MmuINT0078759 @ mm10
Intron Retention
Gene
ENSMUSG00000075588 | Hoxb2
Description
homeobox B2 [Source:MGI Symbol;Acc:MGI:96183]
Coordinates
chr11:96351631-96354012:+
Coord C1 exon
chr11:96351631-96352195
Coord A exon
chr11:96352196-96352949
Coord C2 exon
chr11:96352950-96354012
Length
754 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
TAGGGGTGCTTCCCTCGCAGATG
3' ss Score
7.56
Exon sequences
Seq C1 exon
TATCAGCAATATACAATTATAAAGGCCTAAATTTAAAAAAAAAAGAGAGAGAGCGAAATCTCCCCCCCCCCGCGAAATTGCTCCATTGCATAAACCTGGGGGGGGCGGGAGAGGGGGGTCCCTCTGATTCTCCCTCCTGACGCCCCCCCCAGCAGGCCCCCTCCCCCACCATTGAAAGCCATGAATTTTGAATTTGAGAGGGAGATTGGGTTTATAAACAGCCAGCCATCGCTCGCCGAGTGTCTGACTTCCTTCCCCGCTGTCTTGGAGACATTTCAAACTTCATCAATCAAGGAGTCGACATTAATTCCTCCTCCTCCTCCTCTGGAGCAAACCTTCCCCAGCCTCCAGCTCGGCGCCTCCACCCTTCAGAGACCAGGGAGCCAAAAGCAAGCCGGAGATGGGCCTGCTCTGCGGTCACCGCCGCCACTCCCCGTTGCCCCCCCAGCCCCCGAGTTCCCCTGGATGAAAGAGAAGAAATCCACCAAGAAACCCAGCCAATCCGCCGCATCCCCTTCTCCAGCCGCCTCCTCGGTCCGGGCCTCCGAGGTCGGATCACCATCAG
Seq A exon
GTGGGTAAACGTATTAGGGGCGGGGTGAGGGGCAGTTGGAAGAGAAGGGGAGAATGTGAGGTGATGGGGCTCCTGGTGGGGTTCCCTAGGTCGACGGATCTGGGGCGAGGGAAGCAGAGTATCCCGCTGGGGTTCAGGCCTAGCCACTGTTAGCTTCCCCACCCCCAGAAAATTTTGGAAGCTGATTGAGGGTGGGGAGGATGCTTTTTTTTTTTTTTTTTTTTTAAATGTGCTTAGAAAAAAATGATTCGATTGAAGGGTTTCCCCGGTTTCTGTGTAGAGGAATGAAGCGTGTCTGGGATTGAATCTGGAGCCTGGAAAAGATGCGATGCCTCTAGCTCTCCTAAAGCTAGGGAAGAAGAGGGAATTCAAAAGCTAGGAAGGAAAGGGGTGAAGAACAATCTATGATCCCTCTCTCCCCAGGTTGAGTTGGAAAGTTCTGAATTGAGGGGTCCATTGGGAGGACTTGGGGGAGGGAGACTCTGAGGTCCTGGGAGCTAAGAGAAATTGCTCCCCGCCCCCTACGTGGCCCGTGGGCGGCTCTGAAGGCACCGACTTGACCCGGGCCGGGTCTGCCTACGTGGAAGAGCACTAAAAAAAACCCCAAAGACACAGAAAGAAGCGCTGTGGGGGTGGGGTGGGAGCCCGAGTAGGACTGCTGAGAGTCTTTTAAGCCAAAGGGGTGCTCCCGATCTCAGCTAAACGGAGGCTGCGTTGAGACCTCTCTGATAACATAGGGGTGCTTCCCTCGCAG
Seq C2 exon
ATGGCCCCGGATTGCCAGAATGCGGCGGCAGCGGCTCCCGCAGACTGCGCACGGCCTACACCAACACGCAACTGCTGGAGCTGGAGAAGGAGTTCCACTTCAATAAGTACCTGTGCCGGCCGCGTCGCGTCGAGATCGCTGCCTTGCTGGACCTCACCGAAAGGCAGGTCAAAGTCTGGTTCCAGAACCGACGCATGAAACACAAGCGGCAGACGCAGCATCGAGAGCCGCCCGAGGGAGAACCAGGCGGGCCGAGCGCCCAGGACGACGCGGGAGAGCCAGCCGAGGAACCCACGGTCAGCCCGGGCGACGTCGCGACTCACCGGCTGCGGGAAGCCTGCTTCCACCCCGCCGAGGCCGCGCAGGGACCCCGGGGCGCACCGCCGTCAGCGCTGCCTGCCACCACCCTGGAGAGTGTGGGCGCATCGAGCCCCGGCTGCACAATGCTCAGAGCCGGAGGCCGGCAGAGCGAGCCCCTACCCGAAGACGCCTGCCCCGAGCGGCAGGATTCGCCTTTTCTACCGGACCTCAATTTCTTCGCTGCAGACTCCTGTCTCCAGATGTCCGGAGGCCTTTCACCCAGCCTGCAGGGTTCTCTCGATAGCCCCGTGCCCTTTTCCGAGGAAGAGCTGGACTTCTTCACCAGCACGCTCTGTGCCATCGACTTGCAGTTTCCCTAACTGTTTTCCATCTTTGGTCCTTTCCGTCTGGTCCTCCTTGGCTGTTGGGGGCGGGGGGAATCGGGCCTTCTCCACTCGTGGATACATTTATGCCGTTTTGTTAAAATCCAGATAGTAACGAATTAGCGTTTCATTCACTCCTTTTCGCTTTTTAAAACCACACACAAAAAATTCCACTTGGTAAAACTCCTTCCAACGAAATCTCAGGAATAATTAAACTCTAGTGGGAGAGGGTTTTCTTACAAAGAACTAGAGGGACCTATTTTCCTCTTTTTTAAGTTTTAGATTGTAGATTATTTATTAAAATTGTTTAATAATAGGAAAGGGGGAAAGTATTTATTGTACATTATTTTCATAGCGTAAATAAATGTCTTTATAATATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075588:ENSMUST00000100523:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.729 A=NA C2=0.664
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=25.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCTCTGGAGCAAACCTTCC
R:
GGAACTCCTTCTCCAGCTCCA
Band lengths:
342-1096
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