MmuINT0099841 @ mm10
Intron Retention
Gene
ENSMUSG00000001566 | Mnx1
Description
motor neuron and pancreas homeobox 1 [Source:MGI Symbol;Acc:MGI:109160]
Coordinates
chr5:29473034-29474916:-
Coord C1 exon
chr5:29474756-29474916
Coord A exon
chr5:29474232-29474755
Coord C2 exon
chr5:29473034-29474231
Length
524 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGC
5' ss Score
9.1
3' ss Seq
ACGCCAGATTATGCCTGCAGGTG
3' ss Score
4.31
Exon sequences
Seq C1 exon
CCCAGGCGCAGTCGAACCTCTTGGGGAAGTGCCGAAGGCCTCGCACGGCCTTCACCAGCCAGCAGCTGTTGGAGCTGGAACACCAGTTCAAGCTCAACAAGTACCTGTCTCGACCCAAGCGTTTTGAGGTGGCTACCTCGCTCATGCTCACCGAGACTCAG
Seq A exon
GTGCGCGCGCGCCCGACCACCCTGAAGGCGGGTGCTGATTTGGGACACTGAGCCCTAGTTTCTTTATCTTTACGTTGGGTATTGATTTTCAGCGTGAGGTTCTAGGATGCTCTGGAGGTTTGATTCAGTTAAGTTGGGGAGCAGGCTGAGAATCTGTATTTAACAAGCTATTCTGGAGGTGTCCCTCCGGCCACATTCAAAGAAGTTATTTTTCTAGAAAGGTGCAGACTTGAGAGTTTGGTGACATTGCGAGCTGCCTTGGTGCCTCGGTAGACCGAGGGTATTAAAACGCGCCCAGTTGGGGAGTTAGGGACACTACACCCATGGCGTTATTGTTAAATAGAGTAGATTTAAGGGGCGAAGACGTGGAGACGCCGCTGCCAGTCAGTCTTAGTCCTCTAGCGAAACCTCTTCTAGGGCGAGGGTAGGCCAAGGAGCAGGGGTCCCGAATGCTTGTACGCTCTCACCCTCTGGATTCGTGGGGATGCGGGTGGCCAGTTTCTCACGCCAGATTATGCCTGCAG
Seq C2 exon
GTGAAGATTTGGTTCCAGAACCGCCGAATGAAATGGAAACGCAGCAAAAAGGCCAAAGAGCAGGCTGCGCAGGAGGCGGAGAAGCAGAAGGGCGGCGGCGGGGGCACCGGCAAAGGCGGCAGTGAGGAGAAGACGGAAGAGGAGCTGATGGGGCCTCCGGTTTCGGGGGACAAGGCAAGCGGCCGTCGCCTGCGGGACTTGCGGGACAGTGACCCTGATGAGGACGAGGATGATGAAGAAGAGGACAACTTCCCGTACAGCAATGGTGCCGGTGCCCATGCTGCCTCATCCGACTGCTCATCTGAGGACGACTCGCCTCCTCCAAGACTAGGCGGGCCTGGACACCAACCTCTGCCCCAGTAGTTGCCTCCAGGGCGGAAGCAGGGATGCGAAAGATGGCTACCTGGGGGGCTGCGGGGCTTGGGGGAGTTTACAATCCCATCCTATGGCCTGCAGCCAGGCTGACAGCCTCTCCCCGAACCATGCATCCAAGTGCAGGCTGGGCTGCGGATCCTTTTTGGGACCTCGAGGGGACAGCAAGAGAGAATGAGAGAGGAGCTCCAATGTGAGCTTTTCGTTCTTATACATTTAATTTCGGGTGATGTTGGCCAGAGGTATCTGGGAGAACCTACCCTTTCTAGGAGTGGCTCCTGCCTGACTCTTCCTTCGTCGGAGAAAGGAAAAAACAGTGTTAAGTGACCTAGAAACTTGAACCCTCCTTTGGAGACAACCATTCTGCTGAAAATTTAAAACAGAGGGAGGAAAAAGGTGTTATGCCTATGTATGGGGGGGGGGCGGTAGTGGAGTGAGGTGTTATGTCATGAGCATTCAGATTGCTGAAAAAAATCTCAGAATGGTAGTGTATTTTTGTATATTGTATTTATATATAAAGAAAGAAATGTCTACTTATGCATGCTAAATTATTATTTAGCTTTCCCATCCCCCAGGGTGGAGATGGAATGTAAAATAAATTGGTTTTTTTACTAGATGAGAGTGAGGGGGGGGGAGAAACACCTTTAATTTTGGAAGGAGGGGGACTGAACCCAGGGCCTTGTGCAAGCTGAGTAAGTGCTCTGCCTCTAGCTTATCTTCGCGAACCCAGAAAATGCAAATCTTGTGAGATCTGACTGTCTTGGTTGTGGGGTGATGTCTATTTCGTGATTATCAGCAAAGAGTAAAATTCAGAATTGCAAATGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001566:ENSMUST00000165512:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.121 A=NA C2=0.892
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(73.7=80.8),PF088806=QLQ=WD(100=53.8),PF090735=BUD22=PU(23.0=67.3)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=10.7),PF090735=BUD22=PD(75.2=95.0)
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:
CCAAGCGTTTTGAGGTGGCTA
R:
GTCCTCAGATGAGCAGTCGGA
Band lengths:
356-880
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