MmuINT0091661 @ mm10
Intron Retention
Gene
ENSMUSG00000038765 | Lmx1b
Description
LIM homeobox transcription factor 1 beta [Source:MGI Symbol;Acc:MGI:1100513]
Coordinates
chr2:33560965-33565225:-
Coord C1 exon
chr2:33565082-33565225
Coord A exon
chr2:33564794-33565081
Coord C2 exon
chr2:33560965-33564793
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
GGAACGACTCCATCTTCCACGATATCGATAGTGATACCTCCCTCACCAGCCTCAGCGACTGCTTCCTCGGCTCTTCCGACGTGGGCTCCCTGCAGGCCCGCGTGGGGAACCCCATTGACCGGCTCTACTCCATGCAGAGCTCCTACTTTGCCTCCTGAGAGCCAGCCGGGCCGCATGGACGCTTGGGCCTGGGCCTAGGGTGGAGCCACAGGCCTCTGCAGCCAGCCGGCCCCCCAGCCCACCACCCGCTCAGACTCTTCAGACAGCCATACGGTGCCCTCCCCTCGGCCAGCCAGACCTGGCTCAAGTGCCCACCGGGCACAGCCAGGCAAGGCAGATGGGTGCAGCCTGGGCAGGGACTGTGTCCTGCCCACAGAGACCTTGTGACCCCTGGGGACCCAGAGCTCTTGGACAGTCACTTGCCTCCCAGTCCTTTGACTTCATCACTACCTTCCCCGTCCCCGCCTCTTTTTGGGGGAAGCTTAAATTTGTTCGTTCTTTCTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTTTTTTATAAACATTCTGTTTCCAGCCAACCTCCATTGTCCCTGCAAGGCCAGCCCTGGGACAGTGCCTGGTACCCGAGAAACAGTTATACGGGTGTCCTGCGCTGGAGACCACTTCCCCTTCTGGTTAGCTCGGGGGATGGTTTCTGGGTCCTGGGAGGCCCAGGGTCACTGTTCCCAGCCCTAGGCTGGAGCACAGGAGAGGAGGGCCCATGCAGGTGTGACAGGCTCTTTGGCCCTGCCTGAACTGGGAGTCTCAGCAAGAGGAGGGATGTGGACAAAGCCCAGAGAGACCCAAAGGGACAGAGATGCGCGCACGTAAAGCCACTCACATCTGTAGGCACACCTGTGCAAGCATGCATATATACACCTGGTGCACACGCACACAAAGATGGAAGAGCTGCCTTTCCTTTCCAGAAGCAGCGGTGAGGTCAGCGAGCAGGGCCTACCTCTAAGAGCAATTGGAGAGGGAGGAAGGACGTAGGCCTGAGGTGTGAGCAGACAGACCTGGGTGGACCCCAGGCTCTGTACAGGTCATGACTGCCAGGGCAGGAGGGTAGTCACAAACCTACAGGTCCCAGGGCAAAGCTGGAGTCCAGAGAACCCAGTATACACAGACCTCAGCAGACACTCCAGATGGAGAGGACCTCAAGAGTCTGACCCTTGGTACCATCCGATACTTAACTCCCTCGGTCCTTCTTCTTACCCAGGGCCAGCGATGGCCAGCTGCCCTCCTTGTGGGCTCCCCTGACCCTCAATCTCCTCTTGCCTGTCAGCTGAGGCTGTCCGCTGGCAGGGCTCCTGACCTTAGCCAGCTCGCACTCAACAAGGCCAGCACCTTCTCTGCTCTTGGCACCTTAGCTCTGCTGATGCGGCTTAGGTCTCATGACTTTGGAGCCCCATCCTTGTTCCATAATGACCCCCCTCCCCGGGGCCTCACACAGGCACAGTGACAAGCTACAAACTCCTTCAATATGTGTGGATGGGATGTTGATTGCTTAGAGCCCATGGAAGACCACCGCTTGTACCTGGTTGCCTTTCCTTTTGTTGGCTCAGTCAGCTTGGGGCGTTACTCTGAAGCCACTGTATCTGTTCCCTCTGTCTCAGCTGCATCAGGTCAGCCCTGTGGGGCGCCCCACAGAATCCTTGCACAGTTATAGGCCACCAGCATTTCAGCCTCCTGAGTCACCCCCAGCCCCCAGTCTCCTGGACTCTTCCTGCCTGAAGCTGAAGCAGCCGTGGTTCTTTCCTTGTCACCCCCCCCCCGCACACCACCCCCCAACCTCTGGCAAGCACTGTGTTCCAGGCCAGAAGCCCAGGAGAAGGCTGCCATTCATTTAACGCAGACTCCTAGCCACCCCTCACCCACCAACCCACCCGTCCTGATGTCTGCCGAGCTCTAGCTGTGAGCACGGCAGGATGAGTATCTCTCTGTCGCCCGCCATTTTGGGCTCCTGTGCCTGGTTAGTTAAGCTGCGTGGGTTAATTTCCTGTCTCTGGGGAGACCTCAGACCCCCTTAGCCCCACCCAGATGTCACAATATGGAGTCAGCAGGGAAGAGCAGCTAGCACAGCCCTCCCGTGTCCCCCATTCTATCACTATCCTCCATGCTGAAGGTGTGGTCCTGAGCTAGCTGCTTGTGTGGCTCGCCCTTGCCTCCTCTGGCACAGGCCCCTGGCTGAATGGTACAGTGCATACTCCGGGCAGACCCAGGGTAAATAGGAGCTCCAGGAACCCGGGCCTACTCTCATCCACTTTTTAAGTTGGGAGATGCAATCCAGTAGACTGTGTCGCTGCTGAGAAACCTGAGACAGGAGAAGAGCTGGGATGTGCTCAAGGCTTCACAGCAACGTAGTGACAGAGCCACAGATGAGGAGAGGACATTAGGTCTGTCCCCATCTCTGTCTCACATATGCACCCCACCACCACCACCAGGGACCAATGCGTTCTCACCACACCTGCTGACCCCAAGGGTCCTCCAAACCGAGTCCAGCCCTGGCCTCTGCTGTTGCCATGCTGGTGTCCCCAAGCCAGAAGATGTTATCACTTCTAAGTTGCCAGAGGAGGGTCCCCCCAGCCACCACACCAGAGATGCCCTGGCAGCCACTCTCAGCATTCTTTCACCACGGCTGTGGCCTGCTGCCCTGCTGAGACAACATGGCTGCTGCAGGGACAAGGGCTTCTGTCCCGTGGGAAGAGACAGCCTTTGATCTTGCCCAGACCTTGTTAGATAGCACACTCAGGCTTCTGGAACTGAGGCTGGAAGGAGGCAGTGGTGGAGGGTTGAAGGTGGGGGGTGGGGCTAGCCTGCAGCCTGAAAGGGCAGAGGGATATGGGAGAATGAGGTAGAAATTGAGAGAGAAAATCCAAGTTCCACCTCCTGGCTGGGGGTGTGGCATGTTGAGGCTCAGGCAGAGAGGAAGGAGCCTGTCCAGGTGTCACACAGGAGTGACAAGAACCTGAGCTTTGTCCCAGCCAGGGCCCTATCTGTAGATTCATTCCATGAGGCTTCCCTTCTCTCTGCTGTCCTCAGAGACTCAGAAGAGGCCCCACACACAGACACCACACCAGGGGTGAGAGTCAGACCAAGGGGTGGCACAGACAGCCTGCTGTTATGGAGGCTTCCTTAGTGGCAGGTGGGCATTGAGAAACTGCCCTTACATAAGAGATCCAGCTCAAGGGCAGCCTCTCCTCCTTTAGGGACATCCCTTTGAAGTGAGACCACCTCCCTGTCTGTCTGATTGTACCCCCCCCCCCCCCGCTCAGCAGGGGAAGATGGACTCAGAGCTCTGGGCACCCCTAGGACCAGGGGGACGCTGCAGCCCAGGGCTGACCGATGCGTGGAAGGGGCAGCACACTCACACACGTGCGCACACACTCACACCCGAAACAAGGAGGCTCACACATGGCCTGGGAGCAGGGAGACAGGAAGGACCCTTCAACATGTGGCCCTTGACAGGGGCAATTGCCAATGGTCTCTGGGCTGCTGCCCTGCCCTGGGGTCCCGCTTGGAGGGCGTTTGTTGCAGCTGGACTGGGGCCAGGCCACCCATCGTATTCTTTCCGTTTACCTTGTACAGACTGCCCGCCTGCCATCCCCACACACATTTTATTTAATAACTTGTCATTGTTAAATTATTTATTAGCGTTTCCACATCACCACCCCCGCCTTCCACTCACCTTCTGCCTCTTCCCACAAAAGCAGAAAATGGAAACAGCAAGAAAAAAAGACAAGATGTTGGTATATTTGTAAATAAACAACCTGTACACTCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038765:ENSMUST00000041730:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.965 A=NA C2=0.221
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
- 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