MmuINT0078791 @ mm9
Intron Retention
Gene
ENSMUSG00000043342 | Hoxd9
Description
homeobox D9 [Source:MGI Symbol;Acc:MGI:96210]
Coordinates
chr2:74535820-74538265:+
Coord C1 exon
chr2:74535820-74536890
Coord A exon
chr2:74536891-74537236
Coord C2 exon
chr2:74537237-74538265
Length
346 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
GCAAACCCCCCTCTTCCTAGACA
3' ss Score
5.57
Exon sequences
Seq C1 exon
GCCGCCGCCACCAGGGCGGGCTGAGCCGGGCCAGGCCGGGCTGGTGCGTGGACCTGGGCCCGGCAGCTCTAATTGCAACGCTCCTGTTGATGATGATTTTTTTTTTTTTAAATCACAGCAGCCCCCAGTTTAGCGGACTGATTTACTCCGGGTATTGGTAAATATGATCACGTGGGCCGCGCGACCAATGGTGGTGGCTGCAGCCTGCGAACTAGTCGGCGGCTCGGGCGCCGGCGAGGAGCCGCTCGGCGGTGGGCAGTGGAACCTTGGGTGGGAGCGAGCGGCGCCTCACCATGTCGTCCAGTGGCACCCTCAGCAACTACTACGTGGACTCGCTCATAGGCCATGAGGGCGACGAGGTGTTCGCCGCGCGCTTTGGGCCACCGGGGCCGGGGACACAGGGCCGGCCCGCAGGTGTGGCCGATGGCCCAGCCGCCGCCACCGCCGAGTTCGCCTCGTGTAGTTTTGCCCCCAAATCGTCCGTGTTCTCCGCCTCGTGGTCCGCGGTGGCCGCCCAGCCCCCGGCGGCGGCGACGATGAGCGGCCTGTACCACCCGTACGTGTCCCCGCCGCCCCTGGCTGCCGCCGAGCCGGGACGCTACGTACGCTCCTGGATGGAGCCGCTGCCCGGCTTCCCCGGCGGCGCAGGCGGTGGCGGTGGCAGTGGTGGCGGCGGTGGCGGAGGCCCGGGTCCCGTTCCCAGCCCCGGTGGCCCAGCCAACGGGCGCCACTACGGGATTAAGCCTGAAACCGGAGCGGCCCCGGCCCCCGCTGCAGCCTCCACCTCCTCCTCCTCCTCCACCTCCTCGTCCTCCTCCTCCAAAAGGACTGAGTGCTCCGCGGCCCGCGAGTCCCAGGGGAGCGGCGGCCCAGAATTCCCGTGCAACTCGTTCCTGCGGGACAAGGCAGCGGCGGCGACAGGGAACGGGCCCGGGGTGGGAATCGGGACCGGGCCAGGGGCGGTAGGCTCGTCCGAGCCCTCAGCTTGCAGCGATCACCCGAGCCCGGGCTGCTCGCTGAAGGAGGAGGAGAAGCAGCCGCCGCAGCCGCCGCAGCAGCAACTTGACCCAA
Seq A exon
GTAAGTGCAAAAGAAATTGCCCCCTGATTTATTGCTGAAACCTGTAAGGCTCGAATGTGCAAAACTGATAGTTTTACTAACCTATAAAAACGTCTAGACGCCTACCCAAGCCTAGGCGAGCAACACGTATCCATAAAAAGCTTCCCATAACCACCTACCTTGGGCGCGCGGTTTGTACGGTAAACAGAGCGCGGGCATTAAGGCTTTTTATGATAATTCCCCCAAGTTGTGAAAAGCGTCCATCCTTGGTGAAATTAATTTAACGACCTCTCTTCCCCACCCTGTCGTCTCTCCCTGCCTCCCCTCCGCCCCTCGCTCCCTTGTCTGCAAACCCCCCTCTTCCTAG
Seq C2 exon
ACAACCCTGCAGCGAACTGGATCCACGCTCGCTCCACCCGGAAAAAGCGCTGTCCCTACACCAAATACCAGACGCTAGAGCTGGAGAAGGAATTCCTCTTCAACATGTACCTCACCCGGGACCGGCGCTACGAGGTGGCCAGGATTCTGAACCTTACAGAGAGACAAGTCAAAATCTGGTTCCAGAACCGTAGGATGAAAATGAAAAAGATGAGCAAGGAGAAGTGCCCTAAAGGAGACTGACCCAGTGCGGGTCTGGCCTGCAGCACTCAAAAGGCAGCGGGTTTTTTTGTTTGTTTGTTTGTTTGTTTTGTTTTTTGTTTTTTGTTGTTGTTTGTTTTCTTTGTGGGTGCTTGATTCAGAAACTCTGCAGCGACTCGGACTTTCTTCTTTTTTTAGGTAGAAGTGACTGTGTGGTTGGTCTCTGTGAGTTATCTGGGGGACACTGTATTTGCTCGCATATGTATTGGAGAAACCAAGTGGCTTTGGAGTCTTGTCCTGTCCCACTCCCTCCCTTCCCTGCTCCCCTGATTCCTTAGGAAATGCTATATTTTGTGAGTGCACGCAGGCTTGATGGAGCCCTATTCTATGTAAATGTCCCTCATGTTTCTGAAAAGTGCTGTAGTTTAGTCTCACCCTATCCAGCCTCCCAAACAGGGCCAACGATCTAATTCCGAGAATCTGAAGGAAGACAGAGTGTGGACACCCCCACCCTGCTCTCCCAACTAAAATCCAACTCAGCTGCTCAAGGCAGGAAAACCCCTTTCCTCGGGGAGCCGGCGGACTGACTTCCACAGAGGCCTACCGAGAAACCTTGGGCCCTGGGGCGCGAGATTGGGGGTGGGGTGGGGATAGGCTTAGTCCTCAGAGCACCGGGGAAGCTACTTTCTCCCCGGGAGGGCTGAGCTCCCATTGGGCGGCCTCGGGAGGTTGCCTTCCATATTCCTGCCTGAGGACCAGTTGTAAATGTTACCGCTTCCAACAAATAAATGCTGATCTGAACAAATGGAGCCCAGCCGCTGGCCCTGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043342-Hoxd9:NM_013555:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.742 A=NA C2=0.325
Domain overlap (PFAM):
C1:
PF046178=Hox9_act=WD(100=47.3)
A:
NA
C2:
PF0004624=Homeobox=WD(100=70.4)
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:
TCGCTGAAGGAGGAGGAGAAG
R:
AAAACCCGCTGCCTTTTGAGT
Band lengths:
345-691
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: