MmuINT0078767 @ mm10
Intron Retention
Gene
ENSMUSG00000020875 | Hoxb9
Description
homeobox B9 [Source:MGI Symbol;Acc:MGI:96190]
Coordinates
chr11:96271457-96276595:+
Coord C1 exon
chr11:96271457-96272058
Coord A exon
chr11:96272059-96274623
Coord C2 exon
chr11:96274624-96276595
Length
2565 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TATCGCTACTTCTCTTTCAGCCA
3' ss Score
8.02
Exon sequences
Seq C1 exon
GGTCCGTGTGCCACCTTTTCCCTGCTTGGGCGCCGCGGCGCGAGCGCTTCCCTTCCCCCTGCGAGCGCGCGGATAATGTCTGAGAATGTCCATTTCTGGGACGCTTAGCAGCTATTATGTCGACTCGATCATAAGTCACGAGAGCGAGGACGCGCCTCCAGCCAAGTTTCCTTCGGGCCAGTACGCGAACCCGCGGCAGCCGGGCCACGCCGAGCACCTGGACTTCCCCTCGTGCAGCTTCCAGCCCAAAGCGCCGGTGTTCGGCGCCTCCTGGGCGCCGCTGAGCCCGCACGCCTCGGGGAGCCTGCCGTCTGTCTACCACCCCTACCTGCAGCCCCAGGGCGCGCCGGCGGCCGAAAGCAGGTACCTCCGCACCTGGCTAGAGCCGGCGCCGCGCGCCGAGGCCGCCCCGGGGCAGGGCCAGGCGGCCGTGAAGGCGGAGCCGCTGCTGGGCGCGCCGGGGGAGCTGCTCAAACAGGGCACGCCCGAGTACAGTTTGGAAACTTCGGCGGGCAGGGAGGCTGTCCTGTCTAATCAAAGAGCTGGCTACGGGGACAATAAAATTTGCGAAGGAAGCGAGGACAAAGAGAGGCCGGATCAAA
Seq A exon
GTAAGTTATAAAAAAAAAAAAAAGTGAGGAAATCCCCCCCAGGCTGCAGGCCAGGCCCGGGGGAGGGGAGGGGAGAGGCCATAAAGCGGACAATGTAAAGGGACAGAGCGCCTGGGGCCGCAGGGCTAGAGTGGGTGGAGGGAAGAGGAAGGAAGGGGCTGGCAAAGCAAAAAGCTGGGTGTCCAGGAGGGGGACACTGAGGCTACCCCCCACTCCTCCTTGTGGCGCAGGGACTGAGACTCAGGGACCAAGTCTCTCTAGTCCTTCATTCTTCCCCAGGCTCGGGCTGGAAAAAGGGAGAGGGACCTGCGATAGAACTGTAGGAGGCCGGGCCGATGGCCAGCGCGGCCCGGAGCCCGCGCGGGCACGGGGCCGAAGAGCACTCGGCAGAGCCGCCTGCGCCACGCGCAGACCGTCCCTGCCGGCCAAGGGGAAGGGGGAGGGGGCTCATTAGGATTTTATTTGCGATGCAACAGCTTGGCGGAGGATTGTTCCTAGCAGATCTCACGCAGTAGCCGCGTCGGGTCGGCAGCAGGCGCCGGGAGGGGCGGGGGAAGCCCAGGATGCGGTGACGGAGCCCCCTCCCCGGTGCGCCGGCCCCTCCCCGGGAGCCTTCCCTCCGGGGGTCCCCCGCCCTTCTAGGGCATCCTCGACAGGACGGCCGTTTCTCCTCCTGCGGTTGCACGCTGATCTCCGCGGGGCTTCCGATCACTTAGGCCGGGCAGTTCACCTCTCCGAGAGTCTAGGCATCACTTGCTAAAGACAGGGCCTCCCTCTAGAATGGAGGAGAAGACACCCAAAGGGACCCCGGGGGAGGGAGGGGGAGGACTGCGCAGGGGCGGAGAACTCTACCCTTGGTGGAGAGTTTCTTACCACCTCCCACTCCTAAAAGCACCCTTGCTAAAATAAAACCCCAAGTGGAAACTGCTGCTGGCTGAGAGTAGAGGAGGCTTACTTTTAGGGGTTTGTTTTTAAGGATGGGGAAGACAAACTGGTTTGGGGCTCGCTCTTGGTCCCAAACAATACGGGACAAACTGACAGGTCAACTCCTCACCTCTTCCTCCTCTGGGCAAATAGTTTGGTCCTTGCTCGCCCTATTGGATGCCCCACCAACAGAGAGGCCAATGGGTCCTCTGGGGGCATGCTTGCCCTCTGAAAAGCAAGGAGAGACACTATTCCCCTGTGACCCTTGTGGTCCCCTCATACCTCCAACTTGCCAGGCTGAGTTATTAAGGAGCTCATATCCCCAAAACAGCTCCTCCCAAAGCTCCAGAAAACACCCAAACAGACCCCTCACCCCATGGCCCCAGACTAGGCCTGAGTTGCCCATCATTGCAAGGCAGCCATTTGGCTAGGCTCAATTATTAACAGTTTTTTTTTTTGTTTCCTCTTTCATATTTAATGAAAGAGGAAAAGGCTGCGGGTCCCATCCCAGACAATCACATTAAGGGAATAGCGCTGCAAATTGGCAGGACACGCTACTTAGTGTAGGATGAAGTGAATTTTAAAATATACATAGATATTCAGAGCTTTTCACTTGGGGGCTAAGCTGGTGGAGTGGATCTTGCTTGTAATTGGCTCTGCTTTGGGAGGCAGGTAACTTTTCTGAGTCCCGAGGTCTAAGGAGGGATGCTGGACAGAAAAAGAAAAAAAAACTGTATATGTTATTTGCTCTTTGTGCCCCTCTTCCACTCAATTACACCTTTCTCTGCCTCTCCATTGGGTCCGTTAAAAGGATTGGTATGCTGGGAAGGGCTTTCTGTCGTCCCCCCCGCCCCCCGCCCCCCCCACCTCATCTCTGCTTCTCTATCTTAGAGCTGTAGCAATTTTGCTTCCCAGTTTCCCTGAACTTGTGTTAACCAAACTGTGAGCTGAGTAGCAGAAAAGAAGAGGCTATTGCCACCATAAGTTATCTGGAAGCCCTGGGGCTCCCCGTCCACGGGCTGCAATTGATAAATGGTTGCAATTGGGTTGCTTGTGAGTCGGAGTGTGCAGGGTGTTCATGGCTGTAAATGCAGACTCTTATTTGTGGTGTGTGATGGGGAGGGCTGCTACCCAGACTCACATGTCTGCTGCTTAGGCCTAGGGCTGAAAAATGGCTTCCTAGGCAGGGTTCACTGGGACTGGACTGGAGCACCAGGAGATCTCTTGGCTATGGCTGAACAGAACTCCACTCCTTACCCATTTCTTTCCCCTTTCCCCTGAAACCTAGAGCCAAGGCACCCTTCAGGTCAGCCACCTTTAGCTGGTAGTGTGGTTCCAGCTATACTGAGCTCTTCTGACCTGGGTCCAGGTCTATTTGGATACAAATAGAGGAAGACTGAGATTCCTAGAGCAGTCAAAGCTTTGGAGATGCTTGGGTGGTTTGGCTGCATCTCCTCCAATGCACTGTTCCCTTGGAGCTGTCCATATTCACTCCTGGCCCAGTTAGAGATGCTTTCTGAGATCTTGGAGGCCTGGGTGTGTTTCTCCAATGCCAGGGGAGTAGAGATGTGAGCGCACCTTCTTGGTCTGGGGACCTCCATTCCCTTTCTCTCTTTGATTCTATCGCTACTTCTCTTTCAG
Seq C2 exon
CCAACCCCTCTGCCAACTGGCTGCACGCCCGCTCTTCCCGGAAAAAGCGCTGTCCCTACACCAAATACCAGACGCTGGAGCTAGAGAAGGAGTTTCTGTTCAATATGTACCTCACCAGGGACCGCAGGCATGAAGTGGCCAGACTCCTCAATCTGAGTGAGAGACAAGTCAAAATCTGGTTTCAGAACCGGCGGATGAAAATGAAGAAGATGAATAAGGAGCAGGGCAAAGAGTAAAGATGACCACCCCCCCTTCCCCAGCTCACTCTTATTATTTATGTGATGGTCAAAAAGCCACTGCTGTCTGGGTTGTACCCAAGTGAGTGGGGAAGAGTATCTCCTCTTTAAAATCCCTCATCTGCACCTGGAGCCTGTCTCCTCTCCTTTGCGCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCACTCTCCTGGTGTTAAGAGGAAATTTTATTAAGTTAGAAGCTAGCTATACTTGGTTCCTAGAAAAGTGATGAGCCTCGCTCCGAGGAAAGAGACCCTAGTCGAGCTCCTAGCATCCCTGCTAATTTTTCTGGAAAACCCCAGCCCCTCTCTTCCAGTCTGCCTGTTCCCTCCCTGTAACCTAGCCAGACGCCACCCAGGTACAGTTTAACTGCACACAGCCCAGTGGATGCCCACAGACATAGAGTTTGGAGTCTATGCTAATCATCGTGGAGAAAGGACATCAAGACGTTGTTCATCAAACCAAGCAGGGCAGCTCTCAGATCAGGTTCATTTTGGTTGTGCCCTGATCCAAACACACACTAGGAAGATGTCTAGAGATGCCCTCAATGAGGCACTGCAGTCCCAAAGTCTCAACATCCCAATATGTATCCTATGGAATTGCCAGCTAGACCCCATATCTGGGGAGGCCTGTGGGCAGATGTGGCCATTCCTGTCCCCAAGCTGTTGTGAGCTAGAAAGGGCAAGAAAAAGCAGGGAGTGGTTTTATGAAGGTACCATTAGTGGAGTCCCCTCGTATTTTCCCTGCAGGAAGTGTTTAATTCTGCATGTTTTCCTTTCCTTCCAACTAAAGGAGGTCAAATTGTGGGTTGTAGAGCCCTGACAGTGCTGTTTCCCCATTCATACATTCCTATCCCCATTTGACAGAATGTAACTTTTCTTGCTGACCACAGTCTCAGATTCCTCTCTATCCTCCAACTTTGAAATCAACTCTCCTTTCCACCAAACCCATCTTGCACCAGCAAGACAAGTCTCCCATTGTAGGAAAAAAAAAAAAGTCCCTTTCCTCTCTGCTAGGTCAACCCCACCATAGAGAAGGCTGGGTCAGAAGAGTCTGAAAATTTATTGTGAATCAATTCCCCAGCTCCCTTCCAGAGTAGGCAGTCAGGGCCGGGAGGAGCAATGGCCTCAGCAAGCAGGGCTAGTGGGTATCTTTCCATTTCACCAGTTTCCTGACCCAGGAAGAAGAGAGCCCCTTGGCATCCAGCCAGAGGTCCAAAAGAAGACTCAGAGTGGGGACTTCACCTCCTGCAAAGTCCACTGCTGTATCCATCCTGTTGCTGCTGCATGCATACGCTTCTGGCAAACAGTCCAGTGTGCACAGGAAAGAGGCAAACATCGCACCTCCCCATCGTGCAGAGGGGGGTCCTCTCTGCCTCTCTGCCTCTCTGCTCTCCCTGCTTCTCAATCCCTTCCACCCGTGGACTTTTGTTCCCGCTTCTCCTGACTGCAAAGAGGTCATTCCAGTAGAACTTTGAATTTTATTTTATTAATTTTTTTTTGCTTTTGTCGGTGGCTGTGGTGACATTGTGCTTGTGTTTTGTGATTTCTTTGGCAGTGATTTTCAGTTGTTGCTTATAAGGGAGGGTTGAGGGTGGGAGTGGGGAGGGCAAGGGGCCTAGAGCTCTAATTGTTTGTTTTGGAAGAAAAAGGGGAAAAAAAGAACAAAAAATATACATATCACTCTAGAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020875:ENSMUST00000000010:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.647 A=NA C2=0.393
Domain overlap (PFAM):
C1:
PF046178=Hox9_act=WD(100=99.4)
A:
NA
C2:
PF0004624=Homeobox=WD(100=72.2)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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