MmuINT0040516 @ mm9
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108885379-108885650:+
Coord C1 exon
chr9:108885379-108885411
Coord A exon
chr9:108885412-108885563
Coord C2 exon
chr9:108885564-108885650
Length
152 bp
Sequences
Splice sites
5' ss Seq
CACGTGAGT
5' ss Score
9.3
3' ss Seq
CCGCCTGCTCTGTGCTTCAGGAC
3' ss Score
9.41
Exon sequences
Seq C1 exon
CCTGCCAGGGCCAGTTTATTGCGTCTGGATCAC
Seq A exon
GTGAGTAGCTTTCTGTATCTAGAATGCTCTTCATCCAAGGCACCAACTAGATGCCTATCGCCTGGGTCCTCGCCTGGGTCCTCTCAGTAGGGGTGTGGCTAGGGTGGCTGACCATGATAACCAAGGATGTCACCGCCTGCTCTGTGCTTCAG
Seq C2 exon
GACCCCTCCCCGGTTATGCTGCGGATACAGCTGGTTCCCAGCTTCACCATGTTCCTGTGCTCCGGGTCTCTCATGTTGAGGAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-Col7a1:NM_007738:114
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.583 A=NA C2=0.967
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
AGGGCCAGTTTATTGCGTCTG
R:
TCAACATGAGAGACCCGGAGC
Band lengths:
106-258
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: