MmuINT0040547 @ mm10
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108965050-108965211:+
Coord C1 exon
chr9:108965050-108965076
Coord A exon
chr9:108965077-108965157
Coord C2 exon
chr9:108965158-108965211
Length
81 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGT
5' ss Score
10.75
3' ss Seq
GACCCACTGTTCTTCCCTAGGGT
3' ss Score
10.76
Exon sequences
Seq C1 exon
GGTGACAAAGGTGATCGTGGGGAACGG
Seq A exon
GTAAGTGAGGAGCCAGGTATTCTGGGGATGGCTTGGAGGCTGAGTCTCATGGCCATCTCCTGACCCACTGTTCTTCCCTAG
Seq C2 exon
GGTCCCCCGGGACCAGGCATTGGTGCCAGTGAACAGGGTGACCCTGGACTTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650:ENSMUST00000112070:38
Average complexity
IR
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(13.8=100),PF0139113=Collagen=FE(14.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(6.9=22.2),PF0139113=Collagen=FE(30.4=100)
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:
GTGACAAAGGTGATCGTGGGG
R:
CGGAAGTCCAGGGTCACCC
Band lengths:
80-161
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types