MmuINT0091654 @ mm9
Intron Retention
Gene
ENSMUSG00000026686 | Lmx1a
Description
LIM homeobox transcription factor 1 alpha [Source:MGI Symbol;Acc:MGI:1888519]
Coordinates
chr1:169774763-169778864:+
Coord C1 exon
chr1:169774763-169774933
Coord A exon
chr1:169774934-169776731
Coord C2 exon
chr1:169776732-169778864
Length
1798 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
ATGTTCCATCTTCATTTCAGGTG
3' ss Score
10.32
Exon sequences
Seq C1 exon
CTCAGACAAATGGTAGTGGGAATGCGGGCATGGAAGGGATCATGAACCCCTATACAACGTTGCCCACCCCACAGCAGCTGCTGGCCATTGAACAGAGCGTCTACAACTCTGATCCCTTCCGACAGGGTCTCACCCCACCCCAGATGCCTGGAGATCACATGCACCCCTATG
Seq A exon
GTAAGAGGGATTCAGTCCCCAGAGGTCCCTCTCAGTTCACGCTTGTGGGCTTCTCATTTTTCCTTAAACATATCTACACATTTCCCAGAGACTTGCTGAGTTAACAAATATGAATACGTGTCCCACAAAATATTGCTGACACCACCTATCTGATGGGCACAGAGGATTCCTGAGCACATTCTATGGTAACATTTCCACGTGTCATCATTTTTGAGGCTCCTTTGTTGAGCTTTTCCTTGTCGACCTTGCCAATTAAGGCAATGTTCAAGGGATGTGTCCTGGAGTTTAGTGGGATGGAGTAAATGAGTATAGGGTACCAAGGCCATTACATGTTTACATTAAGAAAGGCAGTGTATGGCTTATACTATAGGTGACTTAATATGTGATACATGTCACAAGTTGTCCTGATGTTTATACAATAAAGTTGAATTCAGCAGTCTTGTCAAATGTAGTAGCAGAGACATAAGGTGTGCACTCTGCCAACTTCTTTCCTTTAGTTAATTTTTTGTTGTTGTTGTTGCTGTGGCCAGGAATGTGACCAATTGGTAAAATGCTTCTAACACATACATGAAGACAAAAGTTCAGGTCCCCAGCATTCATGTTAAAATCAGACATGGCTACAAATATCTGTAGCCCCAGTGCTTGAGGGGCAGAGACAGGTGTGTCCATGAAGACTGCTGGCCAACCAGTCTTAACAAACTTGTGACTTTCAAGAATAAGGAGGAGACCTGCTCAAGAAGATATCTGACATTAGCTTTTGTCCTCTACATGCACACACTCAAACATGTGGCCAACACACATCAACATATACAAGCACATTTGCCACACACACACACACACACACACACACACACACACACACACACACACACTTGTTGTTAAAGTCACCTTTACTTTGGTTTAGTCCAGCTTCAGCAAACACTTAACCATGGTGTTTGTGGACCCTCACTTCCCAACCTCAAGAACACGTACACTCTAGGTTTTTATGTGTGTCTCCCAGTGATGCCCATCCATTTCCTCTTTAGAAGACACATATAACACTCAAAACATATTCTCTGTCACATGGGAGACCAGGGAAGATGTGATTTTGTTGTTCATTTTGCAAATCCTTATGTCAATGACTTTAGCAAAATGAACAATTGAAGCTCAATGATAAGTTTTAGGTACTTGCTTCTGCCTCTCCAGTTGAACTGAAGTGCAGGTATACCCTGCCATGCCGCCCAGGTTGCAAGTTTTTGATTGGTACCTCAGCTGTGTTATAGTGTGACCCCCTGGTCCTTCTCTCCAGGGTGCAGTTGAGGCCAGGTACCTAACTTCCTTTGTTGTGAGGCAGAAATCTGGGGAGACAGAGAAACATTGGTACATCTCTGCTACTGGAAATGACCAATGTTACCAGCAAGATCAGAACTTCACTTGAAGAATCCATGTTCATTTCTTACCATCTGTCCTTGAGGAGCCCTTTGTGAGGCTGAGGACATTCAGAATCCCTGTCTATGTCCCTCCAGCCTTTGGAGATGAGTTCTGCCTACCCCGTGTTTACTGTGTAGATACCCTCACTGTGCATACCTTCACTCATGTGGCTTAATGTTTCCCAACTTTGGACAAGAGCTCTCTATGAGACCCCTAGCATCGTAACCTTTACATTGTTGTGTCTAGTTGTTCCCACCCCATAGCGCATACTTAGTAGGTCCTCATCCCTGGGATGTGTTCAAACACTTGTTGAGGTCAGCTAATTTCCTAGCATACAAGGGTGTTACTTCTTCCAGACCCTCATTGCCATGTTCCATCTTCATTTCAG
Seq C2 exon
GTGCTGAACCTCTTTTCCATGACTTGGATAGTGATGACACATCTCTCAGTAACCTGGGAGACTGCTTCCTGGCAACCTCAGAAGCTGGGCCCCTGCAGTCCAGAGTGGGAAACCCCATTGACCATCTGTACTCCATGCAGAATTCCTATTTCACCTCTTGAGTCTTCTCCTACAATTTTGTGACCTGGGCTCCCATATGGAACAACCATACTGTGTGAAGGGTTGCTGACTTTAGGATGGGGAGGCCAGAGAAGAGGTGGGCTGGGGAGGGAGGTTTGTTGGGGATGCTGTTGTTTAATTATATGGTGTAGCTCAGCATTTCCAAAGACTGAATACATTATGGATTGCATAGTTTAATGTTTCTAATAAGAGTCTTAGTGTTAGATATGAAGATGTGTTTATCATTAAGGGCAGGGTCTTTTAATATAGACATTCTCAAGCAAACTAGATATCTAGGGACTCCTAACAGCTTCCCACCGTTCTGGAGAAGTGCTTGTCAAGAGGTGCCGTATGTCTATTCATCTACACACCAATAGACAGACAGATTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGAGTGTGTGTAAAACCTTTCATACTTTATCATCAAAGTTTATTCCTAATTATAACAGACACCAACTGTACAGCAAAAGTAACTTTATTTTCAGTGTGAACTATATTTAAGGAAATGCTTGATGCACTTAAGTTATAAAATGAGATAATTTACTTTTATAAACTTTATTTTTAGTTTGGAGAGACTCATCGGCAGGGCAGAGAGAACTGTTCCACCGGGCCCCACAGCTCTGAGTGCTTGAGTTCACTCTGTGATCAGAGCATCATTGAGGTCTAGAATACAACTCCAGATGGCAGGCAGCATGCTATAGTGAACTCATGCTCACCCTGGTGTCCAGTCACTGGGCCTGAATGAGATTTTAGGCTTATTGGCATGGGATTGTTGGGCAGCATCAGCAAGGTTGTCCTTACCCCCACCCCCACCCCAGATTCAGCCTCGATGAGTGTGGATGAAGTTGATAGCCACACCTACCTCTCTCTCTATGAGTGTGGATGAGGTGGTTGCCACACCTACCTCCCTGGGGACAATAAGGCTCCATACCAGGACATGATCGAAGTTGAAACTAAAATAAATCTGATATGATTTAAAATATAACCGAGTCATGTACCTGATGATAGAGGATACCTGGGACCACAGAGCAGGAAGTTCTGGTACCCTAAGTCCTATCTCTCTGCATAGCCCATATGGCCACATGACAGAGACACAGCTCTGAGGGGGTGGAGACTACGCTCCATCTGAGAAGGTGGAAGAGGCGTGGTGGATGGAATTCTAGAACAAGTGTTGACTTGCACATCTGTTGTTTTTTTTTTTTTTGTTTTGTTTTGTTTTGTTCTTACTTTTTAAAAAGTCACTTCAACGTGACTGTATGCACCCCCAAAAGCCGGAATTACTTGTGATCTCTGTTTGTCTCTTTCTTGAGGGCCCATAATCTGGGGGCCTGCTCATAAACAGCCTCATGGAGTTCATAGAAGCAGAGGGGACCAGGCAGGTACCCAGGGCTCTTCCCTCCAACTCATGTTGCAGTCCCTGAGCACAGGAAGACCCAGTAGCCATTGTACACAGGGACAATCCCGTGCCCTGAACTCCATTGTATACAGGGACAGTTCCATGCCCTGATCTCCAATTACGGTGCTAGAGTGGGATCTTCTGTGTTAGGATCCTTCTGGGGAAGCAGAATGAGTGTAGGGGGAAGAAAGAAGGGCTCCAGTGAGAGGGGCTGTGACAGGCATGACGTCATGCCCGGGACCATCATCAGAGCCATGACTATGCCCACATATCCACTTCATTCTCTTTAAGGCCAGAGGAAGCATGTCCCTTAGTGGTAGAGTGTGTGTTGTGTGATTTTTGTGCTCTTCTTTATAATTTATACAAACCGTCAGGAAACCTGAACCAGTCTGTGGGCTGAGAATGAGGCGGGTGTAGGGGGCACAGACAGTGTCTGTGTGGCTGATTGGTTGAGGAATGTAGCAGATATGTGAATGAAAGCAAACAGAGATCCTTAATTCTACTCTCTAATGACATACCGAGATGAAATTAAAAGCCTCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026686-Lmx1a:NM_033652:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.793 A=NA C2=0.623
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
ACTCTGATCCCTTCCGACAGG
R:
ACAGCATCCCCAACAAACCTC
Band lengths:
357-2155
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: