MmuINT0078766 @ mm10
Intron Retention
Gene
ENSMUSG00000056648 | Hoxb8
Description
homeobox B8 [Source:MGI Symbol;Acc:MGI:96189]
Coordinates
chr11:96281905-96285315:+
Coord C1 exon
chr11:96281905-96283386
Coord A exon
chr11:96283387-96284162
Coord C2 exon
chr11:96284163-96285315
Length
776 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
CCCTTTTCCCCCATTCCCAGCAG
3' ss Score
7.71
Exon sequences
Seq C1 exon
AAGCTTTAAATATGACTACCTCGTTTGTTTGAAAATATGTTTAGGAGAGGAAGCTGTATGATTTGATAACTTGTATTAAAATACCAATTACATTTATAGGACCTTTTAAAACTCGGTGCAATTAAACCGTGTTCTTTTACATTTTTCCGAAGCGACCCTGACATTTAGAAAGACTCCAATTGCCTCGTTAAAATCGCGAAATTAACAGCGTGCCTACGCCAGGCTCAGCGTTGTGGATGTGTGTGTATGGTGTTTTTCCGTGACTCCCCCACATCAGTCTTTGGGGGTGGTCTGCGAAGGTATTTGATTTGTTGTGAGGCAAGAGATATCTCATTAATGTAGGTAGTTAAACAGATTTAATCCGTATTCGTTCTCTCTCTCTCCCCCCTCCCTCTCCCCCCCTCTCCCCCTCTTTCTCCCTGGGTGTTTTTTTCTCTTCCCCTCCTTTTTTTCTGCCCTCTCCTCACTCCCTGGCGCTCTCTCGCTCTAGCTCTCTCTCGCACTCGCTCTCTCTCGCTCTCACCCTCGCTCTGCGTTCTGTCCGGGAGGAGTACCCAGAAGCCAATAGGATGCGGGGTCTCTAATGGATGCAAATGATGGTGAAAAGACGGGGCAAAATATGAAACAACTCATTTGGAGGGAAGTAAATCACCGAAAACTGTTTATGAACTGGCATCCCTTCTTCGAAATGTAAAGCGAGGACCTCTTTAAGTGGCGGTATATTTTTGTTTGGGGGGTGGGGGGTGGGGGGAGGGCGAGCGAGCCGCGGCTGCCATGCAGGCTTAGACTTTTGCAGGCTTCGCTCTTCTATTCCTGGAAATCACAAAAAGTGTGGCGGCTTTGAGATCTTCTTCGTCTTTTCTTTCTTTTCCTTCCTTCCTTCTTTTTTTTCCCCTCCTCCCTTTTCCTCTCCTTTCCTGGCGAGGGTGACTAGGAGCCGGCGAATCCGCGTTTTTTTTTCTCTCTCTCTCCCTCCCTTTTCCCCCTCCCCACCCCCTCCCCAACAGCCCCCAACTACAGCCTGCGCCGCCGCCGCCGCCGCCTCAAAATTCAATAAAATGAGCTCTTATTTCGTCAACTCACTGTTCTCCAAATACAAAACCGGGGAGTCCCTGCGCCCCAATTATTATGACTGCGGCTTCGCCCAGGACCTGGGCGGCCGACCCACCGTGGTGTACGGTCCCAGCAGCGGCGGCAGCTTCCAGCACCCTTCGCAAATCCAGGAGTTCTACCACGGGCCATCGTCGCTGTCCACAGCTCCCTACCAGCAGAACCCGTGCGCCGTGGCGTGCCACGGCGACCCCGGCAACTTCTACGGCTACGACCCTCTGCAGCGCCAGAGCCTGTTCGGTGCGCAGGATCCAGACCTGGTGCAGTACGCAGACTGCAAGCTCGCGGCAGCCAGCGGCCTGGGCGAGGAGGCCGAGGGGTCTGAGCAGAGCCCGTCGCCCACACAGCTCTTTCCCTGGATGCGCCCTCAAG
Seq A exon
GTGAGCTCCCGTCCGACCTGGACCTGACAGGGTGGGAAGGGGCCAGGGGGGCCCCCATGCCGGTGGGGGGGGGAGGGCTGGTGGGCAGTCCGGGAGTATCTTCTGCTCCTAGAGGACTTGTGGGCTCCGTTCCAAACACCTACCTCCTCTCCCTTCTGTCCCACTTTCTTTTCTTCTTTTTCCCCTTTTCTTTTTGCTTCCTTTGAAGGAGGGGGGGGTGTCTCTAAGCGAATTTCCTGAATCCATAAACCCCTCACCCTCCTTAACTTTTCTTCTTCTCCTCCTTTCCCCTTTTACTGTTTTATGGGGGCTGTGGAGAAAGACTGGTGGGTGTGGGGGCGCTCAACGTTTGCACTTCTCAATTGCTTTATAGTTTAATTACCCTGAAGAAACTTTTCTTCTGGGGCAGAGGCTCTGGGGGCTTTTCAAGGTGGGTTCGAGGTCCCCACTCTGGCTTTTTAGTCTTACTCCCCCCTCCACATCCACCCTCTTAAACTTTATGGCACTTTTAATGTATCTGAACCCCCTATTCTGGTTCTAGTTACCAGAGAAGGGGCTCCTCCTTTATGGCCCCTGCAGATTCAGGGCTGTCTAGTCCCCCCTCGCCCCCCCCCCCGCTGACCGCGTCTTCCGCGCTCCCCCTCCCGCCCCCGCATAAGGGTCCCCTGCCCTTATTATCCTGGTCTCCTAGGCTGGTTCACGAATCTTCCAACCTTCTCTGTCTCTTCCCCCTCCCCCACCCTCCCCTCTGTCTCGCCCTTTTCCCCCATTCCCAG
Seq C2 exon
CAGCCGCCGGACGCAGGCGAGGCCGCCAGACCTACAGTCGCTACCAGACCCTGGAGCTGGAGAAGGAGTTCCTATTTAATCCCTATCTGACTCGCAAGCGGAGGATCGAGGTATCGCACGCGCTGGGACTGACAGAGAGACAGGTCAAAATCTGGTTCCAGAATCGGAGAATGAAGTGGAAAAAGGAGAACAACAAAGACAAGTTTCCCAGCAGTAAATGCGAGCAGGAGGAGCTGGAGAAAGAGAAGCTGGAGCGGGCACCAGAGACCGCCGAGCAGGGCGATGCGCAGAAGGGTGACAAGAAGTAGGCTCCAGCTGGGACTGCTCGGGCCCGGACTAGCCCGCACGTCCGCCGGTCCCCCCCGCGACCACGCCGCCGCCGCCCGCCCCCCGCCTCCGAGAGCTCCGGCCCCGCGAGCGGAGCCAGGAGCTGGGCCTCCCACAGCAGCGTCCCCCGCCGCGCCAGTCCCCGCTAGTGGTAGTATCTCGTAATAGCTTCTGTGTGTGAGCTACCGTGGATCTCCTTCCCTTCTCTTGGGGGTCCGGGGGGAAAAAAAGAAAAGGATTTTAAGCAAGGACTCCCTCGTCCTGCGAGGGTGATCGACTGCGGCCTGGCAGAACCCCCTCGCCCCCGCCCCATGTAAAAAAGCCTCCTTGTGCAATGGTCTGTTTCCTTTGAACGTGCTTCTTTGTAATGACCGAGGTACCGATTTCTGCTAAGTTTTCCCAACAACATGAAACTGCCTATTCACGCCGTAATTCTTTCTGTCTCCCGCTCACTTTCTCTCTTTCTCTCGCTCTCTTTCTCTCACCGCGTCCCCATCTTTCCTCGCAACCCCCTCTCCCCGCTGCCCTCCCTAGCTGGCTTTCTCTCTTGCTTCTCTCTTTTCCTCCTGTCCCCCCACCCCCACCCCCTTTGGTTTGACAATTTTGTCTTAAGTGTTTCTCAAAAGAGATTACTTTAGTTAGCATGCGCGCTGTGAGCATTGTTAAAAGTGTTCTTAGGTTTACTGTGAAGAGAATGTATCCTGTATCTGTGAATTGCTTTATGGGGGGGAGGGAGGGCTAATTATATATTTTGTTGTTCCTCTATACTTTGTTCTGTTGTCTGCGCCTGAAAAGGGCGGAAGAGTTACAATAAAGTTTACAAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000056648:ENSMUST00000052650:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.244 A=NA C2=0.500
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=55.3)
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:
CACCCTTCGCAAATCCAGGAG
R:
AGGAACTCCTTCTCCAGCTCC
Band lengths:
350-1126
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