MmuINT0040520 @ mm10
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108957214-108958235:+
Coord C1 exon
chr9:108957214-108957342
Coord A exon
chr9:108957343-108958091
Coord C2 exon
chr9:108958092-108958235
Length
749 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
CCCACCCTGCCTTTTCTCAGGGG
3' ss Score
8.91
Exon sequences
Seq C1 exon
GGCTAGAGCAGCTGGTGAGCCCGGTGATGAATTTACAAGCCATAGAACTACCTGGGCAGCGGGTGCGAGTGTCTTGGAACCCAGTCCCTGGGGCCACTGAGTACCGTTTCACTGTACGCACCACCCAGG
Seq A exon
GTAAGGCAGAAGCAGCCTGAAAAGTCCCCTCATCCCGAAGTCCCAGCCTGCAGCACCCTCCCACTCTGGCTTGGTTCCTACGGCCTCCTTCATCTTTTTGGCCATCTGCATCCCGGGAACTGTTGACCCCAGAACTGCCTCAGGGTCTGTCTTTCCTCTCCTCTACCCCAGCCTGCTCTTCAGTTGTCTATCTCCACTCTGCCCACACCCCTGCTGTGGCTCATCCATCTCGACCCCCACAGTTCTACGACCCACGCTCTGCTGTCCCTCTCTAGGGAGAAGAGGGCCCCCCTGTGGTCACTGTGGCTCAAAGTAGTCAGAGCCTGACTCAGTCACTTGATTCTTTGCCTGAGCGCTCCTTCAGTCTCTTACATTCCCACCGCCTCCCCACTAAGGATCCTCTAATACTGATCTCTCGCGTCCCCCAACGCTCACCCATCATCCTGTGTCAGTCTATGGGTGACTTGCCAACTTGCATCACAGGCACAGACTCTCATCATGCTATGTCCTAACGCCCCGTCTGTCACCCAGTGTCCCCATTCATTGGCGACCTCCTGTTATCCTGTGTTGCCATCATGGACCCCTTAGCCCCACATCATTTTCTCTTACTGTTTTCCTCTCTCCATTGCCCTTCCCCATCCAATCTCCCCATCTCCCACGATGTCTGGTAGTTTTGCCTATCACTGACTGCTGTTCTAGATCCCTGTGTGGTGCTCACCCCCCTTCCTGCCCACCCTGCCTTTTCTCAG
Seq C2 exon
GGGTCGAGCGGACTCTATTGCTTCCTGGGAGCCAGACAACCTTTGACTTAGATGATGTTCGAGCTGGGCTTAGCTACACGGTGCGGGTGTCTGCTCGAGTGGGTGCTCAGGAGGGTGATGCCAGCATCCTAACGATCCACAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650:ENSMUST00000112070:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.045 A=NA C2=0.041
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(46.8=84.1)
A:
NA
C2:
PF0004116=fn3=PD(51.9=83.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTAGAGCAGCTGGTGAGC
R:
TCTGTGGATCGTTAGGATGCTG
Band lengths:
270-1019
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