MmuINT0091661 @ mm9
Intron Retention
Gene
ENSMUSG00000038765 | Lmx1b
Description
LIM homeobox transcription factor 1 beta [Source:MGI Symbol;Acc:MGI:1100513]
Coordinates
chr2:33420056-33420745:-
Coord C1 exon
chr2:33420602-33420745
Coord A exon
chr2:33420314-33420601
Coord C2 exon
chr2:33420056-33420313
Length
288 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACC
5' ss Score
6.54
3' ss Seq
GTCCCTTCTGCATCCCACAGGGA
3' ss Score
9.83
Exon sequences
Seq C1 exon
AGGTTCTGTCAAGCCGCATGGAGGGCATGATGGCCTCCTACACGCCGCTGGCCCCTCCGCAGCAGCAGATCGTGGCCATGGAGCAGAGCCCCTACGGAAGTAGCGACCCCTTCCAACAGGGCCTCACGCCGCCCCAAATGCCAG
Seq A exon
GTGACCACATGAACCCCTATGGTAAGCTGCCCCACCCCCCATCTGCCCCAGCACTGCCCTCTGTCCCTGCCTAGCCAGGCAGACAGAGGCTACGACAGTCCTTGCTGTCCAGAGCCAAGACCCAGGGCAGCTCACCCAGCACTGCCAGCCTGCCTCCCCCTGACGGGAAGCTAGCCCTAGCCAGTTGGCCTGCCCACAACCCCTGGCCATGGAGCCTGTAGGGCTGCCAGGACCCCCCTGGAGCCCTGAGTCACACCCAGCTCCTGATGTCCCTTCTGCATCCCACAG
Seq C2 exon
GGAACGACTCCATCTTCCACGATATCGATAGTGATACCTCCCTCACCAGCCTCAGCGACTGCTTCCTCGGCTCTTCCGACGTGGGCTCCCTGCAGGCCCGCGTGGGGAACCCCATTGACCGGCTCTACTCCATGCAGAGCTCCTACTTTGCCTCCTGAGAGCCAGCCGGGCCGCATGGACGCTTGGGCCTGGGCCTAGGGTGGAGCCACAGGCCTCTGCAGCCAGCCGGCCCCCCAGCCCACCACCCGCTCAGACTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038765-Lmx1b:NM_010725:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.959 A=NA C2=0.212
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTCTGTCAAGCCGCATGGAG
R:
GAGGCAAAGTAGGAGCTCTGC
Band lengths:
296-584
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: