MmuINT0078751 @ mm10
Intron Retention
Gene
ENSMUSG00000079560 | Hoxa3
Description
homeobox A3 [Source:MGI Symbol;Acc:MGI:96175]
Coordinates
chr6:52169062-52172769:-
Coord C1 exon
chr6:52172121-52172769
Coord A exon
chr6:52170743-52172120
Coord C2 exon
chr6:52169062-52170742
Length
1378 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAT
5' ss Score
8.76
3' ss Seq
TCCTCTCTGTGTCCTGGCAGGGG
3' ss Score
10.83
Exon sequences
Seq C1 exon
GTTTGCGCGCGGCGGCCATTGGCGGCGGAGTGTCACGTGACCGCGGGGGCGTGCCAATGTGCTCCCTTACGGGTGTCAAGCCCTTGTCAGAGAGTGTGATCACGATCGTGAAACATCGCGATGCAAAAAGCGACCTACTACGACAGCTCAGCGATCTACGGTGGCTACCCCTACCAAGCAGCCAATGGGTTCGCTTACAATGCCAGTCAGCAGCCATACGCGCCGTCCGCCGCTCTGGGCACCGATGGCGTTGAGTACCATCGACCTGCCTGCTCCCTCCAGTCTCCCGCCAGCGCTGGGGGCCACCCCAAAACTCATGAGCTGAGCGAAGCTTGTCTGCGCACCCTGAGCGGCCCTCCTAGTCAGCCCCCAGGCCTGGGTGAACCACCTTTGCCTCCACCTCCTCCCCAGGCAGCGCCCCCAGCGCCCCAGCCTCCACAGCCCCCACCACAGCCCCCTGCGCCCACCCCTGCAGCTCCTCCGCCTCCCTCGTCTGTCTCTCCCCCTCAAAGTGCCAACAGCAACCCTACCCCTGCCAGCACAGCCAAGAGCCCCCTGCTCAACTCTCCCACCGTGGGCAAACAAATCTTTCCCTGGATGAAAGAGTCAAGGCAGAACACTAAGCAGAAAACCAGCGGCTCCAGCTCAG
Seq A exon
GTAAATGAATGCCTTTAGGAGGTGGGGCCTCTGGCCTTGTACCAGCTCCACGCTCCAAGCCACTTCTAGCTATTACAGCCAGCCTAGGAGGAGAGAAACATCTCCAGAAATGTGCCCTCCCCGCCCCCCCCCCCCACACACACCAGGGAAAACAAATCTTTCCAGAATCTTTGCTACTTAGGAAGGTGATACGGTTACTGTGAGAGGATCCCTCAGACATAAATCTGACTGAAGTCCCTCTGGGCCTCTCTAAGGCGGTTTGAGCCTGGTGAAGTTGGAATCCCTCCTTGTTCCAGTGTTGGGAATTCTGACCTCTAGATAGAACCATCTTTAGGACCACTGTCTCTCTAAGCACACAACTCCTTTTTTCCTGGGCAAACAGTGGCATCCTCCCCATACTGAAACGTGGCAGAATAAAAGCAGGCCCACTCATCCCCCGGGTCAGAATCAATGCTTGGTCTATGATCAGAGCCAATGTTTTCTGCAGCAGATGGACTGGCTGCCTTACTTCTGGGAAGGCCTTGCTCAGTCTTAGTACAATGCAGGAGGCAGCCGGGCATCCCCTGGGGGAGGGGATTCGGCTTGTCATCCTAATGGGAACCACATGGGGCTTTGGGAACTGGACTCCAGTGGGGGAGCCTTAGCCTCAGGGACTTGGGTTTCCAAGCCTCTAGGTTACCTTGGCCCCTTCCTCTCTGGTTTCCTTTGCTCTCTCCTCCAGAACTGGTATTTGGGAAGCCAAGGAGGACAGGAGGCACAAATGCAATGGTCCAAATTGGGGCAGCCTTCATGGTGACATTGAGAACCAAATGACCAAGACTCTGTAAGGGTCTGGTAGCTAGAACTAGGTATCTCCAGTGAGGTCTAGTCTCCTTTGGTCAGAGAAGGCCTTCCAGTTTGACAATACCAATCTGTTACTCTTTTCTTGGGAGATACTGAAAAACTGGTTAGTAGAAGCTAATGGCTGGTCACACAGGCAGGATGCATGCATACACTAGGTCTCCTACATTTTCCAGCGACTGAAGGAATCAAGATAGTGGCACCCGCTCACAGGAAGCTTGTTGTCTGATGGGCCAGGAAATAAGCTGGCCGAGTAAAATAGAGAGGAAGTTCAGGCCAGCAAGGCAAGCAGGAGGCTCTGCAGCTCTGTCCTCTCCTTGAAGAAGCCCCTGATTCGCTCCTTAGAGGAAGGAAGGGCAGGCTAACCAGGCTGTTTCCGCAGACCAAGAGAGGACCACAGCACTGAAGTCCTGCTCCTCTCTGGCCTTGGACAGAGGCTTCTGTGGGGTGAAGAAAGGAGGGGCAGGCCTAGGACTGGGGAGCTAGGCGGGGTCGGTAGCAGCCCCTGACACCGCTCTTCCTCTCTGTGTCCTGGCAG
Seq C2 exon
GGGAGAGCTGCGCTGGTGACAAGAGCCCGCCTGGGCAGGCCTCGTCCAAGCGCGCGCGCACGGCGTACACGAGCGCGCAGCTGGTAGAGCTGGAGAAGGAGTTCCACTTCAACCGCTACCTATGCCGGCCGCGCCGGGTGGAGATGGCCAACCTGCTGAACCTCACCGAGCGCCAGATCAAGATCTGGTTCCAGAACCGCCGCATGAAGTACAAGAAAGACCAGAAGGGCAAAGGCATGCTGACCTCGTCTGGGGGCCAGTCCCCAAGTCGGAGCCCTGTGCCTCCCGGTGCAGGAGGCTATCTGAATTCTATGCATTCGCTGGTCAACAGTGTCCCATATGAGCCCCAGTCACCCCCTCCTTTCTCCAAGCCTCCCCAAGGCGCCTATGGGTTGCCTCCGGCCTCCTACCCTGCTCCCCTGCCCAGCTGCGCTCCCCCACCTCCCCCACAGAAACGCTACACAGCGGCGGGGTCAGGCGCAGGGGGCACCCCTGACTACGACCCGCATGCTCACGGCCTGCAGGGCAATGGCAGCTATGGGACCCCACACTTACAGGGAAGCCCCGTCTTCGTAGGGGGCAGCTATGTGGAGCCCATGAGCAACTCTGGGCCACTCTTTGGCCTAACTCACCTCCCCCACACCACCTCGGCTGCCATGGACTACGGGGGCACTGGGCCGCTGGGCAGCGGACACCACCATGGGCCGGGGCCTGGGGAGCCACACCCCACCTACACGGACCTTACTGCCCACCATCCTTCTCAGGGAAGAATTCAGGAAGCGCCCAAGCTCACCCACCTGTGATGATGGGCCCAGGGCTGTGAGCCAGGAGAGTTGCCCACCCGACCTTCTTTGGTTACTTTTTCCTTTTTTTGTTTTGTTCTATGTTCTTGCCTTTCCCTTTTCTCCTCTGCACCCCTCCCTCATTTTGTTTTCTTTGGTAATGCGTTTTTATAGTTTATGTGACGTAGCAATCTTGGTTGCTGGAAAGGCTGTCAGTATCAGTAGCAACATTTACCACCACCCCTCCTCGCCCTGGCCTCTGGCCCTGCATCCTTTTCCTTCTCTACTCTTTGATAAGAAACAGGGTATATGAACAAACTTTCTAGTCGAGTTTTCAATGTGAATTTGTTCATACTTTATGGCTCCCGAGAGGAAGCAACTGCGTTTTTTTTTTTTAAGTTTTAGTTTTTAAAATTGCACTTCTTGTACTGATCGAGAAAAAGAAATCAAAGGCGCTTTGAAACAGGGACTCCCTGTGCAAAGATGACTACGTGTACGTCTTTCCGTGTGTGTGTGCTTGTGAACAGTCAGATTTATTTATATTTTTTGCAAGCATTGAATAGTCTAAGTTTTAAATATTATTTATCCCCATCCGTTCGTATTTATATTAAAGAAATTCTGTACCCTGATTGTTCAGAAGGTTTCTTGAGCCTTTTGTTCAATGGTGTATTGGCATACATATAAAATTTATTTGAAAGGGAAATAAAATTCCTTTATTAAAAACCGTAGCAATGCAATAAGAACAGAGAGGACCCAGAGTTTGAAAATAGTGGTTTAGGTTTGTAACATCTGGCCAAACTGAACGCTAAAAATGCTAGATTTGTTTTGAGAGTTTTACATTCCTTGCTGCTCACATTCTGAGAAACAAAACAAAAAAAATAAAGTTTTTATTCTGATTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079560:ENSMUST00000114434:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.870 A=NA C2=0.854
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=21.3),PF132931=DUF4074=WD(100=24.3)
Main Inclusion Isoform:
NA
Other Inclusion 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:
CGTCTGTCTCTCCCCCTCAAA
R:
CAGATCTTGATCTGGCGCTCG
Band lengths:
346-1724
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