MmuINT0040535 @ mm9
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108864411-108864817:+
Coord C1 exon
chr9:108864411-108864557
Coord A exon
chr9:108864558-108864644
Coord C2 exon
chr9:108864645-108864817
Length
87 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
ATTGCTGGATCTCTTTTTAGGGC
3' ss Score
9.04
Exon sequences
Seq C1 exon
GCACAGCCGTGACCACAGCTCACAGATACCTCTTAGCATCCAATGCTCCTGGTCGCCGTCAGCAAGTGCCAGGCGTGATGGTCCTGTTAGTGGATGAGCCTCTGAGAGGGGACATACTCAGCCCCATTCGTGAGGCCCAGACTTCTG
Seq A exon
GTGAGCTGTAGGGCTGTTGGAGAAGGGCCTTGGGAATAGAGGTGGCCCTGGTGACGTTGTCATATAGATTGCTGGATCTCTTTTTAG
Seq C2 exon
GGCTTAAGGTGATGGCACTGAGTTTGGTGGGAGCTGACCCAGAGCAGCTGCGTCGCTTGGCACCAGGCACGGACCCCATCCAGAACTTCTTTGCTGTGGATAATGGCCCAGGCTTGGACAGAGCAGTCAGTGATCTGGCTGTAGCCCTGTGTCAGGCAGCTGTGACCATAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-Col7a1:NM_007738:26
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.040 A=NA C2=0.379
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(27.8=100)
A:
NA
C2:
PF0009223=VWA=PD(25.6=77.6)
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:
TGAGAGGGGACATACTCAGCC
R:
CACTGACTGCTCTGTCCAAGC
Band lengths:
177-264
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: