MmuINT0091655 @ mm10
Intron Retention
Gene
ENSMUSG00000038765 | Lmx1b
Description
LIM homeobox transcription factor 1 beta [Source:MGI Symbol;Acc:MGI:1100513]
Coordinates
chr2:33639489-33640511:-
Coord C1 exon
chr2:33640442-33640511
Coord A exon
chr2:33639676-33640441
Coord C2 exon
chr2:33639489-33639675
Length
766 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TCTCGCCCTGTGCGCTGCAGGCT
3' ss Score
7.91
Exon sequences
Seq C1 exon
ATGTTGGACGGCATCAAGATGGAGGAGCACGCCCTTCGCCCCGGGCCCGCCACCCTGGGGGTGCTGCTGG
Seq A exon
GTGAGTGCTGGGTCGCAACGCTCGAATAGTGCGGGTCAGGGGGTAGGGTTGTCCGTCGTGCCGCTGTGGATACCGGCGTGAGGGGCAAAGAATAAAGAAAATAGGTTTTCAGGACGTGGGGAGGGGGTCCGGACCCCTGGAATGACCACCGGAGGGGTAACAAGCACACCGAGACAGAGCTCCCTGAGGGGAAAACGTTCAGGGACGTCACCTAGACAGAGGACTGAACAGCCTCAGCCGTCACTCACACCGTCCTCTCCGGGTCTGGGTTCTAGTGCTGCTACACTGGACTGAGCTGGGGTGGGAAGCGGGTGGCAGGGATGCTGGAGAACCAAGTTGTCTCCTTAGAGCCCGGGAGAGAGGCCAGGTCACCTGGGGAAGGGGAGCTTTTAGAAGAGAAAACTATCCCCGGGTCTATCCCAACCGCGGTTCTTGGGGTAGAAGGTTCCAACAGCATCGTGGGGCGTGTCAGCCAGCGAGTGTCCTGGCCTCACCTCGCTGGTTGGGTTCCAGCCGGCCACCCCGCGCGGAGCTCCTTCTCGTTGGTAATAACACCATCCGCTGGATCTCCGCGAGCGGGGAGAGCGCAGCGCCCAGCCAAGGCTGCAGGCCCTCGGCCTCACGGCGCCCCAGCTTACGGAAAGGAGCGTGCTGTCTAGGGCTGCCGGGTCTCTGGCTCGCCGGCTGGGGTCCTCAGGCGACGGGAGGCGCTCCGGGGCTGGGCCAAGCGGCGCTGACGGCCCGGCTCTCGCCCTGTGCGCTGCAG
Seq C2 exon
GCTCCGACTGCCCGCATCCCGCCGTCTGCGAGGGCTGCCAGCGGCCCATCTCCGACCGCTTCCTGATGCGAGTCAACGAGTCGTCCTGGCACGAGGAGTGTTTGCAGTGCGCGGCATGTCAGCAAGCCCTCACCACCAGCTGCTACTTCCGGGATCGGAAACTGTACTGCAAACAAGACTACCAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038765:ENSMUST00000041730:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0041217=LIM=PU(94.6=84.1)
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:
TGTTGGACGGCATCAAGATGG
R:
TGTTGGTAGTCTTGTTTGCAGT
Band lengths:
256-1022
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