MmuINT0078754 @ mm10
Intron Retention
Gene
ENSMUSG00000043219 | Hoxa6
Description
homeobox A6 [Source:MGI Symbol;Acc:MGI:96178]
Coordinates
chr6:52206288-52208722:-
Coord C1 exon
chr6:52208186-52208722
Coord A exon
chr6:52206625-52208185
Coord C2 exon
chr6:52206288-52206624
Length
1561 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
CACCTCATTTCTGCCCACAGGTG
3' ss Score
11.25
Exon sequences
Seq C1 exon
TTCGGCCATCCAGAAACAAACCAGTTCGATGACTACTAATAGTTATAGCCAGATGTACTAATACACAACAAATCACAGTCCTGCAGAGGGGCGCGCAAATGAGTTCCTATTTTGTGAATCCCACTTTCCCTGGGAGCCTGCCCAGCGGCCAGGACTCCTTCTTGGGCCAGCTGCCCCTCTACCCGGCCGGCTATGACGCGCTGAGGCCCTTCCCGGCCTCTTACGGGGCGTCGAGTCTTCCGGACAAGACATACACCTCACCTTGTTTTTACCAACAGTCCAACTCGGTCTTGGCCTGCAACCGGGCATCCTACGAGTACGGGGCCTCATGTTTCTATTCTGATAAAGACCTCAGTGGCGCCTCACCCTCGGGCAATAACAAGCAGAGGGGCCCCGGGGACTACCTGCACTTTTCTCCCGAGCAGCAGTACAAACCTGACGGCAGCGTGCAGGGCAAAGCCCTCCATGAGGAAGGCACCGACCGGAAGTACACAAGCCCTGTTTACCCCTGGATGCAGCGGATGAATTCCTGTGCGG
Seq A exon
GTAAGGCTTTTCCCTGCTTCCCCACTCCAGAGAGTGTAGGGAGAATGAAAAGCTGGCAGGGAGACAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAGAGATTAGGAAGGGAGGAGAGAATAGGAAGAAAGAAGGAAAGAATGAACAAAATTTCCTTCTCTCTCTGTTGTTTTTTTTAATTTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAACCCAAACATTCCCATGGGACAATCAGGCCCAGCCAGAGGAAAGGCAGGGCCATGAGATCCCTGTAAGGTGACACTTTAGGGGAGGGTGAAGGATTCACTGCCAAGCCTTATGAACCCTGTAACTTAAGGGACAACAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAACTGGTTGAGATGAGAAAGCCTGCCCAGTTGCACCCTGGTACCACCCCCTCAGGTTTCCAAGCAGAGAGGGCCTCCAGAAGGTAGCATAGGCAAACTCCTCCAGGTTCCTACCCCAATCCTCTCTCTTCTGCCCTTTGGAAGTCCAGAAGCCCAGGCAGACAGATGCAGAGGCCCTCATTTCCACATTTGACCTCTTTCTGTGTCTCCACCAAAGCTTTGGAGGGCCACCTTCTCAGAATATTCATATTCTCTCTCTCTCTTTCTCCCTCCCTCCTCCCTGCCTCCCTCTTTTATCTTCTACTTAACTTTCAACTCTTAGTCAACTTCTGTCTTCTCCTGAGACCCTGCCTGAACCTCACACCTGGCTTGGGGAGTGAGTTGTCTCACCCTTGGGTACCTCTGGCACCCAGACAGCCCAACACAGTCCTCACTGCCAGTCCATCACCACCTCACTCACAGCACCCTCTCTTTGGCCCAGGTTTTCAACGATCTCACACAGAGACTCCCCTTACCCTTTGGAGCAGGGACAGAGCCTAAGGGGAAGTTTGCAACTTACAGTCGCTTTAGAGCTTAAACTCTCCCCAGTGGAGTGTTTTCAGGTGGATCACATAACTTGCTAACAATATGCAAAGATTTGAGAAGACTGGCCATATTTAACTTTCCAAAAGTACATTGAGATCTGAGGAGCCTGGATAGCGTCTTTCACAGACACAATGTAAGCATTCAATTTCCATACTGCTCCCAGAATCCCCACTGCACCCACAGACAAATAATTGCTACACTCCCTCGAAACAGTGACTTTGGCCCCTCAAATTAAGAATGGCCATGCTATTTCTTCAAGTCTAATGGTTCTCTTACAAACCACATTTGTCAAAATCAATAACTTCCCACTCAAATCGTTTTTAGGTGAAAAACATCTTGCTTGGTTATGAAATAATTCTTGCCATCCAGCCGGCTTTTTTCTTTCTTTCTTTCTTTCTCTCGGTTGTGATGTGAGAAGCTGGAGTGAAGCAGAGTAATTTCCAGTTTAGAGACTAATGGCTGGGAGGCACACGGGGCTGGGTAGGTTTTGCCTCGCTTATTCGCACCTCATTTCTGCCCACAG
Seq C2 exon
GTGCCGTGTATGGGAGTCACGGGCGCAGAGGCCGCCAGACCTACACGCGCTACCAGACACTGGAGCTTGAGAAGGAATTCCACTTCAACCGCTACCTGACTCGGCGGCGCCGCATCGAGATCGCTAACGCGCTTTGCCTCACCGAGCGCCAGATCAAGATCTGGTTCCAGAATCGGCGCATGAAGTGGAAAAAGGAAAATAAACTCATCAACTCCACGCAGGCCAGCGGGGAAGACTCTGAGGCCAAAGCGGGCGAGTAGACTCCAGTGCAGGGACCAGGCCAGCGTTGTAACCTCTATTGGCTTTGCCCCCTGGTGCCCTTGTCTGCTCCCCAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043219:ENSMUST00000062829:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.245 A=NA C2=0.267
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=65.5)
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:
AAGCCCTGTTTACCCCTGGAT
R:
TAGAGGTTACAACGCTGGCCT
Band lengths:
342-1903
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