MmuINT0078764 @ mm10
Intron Retention
Gene
ENSMUSG00000000690 | Hoxb6
Description
homeobox B6 [Source:MGI Symbol;Acc:MGI:96187]
Coordinates
chr11:96299067-96301569:+
Coord C1 exon
chr11:96299067-96299591
Coord A exon
chr11:96299592-96300668
Coord C2 exon
chr11:96300669-96301569
Length
1077 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
TTCTCCTCTCTGCGTAACAGGTT
3' ss Score
8.83
Exon sequences
Seq C1 exon
CTAAAACCCAATCTCGGCTATACTACTAATAGGCGCGGCGCTCGGACTATAAAACACAACAAATCATAAACCCGGCGGAGCAGCAGCGGCCTCGCGCGCCTCCCCTCCCGATGAGTTCCTATTTCGTGAACTCCACCTTCCCCGTCACTCTGGCCAGCGGGCAGGAGTCCTTCCTGGGCCAGCTGCCGCTCTACTCGTCTGGCTATGCGGACCCGCTGCGGCACTACCCCGCGCCTTATGGGCCGGGACCCGGCCAGGACAAGGGCTTTGCGGCGTCCTCCTATTACCCACCAGCCGGCGGCGGCTACGGCCGGGCGGCGCCCTGTGATTATGGGCCGGCGCCTGCCTTCTACCGGGAGAAGGACGCGGCCTGCGCTCTCTCCGGCGCCGACGAGCCGCCCCCGTTCCACCCCGAGCCGCGCAAGTCCGACTGCGCACAGGACAAGAGCGTGTTCGGAGAGACCGAGGAGCAGAAGTGCTCCACGCCCGTCTACCCGTGGATGCAGCGCATGAATTCGTGCAACA
Seq A exon
GTGAGTGAGACTTCCCGCTGTCCCGTGTCTGTGTGTGTGTGTGTGTGGGGGGGGGTCGGCAAGCAGAAAGACTGAAAGTGTCAGCATCCCCCAACCCCAATTCTCCCATTGGGAACTAGGTGGGCATCTCAGCAGATAGAGCAAGATTGCCCCCCCCCCCGACCTCCAGATCAGTCCTCTTGCCCGCAGAAGTTGCAAAGTTTGCAAAGTCCCAGCTGCACAGTAAGGCAGGGGGAATAAGTGGGCTCTCCCTACTTAAGTCAGGCTAGGATTGTTGATCCGGAAGAGGTTAGGGGACTCAGTCTCTGGTCCTGTATTCCTTTATGTTCTCCCTAGCTCTTGTCCGGATCTGAGGGGTGGGGGGTGCCCCGCACCCAAAGACCACTCCATTAAAAACAAGAGTGCGTCATGAAAGGGGAGGGGTGGCATGACGCCGGCAAGGGCGAGTTTACTTGGGTCCTGGATTGTGTTTCCCTGGGGCTGGGGGAGGAGAACTGGGGAAGGGGGACCAGGGAGCTGTGAGACACTACCATAGGGTCGTATAGTCTGAGGAAGGAAGAAGAGAGGACAGGCGGAGGGAGTGAGAAGAACAAACTGGCTCCTGGGTCTCAGGTTGGATTATTTGTGGGCTTCAAGTCCCAATTGATGTCCATTAGCAGGACACGAAAGTGAGGGGCTGTTAATGCGGACTATGAATCGATCCACGTCATTAGGGATTAAGGGCCAGAATCTATCATCGAGTAGGGTAGGGAGGGCTGGATGGATGGAAAGGAAGGGAAAGAAAAGATACAGCTCGTAGGAGGCACACCTGGCCAGCCCCTCCCCCAAGCTCAGGTGAGAGTCCAAGTGCCCCTCCTCTCCCCCCACTGAAAGTCTAGGCAGAAAGAAAGCACAGGCCTCGGAGTCCAGGAGGGAATCTGGAGGGGGCGCTGGAGGAGTAGGAAACGGGGACCAGGGAATGGGAGGGGGAAAGACTACTCCCGACAGGCTAGCTTTACGTTTGAGGGCCGAGTGGGGGAGGGGCTATGGGCTTGGTGTGATGACCCCAGGCCTCAGTTTCTCCTCTCTGCGTAACAG
Seq C2 exon
GTTCCTCTTTTGGGCCCAGCGGTCGGCGAGGCCGCCAGACCTACACACGCTACCAGACCCTGGAGCTGGAGAAGGAATTTCACTATAATCGCTACCTGACCCGCCGGCGGCGCATAGAGATCGCGCACGCCCTGTGCCTGACCGAGCGGCAGATCAAGATTTGGTTTCAGAACCGGCGCATGAAGTGGAAAAAGGAGAGCAAACTGCTCAGTGCGTCTCAGCTCAGTGCGGAGGAGGAGGAGGAAAAGCCAGCCGAGTGAAGGTGCTGCAAAGGGAGGGGGGACGCGAAGGGAGAGGTCTGTGGGGGAACCTAGGGCACCCGAAAGCCCCAGAAGGCTCTGCGGTCGGGGGAGTCTGGGGACTTGCTGTCCAGAGCACGACGGGCAGGGCCCAGTGCTTGCCTGGATGCCCCCTTCTGCAGAGCTCTTCCTGGGCGCTTGGCGGATGCCCACCCAGCACCCCCAGCGCCTCCTCCCTCCCCCGAAGAACCCACCTTGGCCTCATCAGGCTCTCTGGTGAGAACTGAGAATCGGACTCACTTGATGTCTCCTGGAAGCAGAGCAGAATGCTCATGTCCTTGTCGAGTCTCATTTCGTCCATGTCCCCCGTGCACGGTTCAATGGTAGATTCGCTGTCCCCTCAGCAGGGACCTGAAAGACTCCCTGACCCCAGACTTGTCTCTCCTACCCCCTCCCCAAAGCCACTGGAAGGAGCACATACTACCTAGAAGGAAGAAGAGGAGCCTCAGAAGAAAACAAAGTTCTATTTTATTAATTTTCTATGTGTTGTGTTTGTAGTCTTGTCTTAGCTCCGGACGTGAAATACTTCGGTAATAATATTAATATTATTAATAATGATTATGATGATGATGATAATAATAATAAAGATGTGAAAACTCGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000000690:ENSMUST00000173432:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.252 A=NA C2=0.279
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=65.5)
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:
CAAGAGCGTGTTCGGAGAGAC
R:
CCCTTTGCAGCACCTTCACTC
Band lengths:
358-1435
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