MmuINT0040546 @ mm10
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108964587-108965076:+
Coord C1 exon
chr9:108964587-108964664
Coord A exon
chr9:108964665-108965049
Coord C2 exon
chr9:108965050-108965076
Length
385 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACA
5' ss Score
5.19
3' ss Seq
GGGTCATATCTGTCTTCCAGGGT
3' ss Score
8.1
Exon sequences
Seq C1 exon
GGGCCCCCTGGATCTCGTGGCCCTGTGGGGGACCCAGGACCCCGTGGCCCCCCAGGGCTTCCTGGAATATCAGTGAAG
Seq A exon
GTGACAGCATGACCCTCAAATAGTCTTATGAATAGCATGTGATTCAGACCTGATGAGCTCACTGGGATCCATACAACCCTTACTGTTTCTTCTGACCTTTAGCCCCCACTGCTCAGTGCCTCGCTATTCCTTTTTGGGGATTAGGTTTTGAGATAATATCTCTCTCTCTCTAGCCCTAGCTGGCCTGGAACTCACTCTGTAGACCAGGCTGGCCTTGAACTCACAGAGATCTGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGGGTGCTCCACCATACCCGGTCCCCATTATTTGTCGAACCAAATTTGACCCAACCACTCTCCTTGCATCTTGGGGATGAGGGCATGGTTTAGAGTCATGGGGTCATATCTGTCTTCCAG
Seq C2 exon
GGTGACAAAGGTGATCGTGGGGAACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650:ENSMUST00000112070:37
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(43.1=100),PF0139113=Collagen=PU(3.6=7.7)
A:
NA
C2:
PF0139113=Collagen=FE(13.8=100),PF0139113=Collagen=FE(14.3=100)
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