MmuINT0040539 @ mm9
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108857240-108857581:+
Coord C1 exon
chr9:108857240-108857399
Coord A exon
chr9:108857400-108857487
Coord C2 exon
chr9:108857488-108857581
Length
88 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTTC
5' ss Score
1.14
3' ss Seq
GCTCTTGGCACCCATCCCAGGTC
3' ss Score
4.86
Exon sequences
Seq C1 exon
GACAGAATTTGGTCTGGATACACTTGGCTCTGGGAGTGACACCATCCGAGCCATCCGTGAGCTCAGCTATAAAGGTGGTAACACTCGCACGGGGGCCGCTCTTCACCACGTTTCTGACCGTGTCTTCCTGCCTCGTCTAACACGTCCTGGTGTCCCCAAG
Seq A exon
GTGTTCCCTATAAACCTACCATGCCTGCAAATGTGACCCCAAAATAAATGTCTGAAACATCCCTGACTGCTCTTGGCACCCATCCCAG
Seq C2 exon
GTCTGCATCCTGATCACAGATGGGAAATCCCAAGATTTAGTGGACACAGCTGCCCAAAAGCTGAAGGGGCAGGGAGTCAAGCTGTTTGCTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-Col7a1:NM_007738:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(30.5=100)
A:
NA
C2:
PF0009223=VWA=FE(17.8=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:
TGGATACACTTGGCTCTGGGA
R:
CCCATCTGTGATCAGGATGCA
Band lengths:
170-258
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: