MmuINT0040515 @ mm10
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108982674-108983366:+
Coord C1 exon
chr9:108982674-108982722
Coord A exon
chr9:108982723-108983333
Coord C2 exon
chr9:108983334-108983366
Length
611 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TCCTTTTCTGTCACTTCCAGCCT
3' ss Score
9.76
Exon sequences
Seq C1 exon
GAGGATGACATTCGGGACTTTGTGCGTCAGGAGATGAGTCAGCACTGTG
Seq A exon
GTGAGTGGGTCTGGTGTGGAGTCTCCTTTCCTAACTGCATCCCGGGACACCTAGATGGGGGCCCGCAATTCCCCAGAACTTACAGAGGGCAAGTGGAGACCGATGGCTATGAGCAACACAGATGTTGAGAACAAACATGCTAACAGGACTTCCTTAATGGGGAGGGGGGCGGGGGAGACAGAGATGTGGGTGGCTACACTGTGTTCTGATGACTATCTGTGTGGAGGGGTAGTGTAAGGCACAGGGCTGGTCCCAGCTGTGACACAAGATGATCCTGGAGCCCTGATTCTTCCTGTCATGACTGCTTTCATCTCCTTGCCTCCTGCGTCTGGCCCTTTCATTGCTGATCTGTTTCTAGCTTCTTGCCCTGAGAGTTCATCTCCTCTACACTCCCTCCTGTCCTCCTCCTCCTCCCTTCCTCCTCTTCCCCCTCACCTGTTCTCTCTCCTCACTCCTTTCTCCCTCCCTGGCTGGCTGGCTCTATCTCTCTGTATATCTTAGCCCCCATGCATGTGCCTTTTGTCTGTTTCTCTTTCCCCATCTTCCTGCCTGCCTTTGCATTTTGTTCTCCATTTCTCGTGGTCTCATTCTTCCTTTTCTGTCACTTCCAG
Seq C2 exon
CCTGCCAGGGCCAGTTTATTGCGTCTGGATCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650:ENSMUST00000112070:114
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.706 A=NA C2=0.583
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(0.1=0.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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