MmuINT0040521 @ mm9
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108860137-108860494:+
Coord C1 exon
chr9:108860137-108860280
Coord A exon
chr9:108860281-108860368
Coord C2 exon
chr9:108860369-108860494
Length
88 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CCCCTATCTTTAACCCCCAGATC
3' ss Score
10.52
Exon sequences
Seq C1 exon
GGGTCGAGCGGACTCTATTGCTTCCTGGGAGCCAGACAACCTTTGACTTAGATGATGTTCGAGCTGGGCTTAGCTACACGGTGCGGGTGTCTGCTCGAGTGGGTGCTCAGGAGGGTGATGCCAGCATCCTAACGATCCACAGAG
Seq A exon
GTGAGCACCTTAGGAGACTTACGGGCGATGGCGACCGACTTGCTCCCTGTCCTCACACTGACCTTTCACCCCTATCTTTAACCCCCAG
Seq C2 exon
ATCCAGAAGCCCCACTTGTTGTCCCAGGACTGCGGGTTGTCGCATCAGATGCAACAAGAATTAGGGTGGCCTGGGGACTTGTCCCTGGAGCCAGTGGATTTCGGATCAGCTGGAGGACAGGCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-Col7a1:NM_007738:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.041 A=NA C2=0.093
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(51.9=83.7)
A:
NA
C2:
PF0004116=fn3=PU(46.2=83.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGAGCGGACTCTATTGCTTCC
R:
CAGTCCTGGGACAACAAGTGG
Band lengths:
172-260
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: