MmuINT0078774 @ mm10
Intron Retention
Gene
ENSMUSG00000001661 | Hoxc6
Description
homeobox C6 [Source:MGI Symbol;Acc:MGI:96197]
Coordinates
chr15:103009573-103011881:+
Coord C1 exon
chr15:103009573-103010005
Coord A exon
chr15:103010006-103010733
Coord C2 exon
chr15:103010734-103011881
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
GAAATCATAGCCCGACCAGGTAAAGGCAAAGGGATGAATTCCTACTTCACTAACCCTTCCTTATCCTGCCACCTCGCCGGGGGCCAGGACGTCCTCCCCAACGTCGCCCTCAATTCCACCGCCTATGATCCAGTGAGGCATTTCTCGACCTATGGAGCAGCCGTAGCTCAGAACCGGATCTACTCGACTCCCTTTTATTCGCCACAGGAGAATGTCGTGTTCAGTTCCAGCCGGGGGCCGTATGACTATGGATCTAATTCCTTTTACCAGGAGAAAGACATGCTCTCAAACTGCAGACAAAACACCTTAGGACATAACACACAGACCTCAATCGCTCAGGATTTTAGTTCTGAGCAGGGCAGGACTGCGCCCCAGGACCAGAAAGCCAGTATCCAGATTTACCCCTGGATGCAGCGAATGAATTCGCACAGTG
Seq A exon
GTGAGTTTTACAGCTCCGAGATATAAATTAAATAAACTGAACTGGCTTTATGACCGGCTTCCCTAGAAGAACGGGCGGAGAGAGTTTTTTATGGCCCCATAAAAACAATCACGCTCGTCTCCTCGCCGACACCGAGACAGGGCCCCCTCTTCAGCCCCCTCTGCTCGCCTTCCGCGCTGGCTCGCAAGGGCCTGGCCCCCTCGGTCCCTGACGGATTGGAGGGCTCCAAGAGGAGCTGAGGGGGTAGAAACAGGGCAGGGAATGAGGGGAGGGGACAGAAGGTGGAGGAGCCCCCCAAAGTCTAGTTAGGCCGGAGAAAAGGAAGGGAGTTAGGAAAGGGCAAAGAAGTGGGGAGAACTTTCCAGGGATCTAGAGTGTTGGGGAAGGTGGGGGAGCCCAATCCTTGAGAGATGGGGTCCTTATCCCCAGTAGTTGGTACTTTTTTTTTAAAAATCAGCTTTTAGACAGCCAGCTTTCTGCCTGTTTTTGCCCCGCCCCCCAGCTTTCTTTGGGACACACTTCTCCCACCTCGTGGGAGAACTGAATGAAGTTGGGGTTCTGGCTGTCCCCCCAGTGGGGGTGGGGCAGGGCAAAAGGGAGAAAGCTAAAGCCCGAAGGGGCTGCGAGCTGTGGGCCAAGTTGAGAGGGTCTGGACTTTGCTAGACGAAAATGTCTGCAGAGGACGCCTTGCTGATTGTTTTTAGTGTGTTTTGTGCCTGGATCTCTAG
Seq C2 exon
GGGTCGGTTACGGAGCGGACCGGAGGCGCGGCCGCCAGATCTACTCTCGGTACCAGACCCTGGAACTGGAGAAGGAATTTCACTTCAACCGCTACCTAACTCGGCGCCGGCGCATCGAGATCGCCAATGCTCTGTGCCTGACCGAGCGACAGATCAAAATCTGGTTCCAGAACCGCCGCATGAAGTGGAAAAAAGAATCTAATCTCACGTCCACACTCTCAGGGGGTGGCGGAGGGGCAACCGCCGACAGCCTGGGAGGAAAAGAGGAAAAGCGAGAAGAGACAGAAGAAGAGAAGCAGAAAGAGTGACCAGGACTGTCCTTGCACCCCTCTCTTCTCCCTTGCTCATCCCAGCTCCCCGAATCACACACTCTGTATTTATCTCTGGCACAATGATGTGTTGTGACTTCCTAAAACAAAACAGGGAGTCAGACGTGGACCTAAAAGTCAGCTTTGGACCCCCTCCCTCACTGCACAACTCTTCACTCGTCTCTTCCTCTAGCTCCCTCGCTAGCTTCTTCCTGGCTTGTCTGCAGGCCCCTTCCCTCGCCTAGGCCTAGGAGACCTGAACCTCGCTTCAGACTCCTCAGATGTCTCTCCAAGTGAGCCCTAGGCTCCCTCCCCACCCCCGACGCCCTTCACCCCCGCCCTCCGGCGCAGAGAGCTGGCTCCAGGGCCTGGGGCCTCCACTCGGGGGCCTCAGGGCCCGGCCTGACAGCCGGAGGGCAGGAGGCCTCAGGAGGGCGCGCCTTGGCCCTGCAACAACCCCCAGGGCCTCTCCCCAGTCCCTGCCCGGTCCCTCTGCCCCAGCAAATGCCCAGTCCAGGCAAATTGTATTTAAAGATTCCTGGGGGTCATTATGGCATATTTCGAACTGTGACCGTTTCTGTGTGAATATTTCTAGCTGTATTTGTGGTCTCTGTATTTATATTTATGTTTAGCACCGTCAGTGTTCCTATCTCATTTAAAAAAGGATTTAAAAAAAAAAGAGGGAAAATAACAAAAAGAGAAAAAAAGTGAATGACGTTTGTTTAGCCAGTAGGAGAAAATAAATAAAGAAATAACCCCCTACGTGTTATCCTCCTGTATAAATCCGACCTCTGGATCCGTTCTCGAATATTTAATAAAACTGATATTATTTTTAAAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001661:ENSMUST00000001711:1
Average complexity
IR
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:
NA
C2:
PF0004624=Homeobox=WD(100=55.3)
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:
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
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types