MmuINT0091658 @ mm9
Intron Retention
Gene
ENSMUSG00000038765 | Lmx1b
Description
LIM homeobox transcription factor 1 beta [Source:MGI Symbol;Acc:MGI:1100513]
Coordinates
chr2:33422405-33422849:-
Coord C1 exon
chr2:33422668-33422849
Coord A exon
chr2:33422483-33422667
Coord C2 exon
chr2:33422405-33422482
Length
185 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TCTCCCTCTCTCCGGGTCAGGTC
3' ss Score
9.93
Exon sequences
Seq C1 exon
TGAAGAGTGAGGATGAAGATGGAGACATGAAGCCGGCCAAGGGGCAGGGCAGCCAGAGTAAAGGCAGTGGAGATGACGGGAAAGACCCGAGAAGGCCCAAACGGCCCCGAACCATCCTCACCACACAGCAGCGAAGAGCTTTCAAGGCATCCTTTGAGGTCTCCTCCAAGCCCTGTCGGAAG
Seq A exon
GTGAGGGGTTCTGGGTGGGGCAGTCTGGGGCCAACGCCCCCCTTTTGCTTATTGTGGGTCTGTTCCTCCCCCATGACCCACTGCTATCACCAGGGGCAGGAATGTTCCTCCCACCCCTCAACCCAGCTGCCACCTTCCAGCTGCCATCTACACAGACCTGACTTGTCTCCCTCTCTCCGGGTCAG
Seq C2 exon
GTCCGAGAGACATTGGCAGCAGAGACAGGCCTCAGCGTGCGTGTGGTCCAGGTCTGGTTTCAGAACCAAAGAGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038765-Lmx1b:NM_010725:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.763 A=NA C2=0.192
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(47.4=44.3)
A:
NA
C2:
PF0004624=Homeobox=FE(43.9=100)
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:
AGAGTGAGGATGAAGATGGAGAC
R:
AGACCTGGACCACACGCA
Band lengths:
234-419
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: