MmuINT0040602 @ mm9
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108877578-108877803:+
Coord C1 exon
chr9:108877578-108877646
Coord A exon
chr9:108877647-108877767
Coord C2 exon
chr9:108877768-108877803
Length
121 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACT
5' ss Score
6.6
3' ss Seq
TTACTGGGCATTCCCCACAGGTG
3' ss Score
10.53
Exon sequences
Seq C1 exon
GGGTCACCAGGTCTGCCCGGCCCTGTTGGACCTAAAGGAGAACCTGGGCCTGTGGGGGCTCCTGGACAG
Seq A exon
GTGACTCTTGCCTCTGCTCCCTACTCCCTGCCCTAAGCCTCAGTTTCCACTTACCATCTGGAATGGCAGGACAGAGCGGGAACCAAGGGCGGCTAGACCACTTACTGGGCATTCCCCACAG
Seq C2 exon
GTGGTGGTCGGGCCCCCTGGAGCAAAAGGCGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-Col7a1:NM_007738:87
Average complexity
IR-S
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(32.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(16.2=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:
GGGTCACCAGGTCTGCCC
R:
CTTCTCGCCTTTTGCTCCAGG
Band lengths:
105-226
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: