTGAGGCTAGGGAGGGGACAAGTTCCAGTGTTGGGTGTCAGAATTAATGGTTGTTAGGAGGCTTGGCTATGTTCCTAGGTCTCTAAGGCCCAAACCCCTGGGGTCATCTTAGTGGTGTTGTGTGTATGGCTGGATGCACATGCTACTTCATGCCACATGTGTCTTAGCATGGAAGTGTCCCTGCCTGTGGGTATAGGCCTCTGTGAGCCTGCAATAGTAAACATCTCTAACAATACAGGTGTGTGCACCCATCAGTGAATCCACTGTGTGTGTGTACACATGCCTGCATGTCCTGGTCCTAAGTACCTCCTGTGAGGATGCCTGGTCCCTGTGTCCCTGGAAGCCTCAAGAAAGAAGGCTCCATCCATTCTTCTCTTTCACCCTGTCCCCAGCTAGCATGATGCTCAGAGGCCAGCAGGAGAAGGTGGCTTTCAAACAGGCTGAGGTGGGGAAGCCCAGGGCCAGCCTGGGCCACAGTTGCCATCTGTCTATTGCAGGAGGCTGCTGGCCTGCAGAGTCACACAAGAGCAGATCTGCCCATGTGTGTGAGCTCCAGAATGCTGCACGTGCTCTAGTGTGTGCCTCTTGCTTATTGTGGGGCCATTCCTCCTCCTCAACCCACTGCTATCACGGGGGCAGAAGTGTCTCTCCCAGCCCTCACCCCAAGCCTTGTGCACAGCCATGCATGTGCACCAGGGTACTAGGTCATGGTCTTCCTGACTGTGTGTGTGTGTGTGTGTGTGCATGCGCGTGCATGCGCGCATACACCTGTGAATGCTATCGAGGAACTTGTGGATCAGCAGGGTTAGACCACCCTGGGACCCCGAATGAGGAAGTGATTATATGTTGGGGCCATGGGACATGGTGAAGAAGGATCTATGGGCCTAGGGAAGGCTCTACATTATCCTGAGGACATTAGGAGCCATAATTGTCAGCAGAGGGTGAGGGAATTCTCGCATACAGGTAAGCTCCAACTGACAGGTTGGGTTGTATCCTCCACAG
Seq C2 exon
TGAAGAGTGAGGATGAAGATGGAGACATGAAGCCGGCCAAGGGGCAGGGCAGCCAGAGTAAAGGCAGTGGAGATGACGGGAAAGACCCGAGAAGGCCCAAACGGCCCCGAACCATCCTCACCACACAGCAGCGAAGAGCTTTCAAGGCATCCTTTGAGGTCTCCTCCAAGCCCTGTCGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038765:ENSMUST00000041730:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.108 A=NA C2=0.762
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.6=2.5),PF0041217=LIM=WD(100=74.7)
A:
NA
C2:
PF0004624=Homeobox=PU(47.4=44.3)
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:
ATGGAGAAGATCGCCCCTACC
R:
GATGCCTTGAAAGCTCTTCGC
Band lengths:
356-2076
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