MmuINT0040553 @ mm10
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108965811-108965962:+
Coord C1 exon
chr9:108965811-108965855
Coord A exon
chr9:108965856-108965926
Coord C2 exon
chr9:108965927-108965962
Length
71 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTGT
5' ss Score
6.64
3' ss Seq
GACCTCTTCTGTTCTCCCAGGGT
3' ss Score
8.65
Exon sequences
Seq C1 exon
GGTGATCGGGGACTGACGGGGACCCCGGGCGAGCCTGGAGTAAAG
Seq A exon
GTGTGTAGAGCCTGTGGGGTGCTTGGGAGCATCCAGGTCATGCTCGGCTCTGACCTCTTCTGTTCTCCCAG
Seq C2 exon
GGTGAACGGGGACATCCTGGTCCCGTGGGACCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650:ENSMUST00000112070:43
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(24.1=100),PF0139113=Collagen=PU(8.2=33.3)
A:
NA
C2:
PF0139113=Collagen=FE(19.0=100),PF0139113=Collagen=FE(18.0=100)
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:
GGGCGAGCCTGGAGTAAAG
R:
CCCACGGGACCAGGATGT
Band lengths:
48-119
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