MmuINT0078763 @ mm9
Intron Retention
Gene
ENSMUSG00000038700 | Hoxb5
Description
homeobox B5 [Source:MGI Symbol;Acc:MGI:96186]
Coordinates
chr11:96164826-96167435:+
Coord C1 exon
chr11:96164826-96165489
Coord A exon
chr11:96165490-96166203
Coord C2 exon
chr11:96166204-96167435
Length
714 bp
Sequences
Splice sites
5' ss Seq
ACGGTAATT
5' ss Score
7.31
3' ss Seq
CTCTCCTCTAACTGCTCTAGATA
3' ss Score
7.99
Exon sequences
Seq C1 exon
GAAGTACAGTGCATCGCTATAATTCATTAATACATCATAAATCGTGAAGCACAGGGTTATAACGACCACGATCCACAAATCAAGCCCTCCAAAATCACCCAAATGAGCTCGTACTTTGTAAACTCCTTCTCGGGGCGTTATCCAAATGGCCCGGACTATCAGTTGCTAAATTATGGCAGTGGCAGCTCTCTGAGCGGCTCTTACAGGGATCCCGCTGCCATGCACACCGGCTCTTACGGCTACAATTACAATGGGATGGATCTCAGCGTCAACCGCTCCTCGGCCTCCTCCAGCCACTTTGGGGCGGTGGGCGAGAGCTCGCGCGCCTTCCCCGCGTCCGCCCAGGAACCCCGCTTCAGGCAGGCGACGTCCAGCTGCTCCCTGTCCTCGCCCGAGTCCCTGCCCTGCACTAACGGCGACAGCCACGGCGCCAAGCCCTCTGCTTCGTCCCCTTCCGACCAGGCGACCCCAGCCAGCTCCAGCGCCAATTTCACCGAAATAGACGAGGCCAGCGCGTCCTCTGAGCCCGAGGAAGCGGCGAGCCAGCTAAGCAGCCCCAGCTTGGCTCGAGCACAGCCAGAGCCCATGGCCACCTCTACGGCCGCGCCCGAGGGGCAGACTCCACAGATATTCCCCTGGATGAGGAAGCTTCACATCAGCCACG
Seq A exon
GTAATTCTCCATCTCTTTTTTGTCCTCTCCGCATTCCTGCCCTGTGTTGGGGGTGGGGGCGAGCAAAGCTTGGCTTTGCCTCAAATATAGATCCCTTTTTTCTTTTCTTTTTTTCTTTTTCTTTCTTTCTTTTTTTTTGCCATCAAGAGGGAAAAGTGTCAGAAAGGGTCCCCACAGCTCCATAGATAGAGCCAAACAGTGTTGTTTTCTGGGCGTAGGCATTTAAAAAAAAAAAAAAAAGGCCAGTTTGTTGCCACGTTCAGCTTAGGTTTTGTTTACCTAGCCAGTCACCGGCTTTAGGATGAAAGATGGGATTTGTGTATTGTGAGGAAGGGTCCTGATTATTACAGAAATTTTGAGACTGCTGCTAGCAAAGGGGGAATGGGCTATAAACGGAGCTTTCTAGGGCAAAAGTGCAGTGGCTCTCTTCCCTCCCGGGCGAGCTGCCGCCTGAACCCAGCCTAGGGTGAGGCACTGGGAAGGAGCCAGAGACAAAGCCGGGAGCATTCACTACCATCAGAAGTGGGGGCTGCTGGAGAAGGGGGGGTATGAAGAAATAGAGGCTGGATGCAGGCATCTGGGGTGAGGAGGATGGGAGCTGCGGTGAGCTGGGTGCTGGGGACGCCTGGGTCCTGCTCCCCGCCCCCTCCCACTCAGTGCCCCCTCCTTTAACCGGAATAACGTTGCCTCGGGGCTCTCCTCTAACTGCTCTAG
Seq C2 exon
ATATGACTGGGCCAGACGGAAAAAGGGCCCGGACCGCCTATACTCGCTACCAGACCCTGGAGCTGGAAAAGGAATTCCACTTCAATCGCTACCTGACCCGGCGGCGACGTATCGAGATCGCCCACGCGCTTTGCCTGTCCGAGCGTCAGATCAAAATCTGGTTCCAGAACCGTCGCATGAAGTGGAAGAAAGACAACAAACTGAAAAGTATGAGTCTGGCTACAGCCGGCAGCGCCTTCCAACCTTGAGCCCATCCGGAGGAGCCCTGGGCGGCCCGAGAGCCCGCACCAACCCCAGCTCGACCCTTCCAATCTTCCCTGCACTGCCGCTGCCCGCTGGGGACCAGTTCCCACGAGCCTGTCACACCCCAGTCCTGTGTTACAATTTTTCGTTTGGTCTTAGGTCTTCCCATGGCTCCCTCTCTCCTGGACTGGTTATCTTGTTATTATTGTTAATAATAATTATTATTATTATTTCCCCCTCCGTGCTCCCCACTTCTCTTGGCTCGCCCCCCCCCAAGTTGCCAGTGTTTCTGAATGTCCTCGTGTCTGTGGTTGCGCTCCTTTCCCCAGGAAAAAGAAAAGAAAAAGAAATTCGCATGTTTAATGTGACTTCCCCTCCCCGTCTGTGTTCTAACTTATTTATAAAAGGATGATGGCTGTATTTTGAGTTTCTGCTGGAAACTTCCATAAGGGGCAGCAGTTGAGGTTGGGTAGTGCTGGGCCCAGCTGAGCTGGCCTGGGAAATGGAGCCCACTGTCTGTGTCTCTTTTCTCCCACCTCATCCTTCTTCAGCCCCACCCAGCCCCCACTCCCTAGGCTCAGGTAGCTTGTTCCTTGGGGTGGGAAGGGAGCTAGGGAAGGGTCAAAGTGTGGACATTGAGAAGAGGAGAGGAAAGGAGCAAGAGCTGAACTCCTGCTGCCTGGTAGGCCCCACAAGGCCTAGTCTGGAAGCGTATGGAATCAGAAATAATCCTCAGTGTAAAATGTCTTGTGATTTTTCTCTGTGAATCCGTGGGTCTGGCTAGAAGGCCCAATGCTGTAAATATGGGGATAGTCTGGGTCAGGCCAATCACTTCCTCTCTCACCCATTTCGCTTCCAAGACCATTTGTAGTGAGCGGGTGGATGCTGTGCTACGTGTGAAATCTGTCTTTGCCAGGCCTGTCTCAGTGATTAGCTTTTGGTATGTCTGTAGCTTTCCTTGAAGTTGAATAAATGTTTCCCCCACTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038700-Hoxb5:NM_008268:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.707 A=NA C2=0.195
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=68.7)
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:
TTCCCCTGGATGAGGAAGCTT
R:
GTGCAGGGAAGATTGGAAGGG
Band lengths:
357-1071
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs: