MmuINT0078740 @ mm10
Intron Retention
Gene
ENSMUSG00000000938 | Hoxa10
Description
homeobox A10 [Source:MGI Symbol;Acc:MGI:96171]
Coordinates
chr6:52231197-52234939:-
Coord C1 exon
chr6:52233959-52234939
Coord A exon
chr6:52232781-52233958
Coord C2 exon
chr6:52231197-52232780
Length
1178 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGC
5' ss Score
8.84
3' ss Seq
TGTATTCTCTTAAACTCCAGGCA
3' ss Score
7.28
Exon sequences
Seq C1 exon
AAGAAATGTCAGCCAGAAAGGGCTATCTGCTCCCTTCGCCAAATTATCCCACAACAATGTCATGCTCGGAGAGCCCTGCCGCGAACTCCTTTTTGGTCGACTCGCTCATCAGCTCAGGCAGAGGCGAGGCTGGTGTTGGTGGCGGTAGCGCGGGGGGCGGTGGAGGTGGCTACTACGCCCACGGTGGGGTCTACCTGCCGCCTGCCAGCGACCTGCCCTACGGGCTGCAAAGCTGCGGGCTCTTCCCCGCGCTGGGCAGCAAGCGTAATGAAGCGCCGTCGCCCGGAGGCGGTGGCGGTGGTGGCAGCGGGGGCCTGGGTCCTGGGACGCATGGCTACGCGCCCGCGCCCCTAGACCTGTGGCTGGACGCGCCCCGCTCCTGCCGGATGGAGCCGCCCGACGGGCCGCCGCCACCGCAGCCACAACCCCAGCAGCAGCAGCAGCAGCCGCCGCCGCCCCCGCCGCAGCCACCTCAACCCCAGCCACAGGCCACTTCGTGTTCTTTTGCGCAGAACATCAAAGAAGAGAGCTCCTACTGCCTCTACGATGCTGCGGACAAATGCCCCAAGGGCTCGGCCGCCGCTGATCTGGCCCCTTTCCCGCGGGGCCCGCCGCCCGACGGCTGCGCCCTGGGCGCCTCCAGCGGAGTGCCAGTACCCGGCTACTTCCGCCTGTCGCAGGCCTACGGCACGGCCAAGGGCTTCGGCAGTGGCGGCGGCGGCACGCAGCAGCTCGCTAGTCCCTTTCCTGCGCAGCCCCCGGGGCGCGGTTTCGACCCGCCGCCCGCACTGGCCTCTGGCTCGACCGAGGCAGCCGGGAAGGAGCGAGTCCTAGACTCCACGCCACCACCCACTCTGGTTTGCACCGGTGGCGGCGGCTCGCAGGGCGACGAGGAGGCACACGCGTCATCCTCGGCGGCTGAGGAGCTGTCTCCAGCCCCTTCAGAAAACAGTAAAGCTTCGCCGGAGAAGGACTCCCTGG
Seq A exon
GTAAGCAGAGCTCAACCGAGGGCTCAAGTCAGACGGGCAGACAGACAGACAGACAGACCCACAAGGAAGGAGCAGAGGACCAGAAGCCCGCGCGGCAGCCGTAGGCCTTGGCCCAAACTGACGGCAGGCTGACCTTCTGAACTTGTTTTTAATATTTGGGCGTGGGGATGCTGTAAAAATCCACGTCCGGCTTAGGGCCCCACACCAAGACGTCCTCAGCTCTGGCCCCTGCTCACCCAGACTTGGGGGATGAGAACACCAGCGAGCAGCCCTCCTCCCGTGCTTGCACTTTCTCGTGGCCCTGAGTACCCCCAAGCCCTGGTCCTTAGCCCAGCCTGCTCAGCGCGGCCCACGCGGGGGGGAGGGGCAGGGAGGAAAAGTGGCTCGCTTGCAGATAGCACGGATGTTTGTAAGGCATCCAAAATAAGCAGCCGCCAGAGCCAATAAATAAGCCCATTAACCGGCGAAGTTCGAGTTTACGATCCCCCATGCGTTTTTCAAAGTTTCTGGAGGGGCGGGAGTCCTGGTTGTAAGAAAAAAGAAAAGACAAATTCGGCCGGAACGCTTGGGCCCAGAGCTGAAAACCTAGGAATGGCCATTCCCCTTCTCCTGGAATCTGGTGCTGCCCAGCTTCACACTCCGGTTACTTGGAGGGACAGGAGCCAAACCCAAGCCCTTGACCCCAGAATCGGGTTTTTGGAACTTCCCCATTGGCCCAACTATGCCCTTCTCCTCTAGCCTGGGGCGATCTAGGAGGCTAGGGTAAGCCAGTGGAGCTGCCAGCCTCTCGTCCAAAGAAGCATTCCCTTACCCCAGCTTGGGGGCCGGCAGGAAATGCTTCCCTGCCCCTGGGTGAGAGGCAGAGAAAGGCGTTAAGTTCAAGATGTACGGCCTCGCCTCCTCCGGCCTTTCATTCTCTCAGCGCCCCGCGGCGTGGTGCTAAAACAGGTGCCTGGAAAAAAGTAGAGGAAAATGTAAATTGGGAGGACCGGGTGTGGATTTGAGGCCGATTTTGTCATGCCTTTTTGGAGGGATTTCTTGCAAAAGGAGGGAGGGCATAACCCTCTCTCTATGACTTCGGGCATCCCACTAAATGGGAAAGACCCGGAATTCACCCCCCTCATACAGCCCGAGTGGCCTCGACTTAACCTTCCCCTCTGTATTCTCTTAAACTCCAG
Seq C2 exon
GCAGTTCCAAAGGCGAAAATGCAGCCAACTGGCTCACAGCAAAGAGCGGCCGGAAGAAACGCTGCCCTTACACGAAGCACCAGACGCTGGAGCTGGAGAAGGAGTTTCTATTCAACATGTACCTTACTCGAGAGCGGCGCCTAGAGATCAGCCGTAGCGTCCACCTCACGGACAGACAAGTGAAAATCTGGTTTCAGAATCGCAGGATGAAACTGAAGAAAATGAACCGAGAAAACCGAATCCGGGAGCTCACAGCCAACTTTAATTTTTCCTGATGAAACTTCCAGACAACGTCTTTTCGCTTCCTGAGCGCCTGGACCCATCCTCTGCCTCCAGCCTCTGCCCCAGAACTCACACCTGTGCCGGAGCCCCTTTCTCCCTCCCACACTCGCCATCTCCCAGGCCGTTTCGTCTGTGCAGGGCTGGTTTGTTCTGGCTTTTTTTGTTTGTTTGTTTCTTTGTCTGTTTGCTTGGTGTTTGTTTGCTTGTTTTCTGGGGGAAAAAGCCATATCGCTAAAATTCTATAGAGGTTGAGATCTTTCTCAGTGTCAAGTCCTGAATGGGCTGGGTTTGCTGCCTCTGGGACCCACTGCTAGGAAAGGGCCCCAGTACTCCTCCACGGATCTGGTTTCCTGCCCAGCCCTGGGTAAACTTAGCCGGAAGCCTTAGGTCCCATTGTCGGCGCTGAGGTGTCTGGCCTGAGGTCAATGGTGCAAGGAGCCGCCACCGGGTTCGCCAGCCTGGAGTGCTGGGCTGTGTTTAATCAGGGAGTCCAGGCCTGGTTTCTCTTTTCTTTCTTCTTTTCTTCCTTGGCCAAGAGCAGAGTATGGAAGCATGGACATTCAGGTTAGCTAAAGGGCTTGACCTGGCTGGTTGAAAAAGTGAAAAAGAAATAATCAGTAAGATTAATTTTTCCTTCTTTTGTAAGATCTCCCAGCTTTAAATGAAAATTAAAATGGGCAAGAGAAGGAAACCTCTCTTCCCGTTTGCCTAAGGTCTTGCTTGCCTGGCTAAAATCCTTCATTCACCTTTGAGTTTCCATATCCCTGCTGTTAACAAATAATGCAGGTTTGTTTATACATGTGGAACTGGTGGATTTTCGTCATTAAAACTGTTACCAATTGGTAACACAAGAAAAGCACACCACAATTCTCCCTATTTAATGGAGGTTGTTTTTTTTTTTTTGCTTTAATTCACTTTTTGTTTTTGTTTTTGTTTTTTATTTTGTAGGCTTTCTGAAATTCATGGAAGCCTAGGTGGGCTGGGGCAAGCAGAAATAAAAATGAGAGAAGGGAGATATTGTTTGGATTTCCTTTATACTGTGAAGTTACATGCATAAAAGGGTCAAACCTGTAGGTGCAGAAAAGAAAAAAAAAACCTATAAATACAAATCTGTATAAATGTCTATTATTATGAAAAATTGCCAATCTTGTTTAAGCAAATGCATTCTATCGTTATTATAAATGTTAGTTCTAGCTTTATTTACTTCAAAATCTTAAATCAGAATAAATTAATATTGTATTGCTGCTGTGCGTGGAAAAAGATGATGTTTATGTTCTTATAGAATAAAAGCTGTGGAATGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000000938:ENSMUST00000125581:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=0.316
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=62.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACAGTAAAGCTTCGCCGGAG
R:
GCTCAGGAAGCGAAAAGACGT
Band lengths:
345-1523
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