MmuINT0078753 @ mm10
Intron Retention
Gene
ENSMUSG00000038253 | Hoxa5
Description
homeobox A5 [Source:MGI Symbol;Acc:MGI:96177]
Coordinates
chr6:52201754-52204587:-
Coord C1 exon
chr6:52203789-52204587
Coord A exon
chr6:52202832-52203788
Coord C2 exon
chr6:52201754-52202831
Length
957 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAAG
5' ss Score
7
3' ss Seq
CGCTGACTTTTTTGTTACAGACA
3' ss Score
8.51
Exon sequences
Seq C1 exon
CTCCACCCAACTCCCCCATTAGTGCACGAGTTTACCTCTAGAGGTCATCAGGCAGGATTTACGACTGGACAACAAAAGCACGTGATTCGAAGTCGTACCCCATATTTGGGTGCCTACGTAGGAGGGAACCGAGTACATGTCCCAGTCATTTCCATAATTCATCATAAATTGTGCAAGGGTGCTATAGACGCACAAACGACCGCGAGCCACAAATCAAGCACACATATCAAAAAACAAATGAGCTCTTATTTTGTAAACTCATTTTGCGGTCGCTATCCAAATGGCCCGGACTACCAGTTGCATAATTATGGAGATCATAGTTCCGTGAGCGAACAATTCAGGGACTCGGCGAGCATGCACTCCGGCAGGTACGGCTACGGCTACAATGGCATGGATCTCAGCGTCGGCCGTTCGGGTTCCGGCCACTTTGGCTCCGGCGAGCGCGCCCGCAGCTACGCGGCTGGGGCCAGTGCGGCGCCCGCCGAGCCCAGGTACAGCCAGCCGGCCACGTCCACGCACTCGCCACCGCCCGACCCGCTGCCCTGCTCAGCGGTGGCCCCCTCGCCCGGCAGCGACAGCCACCACGGCGGGAAAAACTCCCTGGGCAACTCCAGCGGCGCCTCGGCCAACGCCGGCAGCACCCACATCAGCAGCAGAGAGGGGGTTGGCACGGCGTCCGCAGCCGAGGAGGACGCCCCTGCCAGCAGCGAGCAGGCGGGCGCCCAGAGCGAGCCGAGCCCGGCGCCGCCCGCTCAGCCCCAGATCTACCCCTGGATGCGCAAGCTGCACATTAGTCACG
Seq A exon
GTAAAGCCAGCCGTTTTCTGATCCACGCGTCCGTGGGGGCGCGGGTCTTGGTCACTCTCTGTTCTCTGCAGCCTCTCTCCCGTCTCTCTCCTAGTCTCGCCTCTCTCCAGCCCGCAGAGCCTCTCCCTGCGGCTCCCTTTTCCCTGCCTTTCTCTTTACTTCCTCCCAATTACTGCAGCAGCGATCTGCATTCACAGATACTGGGGAGAGGGGAGGGAGGAAAATGGGGTGGCCGAGTAAGTTTAAATGTTGAAAGAGGAAGAAATTCCGTCTGGAACCCCAGTGCCTCGGAACTCTCTTCAGGGTCAGGCCAGCGGAGTAGGGCATGCAGGGGTAGGGATGGCAGTAAGGGCCGTGAATCGGGCTTGTCAGGGGAGATAATTTATGGGAAGGGCTACGCTGGGGAAACAGCGTTACTAATTAGAGCCCCCTAAAAGGGGCTTGGGGGGAATAAGCCAGGCGAGGGCAGGCGGGATTCTGAAGTTTGAGGGCAAGAGGGAAAGCGAAGGAAAGGGAAGAAAAAGAAATCGGGCGCCCCAAGCGTACACTGGAACAGAAGGCGGCTAGCTCGGCTGGAACTTTAACTGAGGGTGACCTAGAGGCCACTTGGGAACTGAGAAAAAAAAGTAGTGCTTCAGTGCGTTTCTGGGCGGTGGGCAGACTGGGAGGGCAGTGCCCCCACTTAGGACAACTCGTAAAGGGCTAAAGAGCAGACTAGGGGGCGAGGGAAAGCCAAGCTGTCTTTAAACCCAGAGTTCCTGCCTCAGGTGGGTCGGTTGTTCCCAGAGTCCAAATCCGGTTGTTTTTCTCGCCAGAAAGGAAGGGAGAAGGAAATTTGGGGAGGGTGGGTGAGGAAGGAGAACTTGTTGAGCCTTCTCCGCAGCTCAGGACCCTGGCTGAGTTTTGGAACCAGGTGCTGAGGAGTTGGTGGCTAAACCGCTGACTTTTTTGTTACAG
Seq C2 exon
ACAATATAGGTGGCCCAGAAGGCAAAAGGGCCCGGACGGCCTACACTCGCTACCAGACCCTGGAGCTGGAGAAAGAATTCCACTTCAACCGCTACCTGACCCGCCGAAGAAGGATCGAAATAGCTCATGCCCTTTGCCTCTCCGAGAGACAAATTAAAATCTGGTTCCAAAACAGGAGGATGAAGTGGAAAAAAGATAATAAGCTGAAAAGCATGAGTATGGCCGCGGCAGGGGGGGCTTTCCGCCCCTGAGCATCTGAGCGGCCAAAGTACTGAGCAGTAGTAGCCGGGCAGCTCTCTGTAGTGTCAGTACTAAGGTGACTTTCTGAAACTCCCCTTGTGTTCCTTCTGTGAAGAAGCCCTGTTCTCGTTGCCCTAATTCATCTTTTAATCATGAGCCTGTTTATTGCCATTATAGCGCCTGTATAAGTAGATCTGCTTCTGTTCATCTCTTTGTCCTGAATGGCTTTGTCTTGAAAAAAAAATAGATGTTTTAACTTATTTATATGAAGCAAGCTGTGTTACTTGAAGTAACTAAAACAAAAAAAAAAAAAAAAGAAAAGAGAAAAAAAAACTACACACACAAAAAGCCCCCCCACCTCGTTTAGTGCCAATGTTGTGTGTTGCACTTGAGTTCTTTAATGTGCATGTACGTGGAAGTGTTCCTGTCTCAATAGCTCCAAGCTGTTAAAGATATTTTTATTCAAACTACCTATATTCCTTGTGTAATTAATGCTGTTGTAGAGGTGACTTGATAAGACACAAATTAACTTGTTCAACGTGTAGTGGCTAGTGGCTCTGTGACGAAAACTGTGACTCCAAGCGGTGTGTCCCTGCGTGCCTTTGTAGGACCCTTTGCACGAACTCTGGAAGTGGCTCTTATAAGCGCAGCTTCAGTGATGTATGTTTTTGTGAAAAAGTTACAAATATTGTCCAAGTCTGGCTGTTTAAGCAAACTGTGATCAGCTTTTTTTTTTTTTTGTATTTGTTTTTAAGGAAAAAAAACACTGACTGGAAACAAAACAAAATAAACTTTCTATTGTAAGTTCTCTTGGTCTGATTTATGCCAAATAGCAAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038253:ENSMUST00000048794:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.819 A=NA C2=0.253
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=67.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
CTCAGCCCCAGATCTACCCC
R:
TGACACTACAGAGAGCTGCCC
Band lengths:
356-1313
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