MmuINT1020842 @ mm10
Intron Retention
Gene
ENSMUSG00000018973 | Hoxb1
Description
homeobox B1 [Source:MGI Symbol;Acc:MGI:96182]
Coordinates
chr11:96365752-96368256:+
Coord C1 exon
chr11:96365752-96366391
Coord A exon
chr11:96366392-96366810
Coord C2 exon
chr11:96366811-96368256
Length
419 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
TCTCCCTGCCCCGCCCCTAGCGA
3' ss Score
8.71
Exon sequences
Seq C1 exon
TGTGACATACTGCCGAAAGGTTGTAGGGCAAGAGGGTGTCTCCCCCAAACGGCCCGACCCTCCTTCGGCCTCTACATGGACTATAATAGGATGAGTTCCTTTTTAGAGTACCCACTTTGTAACCGGGGACCCAGCGCCTACAGCGCCCCAACCTCTTTTCCCCCCTGCTCAGCTCCGGCCGTTGACAGCTACGCAGGGGAGAGCCGCTATGGTGGAGGGCTGCCTAGCTCAGCGCTCCAACAAAACTCGGGGTATCCTGTCCAGCAGCCGCCGTCATCCCTGGGGGTGTCCTTTCCCAGCCCCGCTCCCTCGGGGTACGCCCCAGCCGCCTGCAACCCCAGCTATGGGCCTTCTCAGTATTATTCTGTGGGTCAGTCGGAAGGAGATGGAAGCTATTTTCATCCGTCGAGCTACGGAGCCCAGCTAGGGGGGTTGCCCGACAGCTATGGAGCGGGTGGAGTCGGCTCAGGGCCATATCCTCCGCCGCAGCCCCCATACGGAACTGAGCAGACCGCAACCTTTGCATCAGCCTACGACCTCCTCTCTGAGGACAAGGAATCGCCTTGCTCGTCAGAACCCAGCACTCTCACTCCCCGGACCTTCGACTGGATGAAGGTCAAGAGAAACCCACCTAAGACAG
Seq A exon
GTAGGGCTCAGAGGAGCCACTTCCTCTCCTTGGCTCGGGCATACACAGAGGGGCCTGAGCCAGGGCTTCATTCATTCCTTCAGCTGCTTTTACTGGCAGGTAAGTACTTTCCGGGTTCAAGTCAGCAGATATTTTCCCACGGGCTAAGTTCGGGGCTACCTCCTCCCGAAGGAGGTCTCCGCAGTCTTGTCTGTGCGCCCAGTTTGGAACCAGTATTTCACGTTTCTTGTCTGAAGGTGAGTATGGGCGGAAGGCTGGTTCTAGATTTTGTAATTACTAATGGAGGGGGTGTGTGATGCCACATAGGATCTGCATTGGGTAGATGATGAATGAGGACCAAGCCTGAACTAGGAGGAGTGGACGGGAGGGAGAAAGAGGTGAGAGAACTGACGTGGCTTTTCTCCCTGCCCCGCCCCTAG
Seq C2 exon
CGAAGGTGTCCGAGCTGGGACTGGGCGCTCCCGGCGGTCTCCGCACAAACTTCACCACGCGCCAGCTGACGGAGCTGGAGAAGGAATTTCATTTCAACAAATACCTGAGCCGTGCCCGGAGGGTGGAGATCGCCGCCACCCTGGAGCTCAATGAAACGCAGGTGAAGATCTGGTTCCAGAACCGGCGCATGAAGCAGAAGAAACGCGAGCGAGAGGGGGGCAGGATGCCTGCAGGCCCCCCAGGTTGCCCAAAGGAAGCCGCTGGAGATGCCTCTGACCAGTCCGCGTGCACCTCCCCAGAAGCCTCGCCCAGTTCCATCACCTCTTGAATTGAACTTCCTAAGTAACTGGGCTTCCAACGCTTGACCAGTTCTCTCGAAGACTTTCCCAAACTTCACAGCCTTGGTGACCCTCCTCAAGGCCGAGGCACCAGTTTAGAGCTGCCCAGGAAACTGGGCAGGAGTTGGGAAATGTATTTTTCTCTCTCTCAGATCTAGGGGTGGAGGGATGATTGATGGCTGGGGATCCTACAGGTCTTGGGACCTGGGGAACACTCAACTCATCAGAGGTCGAAGGAAGGCCTTTTGGCTTTGATCTGGAGTCAGCCCATCCTTTCGGGCTTCTCCTTTCCCTTCCAACTCAGTTCAGTGCCTTTGAGCTTAGAGAGTTCTTCTTTCGAATTCTTAGCCCAACTCTTCTTTCTAGGTCTGGGATGTCTAGGCTGGGAGTCCTTGGGGTTTTTCTGGGGGAGGATGCGTTTGAGTGTGAGCCCAATCGCCACCAACCCTTAATCTTAATCCAGCCAACTCACCGCAGACCTTACAATAGCAGACCTTACAATAGCACCGACTGCCTTGTGACATACCAAAAAAAAAAAAAAACAAAAAAAACAAAAAAAAACAAAACAAAACAAAAAAAAACAAAAAAAACCCCACAAAAACAAAAACAAAAAAAAAAAACAACCTTACTCCCAAGTAATCCCACAACCCTTTTCCTGGCACATGTCTTTTGCACTAATGCAGCCCTCAGAGGCTGGCTTACGAGACTCTCCCCTTCCCACTGGCATCACAAAATCACCAAAGTGTTTTGGAACTTGGCACTATGGAGATTTCCAGAGCATCATTGCAAGGACTGCCTCAAGCAAGCCTCAACCAAGAAGGGGCGAATACCCCCTCCCAACTCCCTATTTATTACCTCCGGAAAAGCCCACCCCCCAAACCTCCCTCCCCAGCCCATTCTCCTTTCCATAAAACCACCCTACCCCTGGGGCAGTCTGGGGAGGCCCAGGAATGGTGACAGAGTTTCCAGTCTCTTCAGACATTTCTCCAAACCCCGGAGACAGCAGAGAGGCCACTTGAGTTTCTAGAAAACCAAGCTCCAAGCAAGCCAGGTTCTCTTTGTATCTGCAACTACCTCATTGCAATAAAGTCTGTTTTTCTCCCTCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000018973:ENSMUST00000019117:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.577 A=NA C2=0.697
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=50.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCAGTCGGAAGGAGATGGA
R:
ATTCCTTCTCCAGCTCCGTCA
Band lengths:
358-777
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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