MmuINT1020835 @ mm10
Intron Retention
Gene
ENSMUSG00000038210 | Hoxa11
Description
homeobox A11 [Source:MGI Symbol;Acc:MGI:96172]
Coordinates
chr6:52242106-52245810:-
Coord C1 exon
chr6:52245011-52245810
Coord A exon
chr6:52243593-52245010
Coord C2 exon
chr6:52242106-52243592
Length
1418 bp
Sequences
Splice sites
5' ss Seq
CCGGTGCGT
5' ss Score
9.74
3' ss Seq
TTGCCTCTCTCCTTCCTTAGGTG
3' ss Score
12.96
Exon sequences
Seq C1 exon
AAATTTCTACTTCACGGATCCGCTTCAAAGAGGCAGCTGCAGTGGAGAATCATGTTAAGCTCGGCTACTGCGGAGAGCCCAAGGTAGCCCAATGATGGATTTTGATGAGCGTGGTCCCTGCTCCTCTAACATGTATTTGCCAAGTTGTACTTACTACGTCTCGGGTCCAGATTTCTCCAGCCTCCCTTCTTTTTTGCCCCAGACCCCGTCTTCGCGCCCAATGACATACTCCTACTCCTCCAACCTGCCCCAGGTCCAACCCGTGCGCGAAGTGACCTTCAGAGAGTACGCCATTGAGCCCGCCACTAAATGGCACCCCCGCGGCAATCTGGCCCACTGCTACTCCGCGGAGGAGCTCGTGCACAGAGACTGTCTGCAGGCGCCCAGCGCGGCCGGCGTGCCTGGCGACGTGCTGGCCAAGAGCTCGGCCAACGTCTACCACCACCCCACCCCCGCCGTCTCGTCCAATTTCTATAGCACGGTGGGCAGGAACGGCGTTCTGCCACAGGCTTTCGACCAGTTTTTCGAGACGGCTTACGGCACCCCGGAAAACCTCGCTTCCTCCGACTACCCCGGGGACAAGAACGCCGAGAAGGGGCCCCAAGCAGCAGCTGCGACCTCCGCTGCGGCGGTGGCGGCGGCGGCCACGGGCGCGCCGGCAACTTCAAGTTCGGACGGCGGCGGTGGCGGCGGCTGTCAGGAGGCGGCGGCGGAGGAGAAGGAGCGACGGCGGCGACCCGAGAGCAGCAGCAGCCCCGAGTCGTCTTCCGGCCACACTGAGGACAAGGCCGGTGGCTCCG
Seq A exon
GTGCGTATAAAGGCAGCGCCCAGCGCTTTATGAAAGGGGAGTTGGGAATCTAGCGCAGCACCGCTGTTAAATTTTTATATGCTGTTTTATAAGCATATAAGGTTTATGAAGGGCCTTTAGGTTTCCCCCAACAAAACTTTGTTATAAAAGGAGGGATCACGTGGCGAGTGCTGAAATTGGCCGTGAAATACCCACCGGCCAAAGCATGCCTGCAGAAAAAAAAAAAAATACAACTCCCCTTTTTCCTTTTTTCCCTTCTCAGCTCCCAAACTCAACAGCACGATCCCCGCTAGAGACCAGCTCCAGGCTGGGGAGCCGGAGGTGGGCGCCTGTAAATTCCCCCTACAAGGGCTTCAGGAGCCTTTGATAGCGGGGTAATCCGGAGATTTTTATAAAAGCCATGTGTTGCGGCGGGACTCCAGTCCCGGCTGGGATTCAAAGGCATCGGCTGTTTAATGATGGCGCTAAGAGCGCATTTAACAGATAAAGTAGCCCACTTAGCTCAAGCAATATATTAAAAGAAACAAATTAACTTAAATTTGGCCTTTTTGTCCAAAGGAAGCCATTTTCCTCTGGTCCGGTTGCAATTACATGCTGCCTTCTGTTATTCACAATTGTTTTTAAATCAGTCAAAAGTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTCTTAAAGGTGAGGGTGAACAAATGGATCCTGCCTGAGGCTTAAGGTAGCCTCTCTTTCCTCTACCCTTCCTAAACTAGCATCCCTACCCTGCTGAGGGCCCTCTGGCAGTATGCTGACGGTGTGTACTGAGTGAAGGCCTGGGTAGGGGTTTCCTCTGCCACCTCCCACCTCGAGAGAGCTGGGAGGCTGGCGGAAGAGGCAAGAACTGATCAGAAGTCAGGCTGACAAAGACCCCTCAGCCGCCCCAGATGTTAAGGAGGGCTAAATCATGGCGGCAAGCAGGAAAGCCTGGGGCCAGGATGCATGCCTTTACTGCCTCGGGAACAGGCGGCCCAGGTGCTGAAGGTGAAATGTCCTCGGGCGGCTGTTTGTTTAGTCTGGCGGGGCAAGGAGCAGCCCGCAACCCCCACTTGCCTCCGTTCAAAGCAGTTCAACCAGCGCAAACTCGCCTGTTGCTGTGAGGAGCCTTCCTTTCAGCTCAAGGGGCAGCCTGAGTCCTTTCCCTGGGGGCCTATCTAGTGAGCTGGCTTTTATCTGAAGCCGGCTCCAGACTGCAACTTGTCCCTGACCAGCAATAGAAGCCTGAAGGCAGGGGCCTGGAAAGACTTTGAAAGGGCCTGGATTGGGCCTCCAGACCCTGTGGCCAGACCTTCTCCAATGGGGGTCCTGGGAGAGGGTTGCACCCCTATCGCCCTCTCACTCTTTGCCTCTCTCCTTCCTTAG
Seq C2 exon
GTGGCCAACGCACCCGCAAAAAGCGCTGCCCTTATACCAAATACCAGATCCGAGAGCTGGAGCGAGAGTTCTTCTTCAGCGTCTACATCAACAAAGAGAAGCGTCTGCAACTGTCCCGCATGCTCAACCTCACCGACCGTCAAGTCAAAATCTGGTTTCAGAACAGAAGAATGAAGGAAAAAAAGATTAACAGAGACCGGTTACAGTACTACTCAGCTAATCCACTTCTCTAAGGCTCCAGCCTACTGGAATTGGGAGGGGGGCTTCATACATGTGAAATAATATGCAGATTTTGCCCTTGACAAGGTCAAGCCACATTGCGACTTGGAAAAGGGGGGTGATATAGGAGAGAGGAGAGGTTTCCTTATCAGAGATTCGTCCAATAGGAAGGGGGCCTGAAACTCTCTTGGTTCAGATCTCCGTGGTTAAGCTTCCTATTAGTAATTGAATTCTAAGGGTTGTGAATCAACAGAATGAATGGTTTGGGACCCCTGGTGGTTCACTCTTAGAGCCTGCAAAAGCTTTGAGCTGGGTGTGGTCACTGGAGATTGGGCCCCCTGCCAAACCCTAAGGAGGCCACCCGCTCAAGACCCTCTGCACAGAGCCTGCCCACCCCCAGGTCTCCCAAGTCAAGAAACTGTGTGCCCCAAGCCTAGTTCAGCTTGGGGATAGGAGCAGGAGGAAAGGGGATGACTCCTAGAGATTCAGGCTGGGGTTGCTTTCCAAAAGTAATGTGAAAGACAGTTAACCAAAAGGTGGCTGTGAAAAGGGAGAGAGAGTGGGAGGGGGGTGTCCTGGAGGAAGGAGAAACCTATCCAGATGTCATTAATATCATCCCACCACTGATCTGCACCCAAACCTGAGCTCCTAGCAGCCACCTTCTGCAGCCTACCTGGGTTTTCTACCTCCCAATGGTGGTGATGGGTCTTCCATCTCAGAGCTGACTATTCCTAGGGTAGAAGACATTGAAAACTCCAGAGGCTGTGCTGGTTCCTGGCCCCTCAATCTCTACAGGAAATGCCTGCGGAGGGCTACAGTTTGGCAAACTCTTCACCACATTAAGGAAACTTGGATTTGGTGTCTGTCAGGCAGCAGAGCAGCAGGCCTGGCCAGTGGGTCCTTGGCCTTTGGCTGTGAGGGGCTGAAGTTCCCCCCCCCCTCCCAAATCCCTCATTCCTACCCTGCACTCTGTGCTCATCAACTCAGAACTGAGCTTGGAAGCTTCTGGCAATCTTCTAAGAGCCGGAGAGTGATTTGGAGCTATTTTAAAAGATAAATATTATATTATATATATATATTTCCCCGAAGGAACCAAAGCGAATTTTAAGAAGCAATGTAGAGGGGGGGGTGGGGATAATAAAAATATTTAAAGGCTCTATCTGTTTACAGTGTTCCAAGGTTAAACTCGCTCACTGCTAAAATATTTGAATGTATGCTTCATACAGGGATGGTGTTCAAAAGACTGTAAATAAAGAAACCATAACCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038210:ENSMUST00000048026:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.447 A=NA C2=0.234
Domain overlap (PFAM):
C1:
PF120453=DUF3528=WD(100=62.9)
A:
NA
C2:
PF0004624=Homeobox=WD(100=73.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCAGTTTTTCGAGACGGCT
R:
AGAACTCTCGCTCCAGCTCTC
Band lengths:
358-1776
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