MmuINT0078762 @ mm10
Intron Retention
Gene
ENSMUSG00000038692 | Hoxb4
Description
homeobox B4 [Source:MGI Symbol;Acc:MGI:96185]
Coordinates
chr11:96318267-96321638:+
Coord C1 exon
chr11:96318267-96319223
Coord A exon
chr11:96319224-96320029
Coord C2 exon
chr11:96320030-96321638
Length
806 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
CTCTCTCTGTGTGTGTCCAGTAA
3' ss Score
7.84
Exon sequences
Seq C1 exon
AGCTCCCTCTTATCCTGGGGAGGAGATGGGGCCCTATGGGAGTCAGAGAAAGGTTGGTGGAGATTAGGTAGGGCAGGGGTGGGGGCTACACCCGCAGCCCCAACTTCTGAGGGATGCAGGGTTTGTGCTCTGCCCAGCCCCCTCACCCCCAAACAGGCCCTCCAATTAACCTGCTCACTCTTTCTTAGTTCATCACCCCTCTCTGTTGTGGAGAAAGCCAGGCGAGGAGGGGGTCTCCCCGCGGGAGCCCTATGTAAATCCTGGTGTTGGGTGGGTGGGGAGGGGTAGAGAAGGGGAAATAAACCTCTTTGGCTGGAGTAGGGTCCGGGTGAGCAGATTTCCTTATCCGGGAATCGCAGGCCGGGTGGCCATTGGCTCGGAGGATCACGTGGGCCTCTAACTTTGTTCACTTGACAGTAAGTAGGAGGGCTTTCGGAAACAGGAAAACGAGTCAGGGGTCGGAATAAATTTTAGTATATTTTGTGGGCAATTCCCAGAAATTAATGGCTATGAGTTCCTTTTTGATCAACTCAAACTATGTCGACCCCAAGTTCCCTCCGTGCGAGGAGTATTCACAGAGCGATTACCTACCCAGCGACCACTCGCCCGGGTACTACGCCGGCGGCCAGAGGCGAGAGAGCGGCTTCCAGCCGGAGGCGGCCTTTGGGCGCCGGGCGCCGTGCACTGTGCAGCGCTACGCGGCCTGCCGAGACCCCGGGCCCCCGCCACCTCCGCCGCCCCCGCCGCCCCCGCCACCGCCCGGGCTGTCCCCTCGGGCTCCAGTGCAGCCAACAGCCGGGGCCCTCCTCCCGGAGCCCGGGCAGCGCAGCGAGGCGGTCAGCAGCAGCCCCCCGCCGCCTCCCTGCGCCCAGAACCCCCTGCATCCCAGCCCGTCCCACTCCGCGTGCAAAGAGCCCGTCGTCTACCCCTGGATGCGCAAAGTTCACGTGAGCACGG
Seq A exon
GTGAGTGCGTGGGCACCCCTTCCCCTCCCACCCCCGGCGCTTTACAGTGAAGGGACCTCCGAGGCATGTGGGGGAGGGAGCGAGGGGAAGCCAATTGTCCCCGCTATAAACTCGCCATTGCCAGAGATTTACGGTCTCCTGTTTTCAGAGCCACATAATTACATCGCCCATAAATTTTTATGGCCTAGTGGGCCCTGCGCCTTTGAAGTCATCCTCTTCTTCATTCTCCCAGCGACTTTTTCGCCAGGGATTCGCAGTCCCAGTAAAGTTGGAAGTTGGGGAGGGGTGTGGGAGGAGGGGAGGAGAAGGAAGAGGAGGAGGTAATCCCTATTTAAGCACAGAGTTGAATCAACTTCCTGGATTTCTTTTTTTTTTTTTTTTCCCCTTTCTTCCAATCTGGTACCTTGGCTGGAGAAGTAGGCAAAAGTTTTTACTAAGGGGAAGGCGCTGCTTGGAATCTGAGCAGTGAGGGTGGGAACTAAGCCGGGGAAAGGTCTAGGGCAACACCCCCTCCCACTACCCCACGCCATTGGGGTCCTCAAGCCAAAGAGTGAGATGAAAATCTTTCCAAGATTCCTCACAGTGCCCCTCCCCCAGGCAACAAGGACAACAGTACAGCCCTCCAAAAGTTTGAGTTTTTTTTTTTTTTTTCTTTCACGGGTCTTCCTTTTTCGACCCCCTCCCTCCAAGATGAGGTAGTGGGAGCAGGAGGCTCGGTGTTAGCTGGAAGGAAGAAAGGGTTTCCCTCCTCCCTTTCGGGGGCAATAAAACTTTCTCTTTCTCCCTCTCTCTCTGTGTGTGTCCAG
Seq C2 exon
TAAACCCCAATTACGCCGGCGGGGAGCCCAAGCGCTCTCGGACCGCCTACACTCGCCAGCAGGTCCTGGAGTTGGAGAAGGAGTTTCACTACAATCGCTACCTGACGCGCCGCCGGAGGGTGGAGATCGCCCACGCGCTCTGCCTGTCCGAGCGCCAGATCAAGATCTGGTTCCAGAATCGGCGCATGAAGTGGAAAAAAGACCACAAGTTGCCCAACACCAAGATCCGCTCGGGTGGCACCGCGGGCGCAGCCGGAGGCCCCCCTGGCCGGCCCAACGGAGGCCCCCCTGCGCTCTAGTGCCCCCCAAGCAGGAGTTCGAACATGGGGGGGTGGGGGGAACAGCGAGCACCGAAGGGGGTGCGGGGTATGGGAGGGTCCCCGGGCTTGAGCCCAGAAAAAATCTATCTACCCTACCCTCACTTTATCTATAAGGAATAAACACAGAGAAGGGGGGTAGGGAAGCCTTATTTATAGAAAGGACAATAAGGGAGCCGGGTAAAGTCCTTCGGAGACAAGATTCGAGTCTCTTGCTTTCTTCCTTTAAAAAAAAAAAAGAAAGAAAGAAAGAAGGAAAGAAAGAGAGAGAGAGAAAAGAAAAAGAAGAAAGGAAGGAAGCAAGAAAAGGAGGAAGAAAGGAAAAGACAGAAGAGAAATGGAGGAGTCTGCTGCGCCTGGTTTTCAGCTTTGGTGAAGATGGATCCAGGCTTCATCTTTAATCACGCCAGGCCCGGGCCCATCTGTCTTGTTTACTCTGCCGAGGAGAAGACGGGCGAGCGAGCTTCGGTGGCGACCATTACCTCGACACTTGGCTAACAAATGAGGCCAGGCTCGGCCGCTGCCGCCGCCTCTGCTGCTGTCGCTGCTGGATCACAGCCTGGATTTTTCTTTCTTTGTCCCCTACTCCTGACACCCAGCGAATGCACCCTCAGACTGCCAGATAGCACAGTGTTTTGGCCACGGTAACAAACACACACACATATAACTTTCCTCCCTGTCTGTACCCACTTTGGGGTGGGGGTGGGTGGGAAGACTGCTCACTCCCTTCCACCATAGACTTAGAAGGGGGAACAGAAGGGAATTGAAGGGCAGTCTGCACAACGTGGGTTCCCAAATCCGAGCCCAAGAAATAAATGAAAATGAAAAAAGAAAGGTAGCAATTGGGACACCCAAGAAGGCCTTCTGCTAGAAGGTCCAGCTAGGCCTGGCAGGGTGAGGGGCAGTTGAGTTCTGGGAGCTGGGAATGTCTTCTGGGCAGTTCACAGTAGTAGAGTCAAGGCCTTCTCTTAGGTTACAAATGAATGTGAAATTAGGAAATAAAATACTGTGGCCCTCCTACTCTGGAAGGACAATGTTGCAGAACCCTCTCCCGTTGTTATCATTGTTGCATCGTTTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTTTATGTCATGTGTGTCCTCTCTCCTGTTCTCTTTCTGACATTCCAAAACCAGGCCCCTTCCTACCTCTGGGGCTGCCTGAGCCTAGAACCTTTTGTTGGTGTGAAAATTTGTGTCCTGTACAGAGTGACAACAGAAATAAATGTTTGGTTTCTTGTGACCATCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038692:ENSMUST00000049241:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.724 A=NA C2=0.606
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=57.0)
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:
GATGCGCAAAGTTCACGTGAG
R:
ATGTTCGAACTCCTGCTTGGG
Band lengths:
351-1157
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