MmuINT0078784 @ mm9
Intron Retention
Gene
ENSMUSG00000079277 | Hoxd3
Description
homeobox D3 [Source:MGI Symbol;Acc:MGI:96207]
Coordinates
chr2:74581985-74586328:+
Coord C1 exon
chr2:74581985-74582612
Coord A exon
chr2:74582613-74584378
Coord C2 exon
chr2:74584379-74586328
Length
1766 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGTT
5' ss Score
6.3
3' ss Seq
CTATCTCCCTCCTTGCCCAGGAG
3' ss Score
8.69
Exon sequences
Seq C1 exon
GTTACCTGGAGCCTGAGAGCTGGCCCAGCTCTCTCAAGATTCAGCAGACATTGGCCTTGGAGGAGAAGGAGACCGTGGTAGTCAATGTTATTTGAGCAGGGTCAGCTGACCCTGGAACTTCCTGAGTGCACCATGCAGAAGGCTGCATACTACGAGAACCCAGGACTCTTTGGAGGCTACGGATATAGCAAAGCCACTGACACATATGGCTACAGCACTCCTCATCAGCCTTACCCACCCCCTGCTGCTGCCAACTCCCTGGACAGTGATTACCCAAGTTCTGCCTGCTCCATCCAGAGCTCTGCACCTCTCCGAGCCCCAGCCCACAAAGGAGCTGAACTCAATGGTAGCTGTATGAGACCTGGCACTGGGAATAGCCAGGGTGGAGGTGGTGGCAACCAACCCCCTGGTCTGAACTCAGAGCAGCAGCCACCACAACCTCCTCCTCCACCACCACCCACCTTGCCCCCATCTTCACCTACCAATCCTGGAAGTGGAGTGCCTGCCAAGAAGACCAAGGGTGGACTCAGTGCTTCTAGCTCTTCATCCACCATCAGCAAACAGATCTTCCCCTGGATGAAAGAATCCCGACAGAACTCCAAGCAGAAGAACAGCTGTGCCACTTCAG
Seq A exon
GTAGTTCTCTAAGTAGGTCATCCCTGGACCAAGTCCCTTCAGATGGGCCCCAAGAACCTTTTACCCAGGAACCAAGTCTATTAGGTCTCTTAGGGCAACCTTAGCAACAATGTATCCAAACTCCCACTTGTGTAGAAATGTCTATCCTTTTTAGTGACTTTGATTGGGTACAGAGCCTTGCAGAGATAGGGCACTCTTTCATTGCTGGTTCCACTGCTGGACTGGTCTGATACTTATTAATAGAAAGTCCTTCTTTATATTGATATATTATCTGCCTTCCCAGGCTGCTGGTCCTAAATCCGCCTCCTCTTCTACTCAACAGCCCTTCAATGTGAAGATAGGTTGGGTATAGTTTCATACACCCATAATCCCACCCACCACTCAAGGCTGAGACTGGAGTGTATTGAGTTCAAGGAGAGTCTGGGAAGCATAGTGAGTTTCCAGGACCCTTTAAGAGATCTTGTTTTAAAACAGAAACCCAAGTAGAAACAAACAACACCCATACAGAAGAAAAAGGCCCATGCCCAAGTAAATTATAAACATTATCCATTTATTTTATTTAACTTTCCAAAGAACGCTTGAAAATAGATACAAGGTAACATCCTCACTTTCCCCAGAGCCACAGAACTGCAAAGTGCTGCAGTTGAATCTAACCGGTATGGCTTCAAGGCCTTTAAGGCATAACTGTGAGGTTCAGCCCACTCTAGTGAAGCTGTAAGTGGGAAGAGCATGTTCTGGGGGCGGGGGGGGGGGAGAAAATAATTAGGAACAAGAGCAGCTGTCCCTTTCTTGCCCTTGAAAGGGAGGCTCTAGAGCTGAGAGTGGTCCATTCTGAGTTTGAAAGAAGGTGGGCATGGTGAGGAGCTGATGCCTTCTGGTTGCTTAGATGGCTGCTTCTTGAAAATGTCTAGCTTTGTGTTCTTGATGGGGATTATTTTCCAGGTCTAGGGCTAGTCTGCAATCCAGGATATGGTTTGTTATCAGGTCTCTGTTCTGCCTGATGCTCCCTGGGCTGTTGCTCCTAAGGGAAAGTGTCTTCCTGCCTGAAAGCTCTCTCCTCTGCCCCTCCCTCCTTAGCTCAGACACAGGCCCTCCCTCCCAGGAGAAATCCATTTGTCTTCCCAGTGAAGGAGTGGACAAGCAGCTGAGGGGTGGCAGGGGAGGTGAAGCCAGTGCTGAGCCTGCTACTCCTAGCACTGCCATATGCGACATGCTTTCAGCCTGGCCTTGGGATCCCCTAAAACTCCAGGGCAGTATCTTTGGGGAGGGTATTATCACTTCTGTCTTTGGGTGCACCTGGCTTGACTGGGCCCCCTACTTCCTTCTTGGCTCTTTGGACTGTTTGACCTGTAAACAGACAAGGCAGGCTCGAGCTGCCACCTTAGTCCCCAGCCCCAAGCAGCAGAGGCTGGGAGGGGTGCTCTGAGAAGAAGTCTGCTCTTTTGGTGGAGCATCTCATGAGCTGCTTATAGCCTCACAATAATGCCCTGTATTGCCTTTGGGTTAGGATGAAACGAAGGGCTAGGATGGAGGGGAAAGAGGGCAGAGAAAGGCAGAGAGGTTACAGGTGCGACTGACAGGTAGGCCCAGAAGTGTGTGGGATGAGTGTTCCCAAAAGACTTTTATCTCTCAAAAGACCCCACCCTGCTCTAGGTAGGGATGGAGGTGAGAGTCGGGGAGGAACATGGAGACAGAGAAGCACCTCTTTCCGTTCTGGGATTCCTTACTCCTCACTCAGCACCCTCTCTATCTCCCTCCTTGCCCAG
