MmuINT0091651 @ mm9
Intron Retention
Gene
ENSMUSG00000026686 | Lmx1a
Description
LIM homeobox transcription factor 1 alpha [Source:MGI Symbol;Acc:MGI:1888519]
Coordinates
chr1:169760677-169763025:+
Coord C1 exon
chr1:169760677-169760849
Coord A exon
chr1:169760850-169762947
Coord C2 exon
chr1:169762948-169763025
Length
2098 bp
Sequences
Splice sites
5' ss Seq
AAGGTATAA
5' ss Score
7.08
3' ss Seq
ATGTATTCAATTTCTTCAAGGTG
3' ss Score
6.95
Exon sequences
Seq C1 exon
GCAAAAGCGATGATGAGGAGAGCCTTTGCAAGTCAGCCCATGGGGCAGGAAAAGGAGCATCAGAGGACGGCAAGGACCATAAGCGACCCAAACGTCCCAGAACCATCCTGACCACTCAGCAGAGGAGAGCATTCAAGGCCTCGTTTGAAGTATCCTCCAAGCCCTGCAGAAAG
Seq A exon
GTATAAGGGGATGAAGTCAAGAGAAGGAATCAAGACCTCCTTGTCTGTATGCAGTGGGACTCCCTTGGGATATTAAAGGGCTGCGTGTGTGGGGGGGGAGGTCTGAGTGATAGGGAATGCTGCTCAGAGTCTGTGACAGTTATGAGCCCTGAGGAGGTTTCAAAGATAGCTAAGATATGGCTTGGGAAGTAATAGACTCTCCCCCAACTTTCTATGTGCTTGCCAACTCCTGGCTCACAAACACCTCCCATTTCATGAAGTGCAACAGGGAACAATAAATAGTAACTAAATCATCATGATATTAAGTACTAGTTGTGATATAAGCCAGATACCTAACAGATATTATAAAAATACAGTAGCTTGCAATGTGTGCTTTTTATGGTCGGGTTTTGGCTTATTCTCCTTGGTGTGTGGACTTGGGGATTCCCTGGGTAGAAGTCCACTCCTTCCCATGATATTTTCAATGGAAGAGATGCACTCTTGGTTTTCCACTCACCTAATGATGGGGATTTGGGTTGTGTTTTGTTGGGACTGTTTTGACTAGGGGTCTTGTGAACATTTATGGAAAATTACTCATTGACTTAATGAAAAAGTATTTTCCTTTTATGCCCCATTTTGGAGGAGAGGAGGATAAGACTGGGAGGGCAGTTCTGGTATCTATTACTTGGGTTCTAACAGCTGCTCCAGCTGTCTGCATTTTCCTAGCCACCACGGTGGGGACAGCAGAAGTAGTGAGTGAGCACCTGCCATTTTGAGGACATTCCTGGGGTTTGTGTCCACCTGCTTGTGCATCTCTGGTCCACACAGTAGGGAAAGAATTGGGTATTTGTTGAGCCATAATATATTCTGTCACAACTTTGATCTGGGAGATTTCCTCGTAGACTCTTTCCTTTCCTTGCCTTTGCCACTCCCTACAGTCTATGGGAGGTATAGGTAGGTAGTGAGATACCCCAAATAGGCTTACATGTGGACCATTTACAATGAGGAGGACATGAGTATATACCAGTGGCACACAAGGGAGAAAGCTATAATAACATAACAAAGAGGCTGCCAGGAGCTCTGGGAAAGGGCGAAGCCATTTCATCTGGGCATCCACCAGGCTTTATGGATCAAGTGGGCTTCTGATCTGAGGCTCTGGGACATGGATAGGGTTTCAACAGGTGGGAGGGCCCCTGTGTCCACTCCTTATCGTGACTTAGTAGATGCATGTGCCTCAACTACCTACCCTACTCCTCTCACTTCTGAGCTTTATCCCAATTGCGTGGTCAAGATGATGTGTTTTTTGCAGTCTTAGACCATTTAGTCTACATATTCAGGCTCATTCAGTCCTTCTTCCCTGAATCTGTCAAGAAGGCACAGTGTCTTAGGGTTCCTCTTACTATCACACTAACCCCTCACCATATGCCCAGATGACCTAGATAGCCAAACACATCTCCTTGTTATTTGGATCCCAACTGCCTTCATCTCCACATGACCCCAGTACATTCACCAGTGTTAGAGTTGTTCACCTGACTCTGCTCCATTCCAGATAGCCCTCATGTTTTATATTGCCCCCACCCTGGGAAGGGATCAGTCAAAAAAAATTAGTGAACATGAATATTCAGAAAACACACAAAGTTACTTGGAAATAGACAAAGGCAAAATTTTAAGTCAATGACACGACAGGAGGACAAGCGAGAACCATCTGTTTCTGCAGAGAGATTTTCACTTTAGTTTTCCTTAAGTCAATTAAAGCACATGAAAACCTACAACTAAAAAGAGGCCAACTCCAGTAGATCATATAAAGCCATACCTTCCGAGTACAAGAAACCCAAAGTTCCTCCTGGAAATGTGCATCTAAATAAATGAGCATCTTTTTCTTTCTCTACCTTGTGAAAGATGCCTTTTCTGCCAGAAAGAAGAGTTCTTGTGTTTGGGCATATTTGAACATTAATCATGATCTAGTCTCTACTTAGGAATGTGACCTATGCCCCCACCCGGCACCACCCAGGAAATGGTTTACCTCCTACTCTAAGCGGTCAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTATGTGTGTGTTATACTCATGTATTCAATTTCTTCAAG
Seq C2 exon
GTGAGGGAGACTCTGGCTGCGGAGACAGGGCTGAGTGTCCGTGTGGTTCAGGTGTGGTTCCAGAACCAGCGAGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026686-Lmx1a:NM_033652:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.552 A=NA C2=0.115
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(47.4=46.6)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: