MmuINT0078780 @ mm9
Intron Retention
Gene
ENSMUSG00000042499 | Hoxd11
Description
homeobox D11 [Source:MGI Symbol;Acc:MGI:96203]
Coordinates
chr2:74520450-74522195:+
Coord C1 exon
chr2:74520450-74521224
Coord A exon
chr2:74521225-74521959
Coord C2 exon
chr2:74521960-74522195
Length
735 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
TTGGTTTCTTTTCCTTGCAGTGG
3' ss Score
9.4
Exon sequences
Seq C1 exon
ATGAACGACTTTGACGAGTGCGGCCCCAGCGCAGCCAGCATGTACCTGCCGGGCTGCGCTTACTACGTGGCCCCGTCGGACTTCGCCAGCAAGCCGTCGTTCCTCTCGCAGCCGTCCTCGTGCCAGATGACTTTCCCCTACTCCTCCAACCTGGCGCCACACGTCCAGCCCGTGCGGGAGGTGGCCTTTCGCGACTACGGCCTGGAGCGCGCCAAGTGGCCGTACCGCGGCGGAGGCGGCGGTGGCGCGGGGGGCGGCGGCGGCGGCGGTCCCGGCGGGGGTGGTGGCGGCTCCGGGGGCTACGCTCCCTACTACGCCGCGGCAGCGGCGGCAGCGGCGGCAGCGGCGGCGGCCGAGGAGGCGGCCATGCAACGAGATCTGCTCCCGCCCGCCGGCCGCCGGCCAGACGTGCTCTTCAAGGCTCCCGAGCCGGTGTGCGGCGCTCCCGGGCCGCCGCACGGTCCGGCGGCCGCAGCCTCTAACTTCTACAGCGCCGTGGGTCGCAACGGCATCCTGCCCCAGGGCTTTGATCAGTTCTACGAGGCGGCGCCCGGACCCCCCTTCGCCGGCCCGCAGCCCCAGCCCGCTCCCGCGCCGCCACAGCCCGAGGGCGCCGCTGACAAGGGCGACCCCAAGCCAGGGGCTGGTGGCGGCGGGGGCAGTCCCTGCGCCAAGGCGACTCCGGGCCCAGAGCCCAAGGGGGCGGCGGAAGGCGGTGGCGGTGAAGGCGAGGGCCCCCCGGGGGAGGCGGGGGCCGAAAAGAGCGGCGGCACAG
Seq A exon
GTAGGCGCGGGGCGCGGGCCGAGGGGCTGGCCCGGGGCGGCGGAGGGGGGGCGGTGGGGACCTCCCTCTGCTTGCGCCGTTTTATGTGCTACTTTATAAGCATTCGAGGGGGTTTATACATCCTATAAGATTTCCCGGGTCGTTGTAAAGCGTGTTTATGATAGGAAACCAATTTAGGTGGGCTTAAGGTAGACTTCGAAGAGGACATTAATCGCCGTAGAGAGCTTTCCCTCTATTTGGGTGGGGGGGGGGTGGGTGAGTTGAGGACCTTAGAGGAGGGAAGTACATTTGCAGCCAGTTGATGAGTGGGAACACGAGAGCCTCCTGCCTTTCAGGGAGAGGGTAAGTGATCTGCCGCACTGGACTTAACCCCAACCTCTGGCTGGCGCTCAGCTCGGAGTTGAGCAGATGCTCCTGTGGGCGCGCTCTTGTCTCTCTCCCTTCATGTTCCAGTTCAGAGCCTGCCTTGCCATCATCCTTTTTCCTATCTCAGTGCCAGCCTAGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCCGGGCGTGAACACATGTCCACGCCCGCACTCTACTGTGCCCGCCCATATATCATCCCCCACGACGCAGGCAGGGCCTTTCAACGGCGGCAAGGGACGTCCCTAACTGGGCCAAGGCCTGGCCCTAGCTCAGTGGCCAGAGTGGGTGGGGGCAAGCAGTAGCCTCTCTCACCTCTTGGTTTCTTTTCCTTGCAG
Seq C2 exon
TGGCCCCCCAGAGGTCCCGGAAAAAGCGCTGTCCCTACACCAAGTACCAGATCCGCGAACTGGAACGCGAGTTTTTCTTTAATGTATACATAAACAAAGAGAAAAGACTCCAACTCTCTCGGATGCTCAACCTCACTGACCGGCAAGTCAAAATCTGGTTCCAGAATCGCAGGATGAAAGAAAAGAAACTGAACAGGGACCGTCTGCAATATTTCACTGGAAACCCCTTATTTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042499-Hoxd11:NM_008273:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.602 A=NA C2=0.269
Domain overlap (PFAM):
C1:
PF120453=DUF3528=WD(100=70.3)
A:
NA
C2:
PF0004624=Homeobox=WD(100=72.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTAACTTCTACAGCGCCGTGG
R:
GTTCGCGGATCTGGTACTTGG
Band lengths:
357-1092
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: