MmuINT0078790 @ mm9
Intron Retention
Gene
ENSMUSG00000027102 | Hoxd8
Description
homeobox D8 [Source:MGI Symbol;Acc:MGI:96209]
Coordinates
chr2:74543546-74545364:+
Coord C1 exon
chr2:74543546-74544175
Coord A exon
chr2:74544176-74544570
Coord C2 exon
chr2:74544571-74545364
Length
395 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGG
5' ss Score
4.94
3' ss Seq
TTGTTGTTGTTTTTAATCAGCAG
3' ss Score
5.38
Exon sequences
Seq C1 exon
CGCGACCGAGCTGAGGCGCGCCCCTTACCGGCTCCGCGCCGCCGGCGGCCGCCGCCCCGATGAGCTCGTACTTCGTGAACCCGCTGTACTCCAAGTACAAGGCGGCGGCCGCGGCGGCGGCGGCGGCTGCGGCGGCCGCGGCGGGCGAGGCCATCAATCCCACTTACTACGACTGTCATTTTGCACCCGAGGTCAGCGGCCGCCACGCCGCCGCCCTGCAGCTCTATGGCAACAGCGCCGCCGGCTTCCCGCACGCGCACCCGCACCCGCACCCGCACCCGTCGCCGCCGCCCGGGTGCGGCGGAGGGGGCGGCCCGGGGCCCGGCCAGGACTACTTCCACGCCGGCGCGGGCAGCCCGACCGCTGCCTACCAGGCCGCCCCACCTCCTCCGCACCCTCCGCCTCCGCCGCCGCCTCCCCCCTGCGGCGGGATTGCCTGTCACGGGGAGCCCGCGAAGTTTTACGGATACGATAACTTACAGAGACAGCCGATTTTTACGACCCAGCAAGAGGCCGAGCTGGTACAATATCCTGACTGTAAATCGTCCAGTGGTAATATTGGCGAGGACCCAGACCACTTAAATCAGAGCTCGTCTCCTTCTCAAATGTTTCCCTGGATGAGACCACAAG
Seq A exon
GTTGGGATGCGCTATTTTTTTTTTTTTTTTTTTTTTTTTAAGGAGGGGAGAAAGGGAGAAATCTGCTTTCATCTCACGTTCTAGCTTTAAAACTCCCCTGTCCTTTCCCTCTCCCCTTCCTTTTCCTTCTGGTGTAGCCAATGTGGCTCTTGTACAAAAACTAATACAGACTTTTTAAAAGTGTGTAAAGACGGGGGCAGAATAATTGTGAAGAGCTTGTCTCTGCCTCTCTTGCCTCACACCCTATATCTGTATGAGAATTAAAGACCACTGTGTATTTCACCTCTTAAGCCCGTTCCAGAAAACTCCAACAGCATTCAGAGAATCAACCATTAAAAAACAAAAAAACGTTGATTTTCCTCCCCCCCCCCCTTTTTGTTGTTGTTTTTAATCAG
Seq C2 exon
CAGCTCCTGGTAGACGGAGAGGAAGACAAACCTACAGTCGCTTCCAAACCCTAGAGTTGGAAAAGGAATTCCTTTTTAACCCTTATCTGACCAGGAAGAGGAGAATCGAGGTCTCCCATACTCTGGCCCTCACGGAGAGACAGGTAAAAATCTGGTTCCAGAACAGGAGAATGAAATGGAAAAAGGAGAACAACAAAGACAAGTTTCCTGCGTCCCGGCCGGAGGCAAAGGATGGAGACCCCAAAAAGGAAGTCTCGGGGCTGGAAGAAGACGGAGCTGAAGGCTGCCCCACAAATTAAACTCTACCTTTACACTTCTACCACAGACTATTAAGACTGATGATCAGTATAAGTATATACTGGTGGACACCACCGGTCCTCCCTCTTGTGTTTTGGAAACGGACTTTACCTGTGTTTCAAGCTACCTTAATGTCACTGCTCTTGAGGTTTCTGCGCTTTGAAAGGGATTTCTGTGTTTTTAAAGAGAATAGTTTGTAGTATCGCATAGAAGCAGTCCTTGAGCTGTCCTATAGAAGGGTAATTTGATACGGACCTTGTGGCTATATTTTTATAATGGTAATTTTTAACGTCTGAGCTGGTGGTTTGCCTCAACAACATAAACTTCCTAATGATCAGCGCTAGATGATTGAATATAAAATGCTTTATTAATCAAACAAGTGCACTTGAACATTTTAAATCTTTATGGTGAGTAAATTAAAAGAAGTTTATTAATAATGTTTTTAAAAATTATGCCTGCAGAATATTTACTTTATTATTTGATTAAATGTATTATTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027102-Hoxd8:NM_008276:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.655 A=NA C2=0.527
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=57.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTTACGACCCAGCAAGAGGC
R:
GGGACGCAGGAAACTTGTCTT
Band lengths:
353-748
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs: