MmuINT0078761 @ mm10
Intron Retention
Gene
ENSMUSG00000048763 | Hoxb3
Description
homeobox B3 [Source:MGI Symbol;Acc:MGI:96184]
Coordinates
chr11:96343769-96346507:+
Coord C1 exon
chr11:96343769-96344696
Coord A exon
chr11:96344697-96345545
Coord C2 exon
chr11:96345546-96346507
Length
849 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCA
5' ss Score
7.88
3' ss Seq
CCCTCCCCCCTCGGGTCCAGCAG
3' ss Score
6.17
Exon sequences
Seq C1 exon
GGTTATTTCGGGGTGCCAGAGAGAGGGGCAATGGTCCACGAAGCAGTGGTGTTCTATTCCTAAGCGGTCCTCGAAGGAGTACAGTCTTGATTTTGTTTTAAAAAAAAATGGAAATGAAAATGGATGTTTTCTTTTTCCCGTTAAAATTAAAGTTGAAGTGTGAAGCATCCAAGTCAGGTTAGATACTTGGTCTCAGCGTCTGCTGCAGAGATACTGGCGAGGGGAGAAGAAGAAAAAAAAAAAACTATTGATGTCAGTTCCCTTTTTAGTTCCTAAGATGGATTCGAGGCCCAGTCCTCTTCTCCCCTCTGTCTCTTCTCTCGCCCCGCAGGTCAGCCGCTTGGAACAGACCCGAGAGGAGGGGGGCAGAAAGGGGAGGGGGGTCCGGCGTGTCACGTGACCCCCAGGGGTGCCAATGTCCGGTCGTGAGGGTATCAGGCCCTTGCAAGTTGCCACCCACTGCCCGGGCCTCGCCCAGCGATGCAGAAAGCCACCTACTACGACAACACCGCAGCTGCGCTCTTCGGAGGCTACTCCTCGTACCCTGGCAGCAATGGTTTCGGCTACGACGGGCCTCCCCAGCCCCCCTTTCAGGCCGCCACGCACCTGGAGGGTGACTACCAGCGCTCAGCGTGTTCTCTGCAGTCCCTGGGCAACGCCGCCCCACATGCCAAGAGCAAGGAGCTCAATGGCAGCTGCATGAGGCCAGGCCTGGCCCCAGAGCCCCTGCCCGCACCTCCGGGCTCACCCCCACCCAGCGCCGCACCTACCAGTACCACTAGCAACAGCAATAACGGGGGTGGGCCCAGCAAAAGCGGCCCCCCCAAGTGCGGTGCCGGCTCCAACTCCACCCTCACCAAACAGATATTCCCCTGGATGAAAGAGTCGAGGCAAACGTCCAAGCTGAAAAACAGCTCCCCCGGCACAG
Seq A exon
GTACCAGCTCTCTGCCTTCCTAGTCAGCTTTTGTCCAACCCAGGAATTTCACTGTTATTATAGCATCCGACCCCAAGGCGCCCACAAGGCGGCCTGGAGACAATATTAGATGGCTGCCTAGTGCTTTTTAGCTACCTCTCACTACCTGATGACCTCTGACCTGACCAACACCCAGTCCATCCAACCATCCTCCATCTGGGCTTCCAAGAGTTTCCAGGAGGTGGGATGGTTGGCTTTACAGCCCTTCCCAAGGCCGCACCGCCTGGAGGCACAGAGTCATCAAGGATAGATTATTATTAAGTATGATTATTGTAGGTATTAATCACCATCGCTCAGGCAGCCTGGGGTCCCGGCCTGCAGCCACCCGAGCCTCTATGTGCCACACATCCAGGCCCTGCCCACCAGTGTCCAGTCTCCCCCCCCCCGCCCCCCTCCCAAGGTGTTCTCAGTCACTTGTCTTGTAAAGAGGGCGGACAGAAGGGAGGAATCACCTCAGACTTGGATTTGGATATACGGGGAGGGTGCGCGCACACGCAAAATCCTAGCCCTAAATAAATGGCCACGCAGCTCTGTCTGTTTGACATGATCAAATTTTCATAAGCTGGGGCCGTGAAAGGAGAACAGGTCTCTTAATAAATGCCACTATTATAGAGTGTCCGCTAATGCGACGGGAGGTAGGAAGGGGGGGGGTGGTGGTGTAGAGGAGGTGGGGACGCGAAGGGGAGGGCAGCGGGGCCTCCGAGTCCAGGCCTGGATTTATTAAGAAACGATGCATTCAATTTCGGCGTGTTCAGTAATTATCTTTTATTTCATTTTCTCCCCTTCCCACCCCTCCCCCCTCGGGTCCAG
Seq C2 exon
CAGAAGGTTGTGGTGGTGGCGGCGGCGGTGGTGGCGGCGGCGGCGGCGGTGGCGGCGGCAGCAGCGGCGGGGGCGGCGGCGGCGGCGGGGGAGGGGACAAGAGCCCCCCGGGGTCGGCCGCGTCCAAGCGGGCGCGCACGGCGTACACAAGCGCGCAGCTGGTGGAGCTGGAGAAGGAGTTCCACTTCAACCGTTATTTGTGCCGGCCGCGCCGGGTCGAGATGGCCAATCTGCTGAACCTCAGCGAGCGCCAGATCAAGATCTGGTTCCAGAACCGTCGCATGAAGTACAAGAAAGACCAGAAGGCCAAGGGGCTGGCCTCGTCCTCTGGGGGTCCCTCTCCGGCCGGAAGCCCCCCGCAGCCCATGCAGTCCACGGCCGGCTTCATGAACGCCTTACACTCCATGACCCCCAGCTACGACAGCCCGTCCCCACCAGCTTTCGGCAAAGGCCACCAGAATGCCTACGCGCTGCCTTCCAACTACCAGCCCCCTCTTAAGGGTTGCGGCGCCCCACAGAAGTACCCCCCGACCCCGGCGTCGGAGTATGAGCCCCACGTCCTCCAAGCTAACGGGGGCGCCTACGGGACGCCCACCATGCAGGGCAGTCCGGTGTATGTGGGCGGGGGTGGCTACGCGGATCCGCTGCCGCCCCCTGCCGGCCCCTCCCTCTACGGCCTCAATCACCTTTCCCACCACCCCTCGGGGAACCTGGACTACAACGGGGCGGCCCCTATGGGCCCCAACCAGCATCATGGACCCTGTGACCCTCACCCCACGTACACAGACCTCTCCTCTCACCACGCACCGCCTCAGGGTAGAATCCAAGAAGCGCCCAAACTGACACACCTGTGATGGGAGGGGCGGGCTGGGGAGGGAGGGGTGAGGTTAAGGGCCAGGGAGACGGCGGACTTGGGGGATGGGCGCGGTTTAGAGTCCTGAAAGAGGTGTGGGATGGGGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000048763:ENSMUST00000055334:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.840 A=NA C2=0.856
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=20.0),PF132931=DUF4074=WD(100=22.8)
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:
AGGCAAACGTCCAAGCTGAAA
R:
CCCTTGGCCTTCTGGTCTTTC
Band lengths:
353-1202
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