Seq C2 exon
GAGAGAACTGTGAGGACAAGAGCCCACCCGGCCCAGCATCCAAGAGGGTGCGCACGGCGTACACGAGTGCTCAGCTGGTGGAGCTGGAGAAGGAGTTCCACTTCAACCGCTATCTGTGCCGGCCGCGCCGCGTGGAGATGGCCAACCTGCTGAACCTCACCGAACGCCAGATCAAGATCTGGTTCCAGAACCGTCGCATGAAGTACAAGAAGGACCAGAAGGCTAAGGGCATCCTGCATTCTCCAGCCGGTCAGTCCCCGGAGCGCAGCCCACCTCTTGGAGGAGCGGCGGGCCACGTGGCTTACTCCGGCCAGCTGCCGCCGGTGCCCGGCCTGGCCTACGACGCACCCTCGCCGCCCGCTTTCGCCAAATCGCAGCCCAATATGTACGGCCTGGCCGCCTACACGGCGCCGCTCAGCAGCTGCCTGCCTCAGCAGAAGCGGTACCCGGCGCCCGAGTTCGAGCCTCACCCCATGGCGAGCAACGGCGGCGGCTTCGCCAGCGCCAACCTGCAGGGCAGCCCGGTGTACGTGGGCGGCAACTTCGTCGACTCCATGGCGCCCACGTCCGGGCCGGTCTTCAATCTGGGCCACCTCTCGCACCCGTCTTCGGCCAGCGTGGACTACAGTTGCGCCGCGCAAATCCCTGGCAACCATCACCACGGACCCTGCGACCCTCATCCCACCTACACAGATCTCTCGGCTCACCACTCGTCTCAGGGACGCCTGCCCGAGGCCCCCAAACTGACACATCTGTAGCTGTTGCCGCCGGCCAGGCGCAATTACCTCTCTGGTTTTGGTGGCAGAGGTGGTGGTGGGGCGGGGCGGGGCCCGAGGGGCAGTTTAGGGGATCCCCCTCCCTGATCTGGCCTGGCGGATGCCTCACGAGTGGCTTCCAGCGGCCAGGGCTGACGCGACTGGGCCTCCCTCCAGGCGCGTCCTCCTTTGGGTGACTCGCCATAAATCAGCCGCAAGGATCCTCCCCAGTAAACCTGACAGTGCCATAAACTGCGGACCGAGGGACTCTAATCTGGTAATGGTGTCCCTAAGGTAAGTCCTCGACCCATCCGTGGCGAGTCCTGAAGAGGGACTAGGGCCTGGAGAACCCTGGGCCTGGCCCTTCTGTCTAGCTTAGTTTCAGAGACCTTAATTTATAATGCTCCGTCCCCTCCTGTAAAGATTGCATCGGACTAAACAATCTGTATTTATTATTTGAAGCGAGTAATTTCGTTTCCCTGATTATTTATCCTCGTCTTAATGTATTTATGTGTATATTTGTAGAATTCTGAGGCTGGGCCTAGGTACACGCTCCCAGGCCTTGGGGGGGCCACTTTTCACCTCTTTAGTCCCCTTGGTCTGAACTAGTTGAGAGGATAGTTTTGAACAGTTGTAACCATGGCTGGTGTCTGTAGTTGATGTTAAAGGATTGAGATCACAAATGGTCCTTCATGGGTAGAGTCAGGCAGCCCGGTGGCAGGACTCACGCTAGTCGTTTCTCAACAGCCGAAGCCCTCACCACTCGACACAGCTTATTGATTTCAAATTGTCTGGTACTATTTGAACAAACATTTAGAATAAAACCTTTTTTTCAGTTGGAAGTGTATCTGTGTTAATCGCACACATCTGCAAGCAGATCACTCTGTCTTCATCCCTCTGTATGATCCCGGGTTGGGGGAAAAGGACCCTCTGAAACATTTTATTTATTCGGAACCTATTGCACAAAATTGGCGTGGAGAAATACTTGATTACATTTAAGCTCTTAAAACTGAGCGGCAGTAATTGGAGGATGCAAACTCGATATCACCTAAGTGGGGGGCAGTCGCAATAGGATTTTGCCAGAGCAGCGCCTGCATGCTCTTTCTATACATGATCGTCACATGGGCGGGTGTGTGTTCATTTTTTCTGCATTAAATAATAAAAAAATAAACTTTGGGGAAAAACCCTGACAATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079277-Hoxd3:NM_010468:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.797 A=NA C2=0.496
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=22.5),PF132931=DUF4074=WD(100=24.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAATCCTGGAAGTGGAGTGCC
R:
CTTCATGCGACGGTTCTGGAA
Band lengths:
349-2115
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: