MmuINT0078781 @ mm9
Intron Retention
Gene
ENSMUSG00000001823 | Hoxd12
Description
homeobox D12 [Source:MGI Symbol;Acc:MGI:96204]
Coordinates
chr2:74513087-74515762:+
Coord C1 exon
chr2:74513087-74513711
Coord A exon
chr2:74513712-74513870
Coord C2 exon
chr2:74513871-74515762
Length
159 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAAC
5' ss Score
5.88
3' ss Seq
GGGTCGGGGCTCTGTTGCAGGCC
3' ss Score
4.87
Exon sequences
Seq C1 exon
CTATTCCGGGTTGTAACTAAATACTGTTGCGAGCACAGCCGAGGCCCTTTGTTGGAGATGTGTGAGCGCAGTCTCTACAGAGCTGGCTATGTGGGCTCGCTTCTGAATTTACAGTCACCGGACTCTTTCTACTTTTCCAACCTGAGAGCCAATGGCAGCCAGTTGGCCGCGCTTCCCCCCATCTCATACCCTCGCAGCGCGCTGCCCTGGGCTACTACGCCCGCCTCATGCACCCCTGCGCAGCCTGCCACCGCCTCTGCCTTTGGAGGCTTCTCTCAGCCTTACTTGACCGGCTCTGGGCCAATTGGCCTGCAGTCTCCAGGCGCCAAGGACGGACCCGAAGACCAGGTCAAGTTCTATACGCCTGATGCGCCCACCGCATCTGAGGAACGCAGCCGGACTAGGCCGCCCTTCGCCCCCGAGTCTAGTCTGGTTCATTCGGCTCTCAAAGGCACCAAGTATGACTACGCGGGTGTGGGCCGGACCGCTCCAGGCTCTGCGACCCTGCTCCAGGGGGCCCCCTGTGCCTCCAGCTTCAAGGAAGACACCAAAGGCCCGCTCAACTTGAACATGGCAGTGCAAGTGGCCGGGGTGGCCTCTTGCCTGCGATCTTCACTGCCCGACG
Seq A exon
GTAAACAGTGCCCATGCTCCCCCAAGCCAGTTTAGGCAGGGACGGGAGGTGGGGTGTCAGGGACAGTTGGACAGGGAGGAGACCCGCCAGCAGTGGTGAACGTCTGTGGGGCGGGCAGTTGATCTGAGCGAGCTGACATGGGTCGGGGCTCTGTTGCAG
Seq C2 exon
GCCTGCCGTGGGGGGCGGCCCCGGGGAGGGCCCGCAAGAAGAGGAAACCCTACACAAAGCAGCAGATTGCGGAGCTGGAGAACGAATTCCTGGTCAATGAATTCATCAACCGGCAGAAGCGTAAGGAATTGTCTAACAGGCTGAACCTCAGCGACCAGCAGGTCAAAATCTGGTTCCAGAACCGGCGTATGAAGAAGAAGCGGGTAGTGCAGCGCGAGCAAGCACTGGCCCTCTATTAGCTGCCCACGGGGGCCTGAGGCCTTGCCAAGCCTGCCCTTTTGGACCAAGGCCTGGCTGTGGAGGAGGTGTTGGGGCTGCAGATTTCCCTCCCACTCCTCTGGTCCTGGGCGCCCTTCGGCTCAGTCTGTAGCTGAGGAACCAGGAGGAGATTTGGAGATGAGGCCAGTGGAGCCCCCTTCGCTTTCAGCTCTCTTTGGGACCCTCCTGAGAGGTGTTTGGGAATTGCAATCTAACACTGGCTTTAAACATTCAGCATGGTGTCTGGGGGTCACCTGTCCTTGTCTATGATGTTTACATCCGGGGCTCACTATTGAAACACTGTATGAGGGTTTGTTTTTTCCGGTTTTCAACGTGTTCTTTTTCTTTTTCTTTCTCTATCCAGCTCTTTCTGCATGAAACAGGAGCCTAGCTAGAGCTCCGGGTATAAGTGCAGGTAGAAAGGCCCTGAGACCCCGCTGCAGTGCAAGGGGCTGGGGATAACTCTAGCCCCTTCGCAGCAGAAGCCCTTTGTGACAAAGCTGGGCTCTCCACTCTGCAGGAAGGAAAGGGCCTGATTCCACAACCCCCATCTGCCCTGAATGATTTGGGAGGACAAAAGCTACCCTAGACCTTCAGACTTGTGGGGGGGGGGGGAGGAAAGGATACCCTGGAACCTCAGCGCTTCAAAGGTTCTCCTGCTGAGTAAAACAGGCTGGAAGATCTCCTTCTCAGAGACAGGGAGAGAAACTGGGACTCCAAAACAAAGTATGGTCTCTAGACTGTCATAATTCCCCTGCTCCAGCCTCACCTATCCCTGAGCCAAGGCCAAGCACTCTGTAACTAGATCCCCAGAACTGAGCTATGGGTGAGGGGAGCTGCTGGCCTGTTTTGAGGCTTGGCTGCACAGGGAAGAAAGAAGAGTAAGCGAGGCGGAGGAGGATCTGCACTCTGTAACCACGACTCTCCTCTTGAATGAATGAAGTTATCCATATGTCTGTCTTTCTTGAATTTCCTTAATGTATCACCACAGGAAGAGACCCCCCCCCCAAAAAAAATGCCTCCTTGAGGAGTCTGAAGGGTGGGAGAAGAAACCTCTCAGATTCTCAGACTGTAGTTGCTGCTCTTGAAGGACAGAAAACCAGCACTTCTTCCCCATCCTCTCCACCACCCACCAACTCCATCAGAACTTAGCTAGGGTGTCTCTTCTCAGAGACTGGTGGTCAGCTCTTGTAAAGCTTTTAAGGCCCCAAGCCCTGCCAGGTTTACCTTGAGAAACCTAGGTTTTCTGAATTGTGAATGAAGTTGCTCTACGCCTGTTATAGAATCTGTCCAGCCTCATTCCCAGTGAATTCAACTCCGCCTTCCCCTACAATCTTTGCCTCTTCTTTTGAGCTTTAAGCCCCACCCCCAACCTTTAGCAAGATGCACAACATCCCAAAGGCTCATGATTCCTTCCCCAAGTCCAATGGCTTTCCTTTAGAGAAGGTCTCCAGGAACTGGACCTCGAAGGGCATCTCACAAGGACCTTTGAGCCTCGCCCCAACTGACCTCGGTTGGTGTGTTAAATATTATTTCCTGTGCTAACAGTTGCCGTTTATGTTTTGTTTTGATTTTGTAAAATAACACTTCCCTGTATATATTAGCTTCATAGTGAAAATAAATATCCAGATCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001823-Hoxd12:NM_008274:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.300 A=NA C2=0.241
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=71.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAAGTATGACTACGCGGGTG
R:
GTTCTCCAGCTCCGCAATCTG
Band lengths:
254-413
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: