MmuINT0078772 @ mm9
Intron Retention
Gene
ENSMUSG00000075394 | Hoxc4
Description
homeobox C4 [Source:MGI Symbol;Acc:MGI:96195]
Coordinates
chr15:102864826-102867283:+
Coord C1 exon
chr15:102864826-102865592
Coord A exon
chr15:102865593-102866067
Coord C2 exon
chr15:102866068-102867283
Length
475 bp
Sequences
Splice sites
5' ss Seq
CGGGTAGGC
5' ss Score
7.5
3' ss Seq
TTCCCCTCCCCCTTCCCCAGTGA
3' ss Score
9.67
Exon sequences
Seq C1 exon
ACATTGGAGTCGAGCTGGGAGCCACCCATCTTTAGCAAGGAAGGATTGTCAGTCTGGTGGGGTGTGCAATGGTGAGCACCCCAGCTTCTGCCAGCCATCCCCCACCCCCACCCCCAGCAGCAGCAGCACCACCACCACATACACAAAAAATTGGATACATTTTGAATAAAGCGATTCGGTTCCTTATCCGGGGACTGGGTTGCTCGGTGTGATTGGCCGGCGGAGTCACATGGTGAAAGTAACTTTACAGGGTCGCTAGCTAGTAGGAGGGCTTTATGGAGCAGAAAAACGACAAAGCGAGAAAAATTATTTTCCACTCCAGAAATTAATGATCATGAGCTCGTATTTGATGGACTCTAACTACATCGATCCGAAATTTCCTCCATGCGAAGAATATTCGCAAAATAGCTACATCCCTGAACACAGTCCGGAATATTACGGCCGGACCAGGGAATCGGGATTCCAGCATCACCACCAGGAGCTGTACCCACCACCGCCTCCGCGCCCTAGCTACCCTGAGCGTCAGTATAGCTGCACCAGTCTCCAGGGGCCTGGCAATTCGCGAGCCCACGGGCCGGCCCAGGCGGGCCACCACCACCCTGAGAAATCGCAGCCGCTCTGCGAGCCGGCGCCTCTCTCAGGCACCTCTGCCTCCCCGTCCCCAGCCCCGCCAGCCTGCAGCCAGCCAGCCCCTGACCATCCCTCCAGCGCCGCCAGCAAGCAACCCATAGTCTACCCTTGGATGAAAAAAATTCACGTTAGCACGG
Seq A exon
GTAGGCAACTTTGCTTTTTGCCCCCCTCCCTTTCCCGGCGCTCCCCACCCTCCCTGGCCCCCTCTGGCCCCGTCCTCCTTTCTCTCCTTCCCCCTCTCTCTCCAGGAGCGACTCTGGGTTAGCACAATTGAACTGGATTTACGAGCGAGAATGGGTAATTACATCCCCCATAAATTTTATGGCTTAGCTACTCTGGGCAGTCCGAGCCATGTGCTACGATCTGTTATGTATGTGTGAAAACTATGCTTGCTTTCTAAGGGCGCATAAATAATTCAGTGTCGTTACAATGAGGATTCCCCTCTTATTACACTACAAAGTCTCTAGCTTCCTTCAACTTCTTTATAACCCATTTAGCTTGATGACTTTATTTCCACCACTCCCTCCTGTTCCTCAAAGCTGAGGATGGGGTGAGGGTGGGGGCAGGGAGCCTGCTGCCTCTGAACCCCACTATTTGCTTCCCCTCCCCCTTCCCCAG
Seq C2 exon
TGAACCCCAATTATAACGGAGGGGAGCCCAAGCGCTCGAGGACAGCCTACACCCGGCAGCAGGTCCTGGAATTAGAGAAAGAGTTTCATTACAACCGCTACCTGACCCGAAGGAGAAGGATCGAGATCGCCCACTCGCTGTGCCTCTCTGAGAGGCAGATCAAAATCTGGTTCCAAAACCGTCGTATGAAATGGAAGAAGGACCACCGACTCCCCAACACCAAAGTGAGGTCAGCGCCCCCGGCCGGCGCTGCGCCCAGCACCCTCTCGGCAGCCACCCCCGGCACTTCTGAAGACCACTCCCAGAGCGCCACGCCGCCGGAGCAGCAACGGGCAGAGGACATCACCAGGTTATAAGACATAACTTACACCCCTGCCCCCACCCTGTGCTCCGTGCCCCCCTCACACACAAATTGACTCTTATTTATAGAATTTAATATATATATATATATTTTGGTTCTTTTCTCTCTCTTCCTCTTGCCTCCTCCCTTGTCAGTTCCAAACAGACAAAACAGATAAACAAACAAGCCCCTTGCCCTTTTCCCTTGCTGTTAAAGACCCCTTTAAGCATGTGGTGTTGTCTTAGCATGGTACCTGCTGGGTTTTTGTTGTTGTTGTTTTGTTTTGGGTTTTTTGTTTTGTTTTGTTTTGCTTTGCTTTGCTTTTAAGGCCATTGGGGGGGGTATTTATTTTTTAAGAAAAAAAGCTGCAAAAATTATATATTGCAAGGTGTGATGGTCTGGTTTGGGTGAATTTCAGGGGAAATGAGGAAAAGAAAAAGGAAAGGGAGATTTGTAAGTGGAGTCTCATCCTCTCTCCTCCTCCTTTCCCCCCATCTCTTTCCTTAGGCCTTTTGCATTGAAAATGCACCAGGGGAGGTTAGTGAGGGGGGAAGTCATTTTAAGGAGAACAAAGCTATGAAGTTCTTTTGTATTCTTGTGGGGGGGTGGAAGGAGGGGGGAGGACAGCAAACAAAGCTAAATGCATCTGGAGAGCCTCTGGGAGCTGTTCAGTTTGAGGAGCCAAAAGAAAATAAAAATGAACTTTCAGTTCAGAGAGGCAGTCTGTAGGTAGATGCTCCCCCTACCCTCATCGTGGTTATTGTGTTTTTTGGACTGAATTTACTTGATTATTGTAAAACTTGCAATAAAGAATTTTAGTGTTGATGTGAAATGCCCCGTGATCAATAATAAACCAGTGGCTGTGAATTAGTTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075394-Hoxc4:NM_013553:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.796 A=NA C2=0.669
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=47.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
GGATTCCAGCATCACCACCAG
R:
CTTGGGCTCCCCTCCGTTATA
Band lengths:
342-817
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: