MmuINT0091659 @ mm9
Intron Retention
Gene
ENSMUSG00000038765 | Lmx1b
Description
LIM homeobox transcription factor 1 beta [Source:MGI Symbol;Acc:MGI:1100513]
Coordinates
chr2:33422191-33422482:-
Coord C1 exon
chr2:33422405-33422482
Coord A exon
chr2:33422258-33422404
Coord C2 exon
chr2:33422191-33422257
Length
147 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TCTGGACTGTTCCTCTACAGATG
3' ss Score
9.27
Exon sequences
Seq C1 exon
GTCCGAGAGACATTGGCAGCAGAGACAGGCCTCAGCGTGCGTGTGGTCCAGGTCTGGTTTCAGAACCAAAGAGCAAAG
Seq A exon
GTGAGAGGTCACGACTAATCCAGTGCTCCAGGGCAGACCTGGGAGACGGGGATGGGCAGGAGACAGGGAAGGGTCCAGATGTGGGAAGGAGGCAGAGCCTTGTGTTGGGACGGGGACTGAGTGGGCGTCTGGACTGTTCCTCTACAG
Seq C2 exon
ATGAAGAAGCTGGCCCGGAGACACCAGCAACAGCAGGAGCAGCAGAACTCCCAGCGGCTGGGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038765-Lmx1b:NM_010725:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.192 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(43.9=100)
A:
NA
C2:
PF0004624=Homeobox=PD(3.5=8.7)
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:
GTCCGAGAGACATTGGCAGC
R:
CAGCCGCTGGGAGTTCTG
Band lengths:
138-285
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: