MmuINT0091652 @ mm10
Intron Retention
Gene
ENSMUSG00000026686 | Lmx1a
Description
LIM homeobox transcription factor 1 alpha [Source:MGI Symbol;Acc:MGI:1888519]
Coordinates
chr1:167832817-167840972:+
Coord C1 exon
chr1:167832817-167832894
Coord A exon
chr1:167832895-167840902
Coord C2 exon
chr1:167840903-167840972
Length
8008 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACC
5' ss Score
9.24
3' ss Seq
TGTGATCTTCTCTTTGTCAGATG
3' ss Score
9.01
Exon sequences
Seq C1 exon
GTGAGGGAGACTCTGGCTGCGGAGACAGGGCTGAGTGTCCGTGTGGTTCAGGTGTGGTTCCAGAACCAGCGAGCCAAG
Seq A exon
GTAACCTGCTTCTCATCTTTATCTGTCTTTGTCTTACTGGTTTCTTCCAACAACAGCCGATGGACATCGGACTTGCTGTCAGCCTTTCTAAGCTAACTTATGGGGTAGAGTCGTTCTCTTGATTAAAAACGCCTATCATCAGCAATTATTTCAGCCACAGCGCCTGGAGGAAGGGAGAAGCGAAGTGTCTGTGTTAGTGGTTAGTCAAACAGTGAAACAGTTGTTTTTGTTGTGGCAGGCAGAATGCATGTGTCCACTCCCAGCCTTCAGTGTCTGGCCTCTCTAACTCCAGCCTTAGTGTCCTAGGTAACAGACAAGTCCTGGGTTACTTATTTTCTTCCAGACTCTAAAAATATACATGCCCTGGCCATTTTCCCATAATCTTGGTTTTATTTATCCTTCTTTCTTTCATGTATGTTCATGGACATGGAGTGTACATGGAGTTATGTGCATGGAAGTGTGTGCATTTACACGAAGGCCAGAGGTCTTCAGGATAGTAACTCACCTTGGTTTTTGTTCTTTTGAACAGAATGTCTCTCTAGGACCTAGAGTTCCTCAATTAGTCAGATCCTGGGGTCCAGGCAGCCCTAGGCATCCTCTTTGTCCCCATTCCTCAGCACTGGGTAACAGTGCGTACCAATACTTTTTGCTCTAGTTCTTAAACATTGAACTCAGGTCTGTGCTTACTCAGCATCACTTTGCAAACTGAGCTATCTTCCCAGTCCTTAGATGGTGATAAATTACCCTTCTCATTAAGTCGCAATTCTGCAACAGAATTCCTCAGATCAGGGCTGTTGTTGGTGTGTTGCTATTCCATCAATAGAAGAATTCATGGTGCAGTTACTGTTCGGGAGCTCATGGGGTGTGCGTTCAACAAAGCAGGAGCACACTGAAAACTCTGGGGAATTGTATGGCCAAGGAATTCATTTTTCTAGTATCTCACTGTAGTGGCTATTCCTGGTTGTCAACTTGACAATATTTGGAATGAACTACAATTCGGAATTGGAAGGCTCACCAGTGACCCTTATCTGGAGGCTTGGAGATCCTTATCTGGATCTTGGTTTGAAGATCTTGAGCCATAGTGGCTATGGATTCCAGAAGATTGAATCTCCGAGTTTAAGGAACACACCTTTAATCTGGGCTACTCCTTTCATCTGGGATTAAAGGTGTGGTGGAACACACCTTAATCTGGGCTACACCTTCTGCTGGAGACAATATAAGGACATTGGAAGAAGGGAGTCTAGCTCTTGCTCCTGCTCCTTCGCCTGCTTGCTGCGTGAGACTGAGTAACTGCTAGATCCTTGGACTTCCATTCACAGCTGTGACTGAACGATTGTTGGGAATTGAGCTGCCGACTGTAAGTCATCAATAAATTCCTTTATTATCTAGAGACTATCCATAAGTTCTGTGACTCTAGAGAACCCTGACTAATACAGAAGTTGGTACCAGGAGTGGTTCTAGAGTAACAGAAGTACAAGGATGAATCTTTTAAAATTCTGGAATTGGCTTGTTGATCCACCAGCACTTTCAACTATTGAAACCTCTACAGATTCTCTCCCTCCTGGGAGCTCAGAGAATTTTGAAGACCCATGGTTGAAACTATATTCCGAACTTAAAGAAGCTAATGCCCTTGATTTTCTTAATGAATTAGGTGATTCAGTGCACAAAGCTTTCTACAAGATGGGGAAAAAATCGAAAAATGATTTTACTGGCTGGCTGCTCTTAGTATCTGTGGAAAAAATGATGAATGAAAGGAAGGAGTTGTGTGATAAAATCGAAAGGCTCCAGACACAAGTAAACAATCTAAAAGTTGCTAAGTGTGTCCTTGAGGAGAATCTTCTCTCTTGTAGCAATAGAGCTCAAGTTGCAGAAAATCAAACGGAAACTCTCATTGTAAGATTGGCTGAACTACAGCGAAAATTCAAGTCTCAGCCTCAGAGTGTGTCGACAGTTAAAGTAAGGGCTCTAATTGGCAAAGAATGGGATCCTACAACATGGGATGGGGATGTGTGGGAAGACCATGTTGAAGCTGAGAATTTTGAATCCTCAGATTCTCAAGGGTTTGCCCCACCTGAGGAAGTAGTACCCTCAGCCCCACCTCTTGAAATAATGCCTTCCCCACATGAGGAAATTAATTTTGCAGAGTCTGCTCACGGCCCACCAATAGTTTCTTCTAGACCTGTAACCAGACTCAAAGCAAAACAGGCTCCTAGAGGGGAGGTAGAAAGTGTAGTCCATGAGGAAATTCGCTACACTACTAAGGAGCTTAATGAGTTTGCTAATTCATTCAAGCAGAAACCTGGTGAATATGTGTGGGAATGGATTTTAAGGGTGTGGGATAAGGGTGGAAGGAACATAAAACTAGAGCAGGCTGAGTTTATTGACATGGGTCCTCTGAGTAGAGATTCTAGGTTTAATACGGAAGCTCGCATAGTTAAAAAAGGTGTCAAAAGTTTGTTTGAATGGTTGGCTGAGGTGTTTATCAAAAGATGGCCTACTGGAAATGACTTGGAGATGCCTGATACTCCATGGCTTAGTGTTGATGAAGGGATTTTAAGACTTAGGGAAATTGCAATGCTAGAGTGGATATATTGTGTAAAGCATAATTGTCCACAATGGGAAGGTCCAGAAGATATGCCTTTCACCAGCTCTATAAGACGCAAATTGGTGAGAGGGGCACCAGCACATTTGAAGGGTTTTGTTCTTTCCCTTTTCCTTGTGCCAGATCTTAGCATTGGAGATGCTTCTGCTCAATTAGATGAATTAAATTCACTGGGTTTAGTTGGATTCCGAGGTAACAAGGGCCAGGTGGCAGCATTGAATCGCCCGAGACAAGGTGATTCTAGTTATTATAATGGACAGCGTAGACAAAAGAATGTTTATAATAACATACCCAGTAATGGTCAGCACAGGAGAGGTGAAATTTATAATGGCATGACTCGGTTGGACCTTTGGTACTGGCTAACCAATCATGGTGTTTCCAGGAATGAAATACATAGGAAGCCTACTGCATATTTGTTTGATCTGTATAAGCAGAAAAATTCTCAAACAAATGAAAGAAAGGCTACATTAGATCGTGGTAAACAGCCAAATGAAAGAAAGGCTACATTAGATCGTGGTAAACAGCAATCTCGGCCAGTGAATCAATTTCCAGACTTGAGACAGTTTGCAGATCCAGAACCCCTTGAATGAAGGGGTGGCCAGGTTCCGCTGAGGAAGGATCTTGATAAGACACTCAAAGGTTTTGCTGTTACCCTTTCTCCAGTTCTTCCCCAGAGGGACCTACGGCCTTTTACAAGGGTAACTGTACACTGGGGAAAAGGAAATAATCAGACTTTTCGGGGTCTGCTGGATACTGGTTCTGAGTTGACACTGATCCCAGGGGATCCCAAGAAACATTGTGGCCCTCCAGTTAAAGTAGGGGCTTATGGAGGGCAGGTGATTAATGGAGTTTTGACTGATGTCCGACTCACAGTAGGTCCAGTAGGTCCCCGGACACATCCTGTGGTGATTTCCCCAGTTCCAGAATGTATAATTGGGATAGATATACTCAGAAATTGGCAGAATTCTCATATTGGTTCCCTGAACTGTAGAGTGAGGGCTATTATGGTTGGAAAGGCCAAATGGAAGCCTTTAGAGTTGCCTTTGCCAAAGAAAATAGTGAATCAAAAACAGTATCGTATTCCTGGAGGCATTGCAGAAATTACTGCCACTATCAAGGACTTGAAAGACGCAGGGGTGGTGGTTCCCACCACATCTCCGTTTAACTCTCCTATCTGGCCAGTGCAGAAAACAGATGGATCATGGAGAATGACAGTTGATTATCGAAAACTAAATCAGGTAGTAACTCCAATTGCAGCTGCTGTACCAGATGTAGTTTCGTTACTTGAGCAAATTAACACATCTCCTGGCACCTGGTATGCGGCTATTGATCTGGCAAATGCCTTCTTCTCAGTACCTGTCCATAAGGACCACCAGAAGCAATTTGCTTTCAGTTGGCAAGGCCAACAGTATACCTTCACAGTTTTGCCTCAAGGATATATTAACTCTCCTGCCCTGTGTCATAATTTAGTTAGAAGGGATCTTGATCGTTTGGATCTTCCACAAAATATCACATTGGTGCACTATATTGATGACATTATGCTGATTGGAACAAGTGAGCAGGAAGTAGCAACCACTTTGGACTCATTGGTAACACATATGCGTATCAGAGGATGGGAAATAAATCCAACCAAAATTCAAGGACCATCTACCTCAGTGAAATTCTTAGGAGTCCAGTGGTGTGGGGCATGCAGAGATATTCCTTCTAAGGTGAAAGATAAATTATTGCACCTGGCCCCTCCTACAACCAAGAAAGAAGCACAACGTTTAGTGGGTCTATTTGGATTCTGGAGACAACACATCCCTCACTTGGGTGTGTTACTTAGGCCTATTTACCAAGTGACTCGGAAAGCTGCTAGCTTTGTGTGGGGCCTGGAACAGGAGAAGGCCCTTCAACAGGTCCAGGCTGCTGTGCAGGCTGCTCTACCACTTGGACCATATGACCCAGCAGATCCGATGGTACTTGAGGTGTCTGTGGCTGATAGAGATGCTGTTTGGAGCCTCTGGCAGGCCCCTGTAGGTGAATCACAGAAAAGACCTTTGGGATTTTGGAGCAAAGCTCTACCATCATCGGCAGACAACTATTCTCCCTTTGAAAAACAGCTCTTGGCCTGCTATTGGGCTTTAGTGGAAACTGAACGTTTGACAATAGGACACCAAGTTACTATGCGACCTGAACTACCCATCATGAGCTGGGTACTATCAGACCCTGCAAGTCATAAAGTGGGACGCGCACAGCAGCAGTCTATTATCAAATGGAAGTGGTACATACGTGATCGGGCCAGAGCAGGTCCTGAAGGCACAAGCAAGTTACATGAAGAAGTTGCTCAAATGCCTATGGTTTCTACTCCTGTTACAATGCCATCTGCTGCCAAACATGTGCCTATAGCCTCATGGGGTGTTCCCTATGATCAACTGACCGAAGAGGAGAAGACTAGAGCCTGGTTTACTGATGGCTCTGCACGTTATGCAGGCACCACCCAGAAGTGGACAGCTGCAGCATTACAACCCCTTTCTGGGACAACCTTGAAAGACACAGGTGAAGGGAAATCTTCACAGTGGGCAGAACTTCGGGCAGTACACATGGTATTACAGTTTGTTTGCAAGAAGAAATGGCCAGATGTACGATTATACACTGACTCATGGGCTGTAGCCAATGGATTGGCTGGATGGTCAGGGACTTGGAAAGATCACAATTGGAAAATTGGTGAGAAAGACATCTGGGGAAGAAGTATGTGGATAGATCTCTCCAAATGGGCAAAGGATGTGAAGATATTTGTGTCCCATGTAAATGCTCACCAAAAGGTGACTTCAGCCGAGGACGAGTTCAATAATCAAGTGGATAAGATGACCCGTTCTGTGGACAGTCAGCCTCTCTCCCCAGCCATCCCTGTCATTGCTCAATGGGCACATGAACAAAGTGGCCATGGTGGTCGAGATGGAGGTTATGCTTGGGCTCAGCAACACGGGCTTCCACTCACCAAAGCTGACCTGGCTACAGCTGCTGCTGATTGCCAGATATGCCAACAGCAGAAACCAACACTGAGCCCCAGATATGGCACCATTCCTCGAGGTGACCAGCCAGCAACCTGGTGGCAGGTTGACTACATTGGACCACTTCCTTCATGGAAAGGACAGCGTTTTGTTCTTACTGGAGTAGATACTTATTCTGGTTATGGATTTGCCTTTCCTGCACGTAATGCCTCTGCTAAAACCACCATTCACGGACTGACAGAATGCCTTATCTATCGTCATGGTATTCCACACAGTATTGCTTCTGACCAAGGAACTCATTTCACAGCCAGAGAAGTAAGACAGTGGGCCCACGATCATGGAATTCACTGGTCTTACCACATTCCCCATCATCCTGAAGCAGCTGGTCTGATAGAAAGATGGAATGGCCTTTTGAAGACGCAGTTACAGTGCCAATTAGGTGGTAACAGCTTGGAAGGTTGGGGCAGAGTTCTTCAGAAGGCAGTATATGCTTTGAATCAGCGCTCGATATATGGTACAGTTTCACCCATAGCCAGGATTCATGGGTCCAGGAATCAAGGGGTGGAAAACGGAATAGTTCCACTTACTATCACTCCTAGTGACCCTCTAGGAAAATTTTTGCTTCCTGTCCCCATAACTCTAGGTTCTGCTGGCCTAGAAGTTTTGGCTCCAGAGAGGGGAGTGCTCCTACCAGGAGCTACAACAAACATTCCATTGAACTGGAAGCTCAGACTTCCCCCTGGTCATTTTGGGCTTCTAATGCCCTTAAACCAACAGGCTAAAAAAGGAATAACAGTGTTAGGAGGGGTGATAGATCCAGATTACCATGGGGAAATTGGATTACCTCTTCACAATGGTGGTAAGCAAGATTATGTCTGGAGTGCAGGAGATCCCTTAGGGCGTCTCTTAGTACTACCATGTCCTGTGATTAAAGTCAATGGGAAACTACAACAGCCTAATCCAAGCAGGATGACAAAGGACGCAGACCCATCAGGAATGAAGGTATGGGTCAATCCTCCAGGAAAAGAGCCAAGACCTGCTGAGGTGCTGGCTGAAGGTGAAGGAAATACAGAATGGGTAGTAGAGGAAGGTAGTTATAAATACCAATTAAGGCCACGTAACCAGTTGCAGAAACGAGGATTATAAAGTAATATGAATGCCCATTGTAAATTTACTAATGCGTTTGCGATTGTACGAGGGATAGTTATATCATGTTAGGCGTATTTACAACCTTGTTATTGTTTCATGTGAACATGAGATATTATTTGTGTCAAGTTGACAAGGGGTGGATTGTAGTGGCTATTCCTGGTTGTCAACTTGACAATATTTGGAATGAACTACAATTCGGAATTGGAAGGCTCACCAGTGACCCTTATCTGGAGGCTTGGAGATCCTTATCTGGATCTTGGTTTGAAGATCTTGAGCCATAGTGGCTATGGATTCCAGAAGATTGAATCTCCGAGTTTAAGGAACACACCTTTAATCTGGGCTACTCCTTTCATCTGGGATTAAAGGTGTGGTGGAACACACCTTAATCTGGGCTACACCTTCTGCTGGAGACAATATAAGGACATTGGAAGAAGGGAGTCTAGCTCTTGCTCCTGCTCCTTCGCCTGCTTGCTGCGTGAGACTGAGTAACTGCTAGATCCTTGGACTTCCATTCACAGCTGTGACTGAACGATTGTTGGGAATTGAGCTGCCGACTGTAAGTCATCAATAAATTCCTTTATTATCTAGAGACTATCCATAAGTTCTGTGACTCTAGAGAACCCTGACTAATACACTCACACACATACATACATACATACACACATGTGTGCGTGCTTGGCAAATATTAAGATCTCACTGAGGGCTAATGTTTCCCAGAGCAAGAGTTGAGAAACATTGGTGAAAATAAGCTGTCACTTTGGCGGACAGGCTTCTGATTTAGAGATAGGGATCTCAAAAGAAAGGCTTCAAACACAGGGTCGGCAGATAGGAAGGAGGTAAAAGAGTGTCTGGGCTCATCCCAAGTCTCACCCACTGGGCAGTTCATGCTCCACAACTCCATGAAACACACATCCACATACTTCCTGCCTCACCCGAAGCAGTTCCAGAGAAAGCGGCATGCGGTCCTTGCTGGGAAGAAGTCTGTTTCTGAGAAGACAGGATGCACTTTGCATCTTTGGCAGCTGCATTCCTGCTGCTTCAAACTAAGAGAGCCCTTGGCCCTAAGCATCTGAGTCGCAGTGTTGTGCCTGATGTGTGTGTGTTTCCTGGACAGAGTAAGACCTGGGAGGGGGTTGCTTCCTCTGCTTTAGAAACATTCCTCTTACCAAAGGGCAAAGGTCTCACCCTTTCTGATCCTTTCTGATCATCCTGTGGACCCAACCCAGGCCTCTGACTTCTAACCCTGTGATCTTCTCTTTGTCAG
Seq C2 exon
ATGAAGAAGCTGGCCCGGCGACAGCAGCAACAGCAACAGGACCAACAGAACACCCAGAGGCTGACTTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026686:ENSMUST00000028003:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.115 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(43.9=100)
A:
NA
C2:
PF0004624=Homeobox=PD(3.5=8.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
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
- 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