MmuINT0078774 @ mm9
Intron Retention
Gene
ENSMUSG00000001661 | Hoxc6
Description
homeobox C6 [Source:MGI Symbol;Acc:MGI:96197]
Coordinates
chr15:102839993-102842312:+
Coord C1 exon
chr15:102839993-102840436
Coord A exon
chr15:102840437-102841164
Coord C2 exon
chr15:102841165-102842312
Length
728 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TTTTGTGCCTGGATCTCTAGGGG
3' ss Score
7.1
Exon sequences
Seq C1 exon
TAAATATTAAAGAAATCATAGCCCGACCAGGTAAAGGCAAAGGGATGAATTCCTACTTCACTAACCCTTCCTTATCCTGCCACCTCGCCGGGGGCCAGGACGTCCTCCCCAACGTCGCCCTCAATTCCACCGCCTATGATCCAGTGAGGCATTTCTCGACCTATGGAGCAGCCGTAGCTCAGAACCGGATCTACTCGACTCCCTTTTATTCGCCACAGGAGAATGTCGTGTTCAGTTCCAGCCGGGGGCCGTATGACTATGGATCTAATTCCTTTTACCAGGAGAAAGACATGCTCTCAAACTGCAGACAAAACACCTTAGGACATAACACACAGACCTCAATCGCTCAGGATTTTAGTTCTGAGCAGGGCAGGACTGCGCCCCAGGACCAGAAAGCCAGTATCCAGATTTACCCCTGGATGCAGCGAATGAATTCGCACAGTG
Seq A exon
GTGAGTTTTACAGCTCCGAGATATAAATTAAATAAACTGAACTGGCTTTATGACCGGCTTCCCTAGAAGAACGGGCGGAGAGAGTTTTTTATGGCCCCATAAAAACAATCACGCTCGTCTCCTCGCCGACACCGAGACAGGGCCCCCTCTTCAGCCCCCTCTGCTCGCCTTCCGCGCTGGCTCGCAAGGGCCTGGCCCCCTCGGTCCCTGACGGATTGGAGGGCTCCAAGAGGAGCTGAGGGGGTAGAAACAGGGCAGGGAATGAGGGGAGGGGACAGAAGGTGGAGGAGCCCCCCAAAGTCTAGTTAGGCCGGAGAAAAGGAAGGGAGTTAGGAAAGGGCAAAGAAGTGGGGAGAACTTTCCAGGGATCTAGAGTGTTGGGGAAGGTGGGGGAGCCCAATCCTTGAGAGATGGGGTCCTTATCCCCAGTAGTTGGTACTTTTTTTTTAAAAATCAGCTTTTAGACAGCCAGCTTTCTGCCTGTTTTTGCCCCGCCCCCCAGCTTTCTTTGGGACACACTTCTCCCACCTCGTGGGAGAACTGAATGAAGTTGGGGTTCTGGCTGTCCCCCCAGTGGGGGTGGGGCAGGGCAAAAGGGAGAAAGCTAAAGCCCGAAGGGGCTGCGAGCTGTGGGCCAAGTTGAGAGGGTCTGGACTTTGCTAGACGAAAATGTCTGCAGAGGACGCCTTGCTGATTGTTTTTAGTGTGTTTTGTGCCTGGATCTCTAG
Seq C2 exon
GGGTCGGTTACGGAGCGGACCGGAGGCGCGGCCGCCAGATCTACTCTCGGTACCAGACCCTGGAACTGGAGAAGGAATTTCACTTCAACCGCTACCTAACTCGGCGCCGGCGCATCGAGATCGCCAATGCTCTGTGCCTGACCGAGCGACAGATCAAAATCTGGTTCCAGAACCGCCGCATGAAGTGGAAAAAAGAATCTAATCTCACGTCCACACTCTCAGGGGGTGGCGGAGGGGCAACCGCCGACAGCCTGGGAGGAAAAGAGGAAAAGCGAGAAGAGACAGAAGAAGAGAAGCAGAAAGAGTGACCAGGACTGTCCTTGCACCCCTCTCTTCTCCCTTGCTCATCCCAGCTCCCCGAATCACACACTCTGTATTTATCTCTGGCACAATGATGTGTTGTGACTTCCTAAAACAAAACAGGGAGTCAGACGTGGACCTAAAAGTCAGCTTTGGACCCCCTCCCTCACTGCACAACTCTTCACTCGTCTCTTCCTCTAGCTCCCTCGCTAGCTTCTTCCTGGCTTGTCTGCAGGCCCCTTCCCTCGCCTAGGCCTAGGAGACCTGAACCTCGCTTCAGACTCCTCAGATGTCTCTCCAAGTGAGCCCTAGGCTCCCTCCCCACCCCCGACGCCCTTCACCCCCGCCCTCCGGCGCAGAGAGCTGGCTCCAGGGCCTGGGGCCTCCACTCGGGGGCCTCAGGGCCCGGCCTGACAGCCGGAGGGCAGGAGGCCTCAGGAGGGCGCGCCTTGGCCCTGCAACAACCCCCAGGGCCTCTCCCCAGTCCCTGCCCGGTCCCTCTGCCCCAGCAAATGCCCAGTCCAGGCAAATTGTATTTAAAGATTCCTGGGGGTCATTATGGCATATTTCGAACTGTGACCGTTTCTGTGTGAATATTTCTAGCTGTATTTGTGGTCTCTGTATTTATATTTATGTTTAGCACCGTCAGTGTTCCTATCTCATTTAAAAAAGGATTTAAAAAAAAAAGAGGGAAAATAACAAAAAGAGAAAAAAAGTGAATGACGTTTGTTTAGCCAGTAGGAGAAAATAAATAAAGAAATAACCCCCTACGTGTTATCCTCCTGTATAAATCCGACCTCTGGATCCGTTCTCGAATATTTAATAAAACTGATATTATTTTTAAAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001661-Hoxc6:NM_010465:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.172 A=NA C2=0.422
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
PF0004624=Homeobox=WD(100=55.3)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGTGAGGCATTTCTCGACC
R:
TACCGAGAGTAGATCTGGCGG
Band lengths:
356-1084
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: