MmuINT1020851 @ mm10
Intron Retention
Gene
ENSMUSG00000075394 | Hoxc4
Description
homeobox C4 [Source:MGI Symbol;Acc:MGI:96195]
Coordinates
chr15:103035267-103036405:+
Coord C1 exon
chr15:103035267-103035315
Coord A exon
chr15:103035316-103035636
Coord C2 exon
chr15:103035637-103036405
Length
321 bp
Sequences
Splice sites
5' ss Seq
TGGGTAATT
5' ss Score
6.19
3' ss Seq
TTCCCCTCCCCCTTCCCCAGTGA
3' ss Score
9.67
Exon sequences
Seq C1 exon
GAGCGACTCTGGGTTAGCACAATTGAACTGGATTTACGAGCGAGAATGG
Seq A exon
GTAATTACATCCCCCATAAATTTTATGGCTTAGCTACTCTGGGCAGTCCGAGCCATGTGCTACGATCTGTTATGTATGTGTGAAAACTATGCTTGCTTTCTAAGGGCGCATAAATAATTCAGTGTCGTTACAATGAGGATTCCCCTCTTATTACACTACAAAGTCTCTAGCTTCCTTCAACTTCTTTATAACCCATTTAGCTTGATGACTTTATTTCCACCACTCCCTCCTGTTCCTCAAAGCTGAGGATGGGGTGAGGGTGGGGGCAGGGAGCCTGCTGCCTCTGAACCCCACTATTTGCTTCCCCTCCCCCTTCCCCAG
Seq C2 exon
TGAACCCCAATTATAACGGAGGGGAGCCCAAGCGCTCGAGGACAGCCTACACCCGGCAGCAGGTCCTGGAATTAGAGAAAGAGTTTCATTACAACCGCTACCTGACCCGAAGGAGAAGGATCGAGATCGCCCACTCGCTGTGCCTCTCTGAGAGGCAGATCAAAATCTGGTTCCAAAACCGTCGTATGAAATGGAAGAAGGACCACCGACTCCCCAACACCAAAGTGAGGTCAGCGCCCCCGGCCGGCGCTGCGCCCAGCACCCTCTCGGCAGCCACCCCCGGCACTTCTGAAGACCACTCCCAGAGCGCCACGCCGCCGGAGCAGCAACGGGCAGAGGACATCACCAGGTTATAAGACATAACTTACACCCCTGCCCCCACCCTGTGCTCCGTGCCCCCCTCACACACAAATTGACTCTTATTTATAGAATTTAATATATATATATATATTTTGGTTCTTTTCTCTCTCTTCCTCTTGCCTCCTCCCTTGTCAGTTCCAAACAGACAAAACAGATAAACAAACAAGCCCCTTGCCCTTTTCCCTTGCTGTTAAAGACCCCTTTAAGCATGTGGTGTTGTCTTAGCATGGTACCTGCTGGGTTTTTGTTGTTGTTGTTTTGTTTTGGGTTTTTTGTTTTGTTTTGTTTTGCTTTGCTTTGCTTTTAAGGCCATTGGGGGGGGTATTTATTTTTTAAGAAAAAAAGCTGCAAAAATTATATATTGCAAGGTGTGATGGTCTGGTTTGGGTGAATTTCAGGGGAAATGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075394:ENSMUST00000165375:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.669
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=47.9)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGACTCTGGGTTAGCACAAT
R:
GAGTGGTCTTCAGAAGTGCCG
Band lengths:
348-669
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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