MmuINT0040549 @ mm10
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108965301-108965497:+
Coord C1 exon
chr9:108965301-108965363
Coord A exon
chr9:108965364-108965437
Coord C2 exon
chr9:108965438-108965497
Length
74 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
GTCATTTGTTTCTCCTTCAGGGT
3' ss Score
10.74
Exon sequences
Seq C1 exon
GGGCTTCCTGGAAGCCCTGGACCCCAAGGCCCAGCTGGCCGACCTGGAGAGAAGGGAGAAAAG
Seq A exon
GTAGGAGCCTGACCTCTGGGTGGCCCATAGGCAGGGCCTCCCCTGGGTTTTCCTGTCATTTGTTTCTCCTTCAG
Seq C2 exon
GGTGACTGTGAGGATGGAGGTCCAGGCCTCCCAGGACAGCCTGGGCCCCCAGGGGAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650:ENSMUST00000112070:40
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(35.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(7.1=20.0),PF0139113=Collagen=PU(31.0=90.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGAAGCCCTGGACCCC
R:
CTGTCCTGGGAGGCCTGG
Band lengths:
95-169
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