MmuINT0040612 @ mm10
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108977821-108978012:+
Coord C1 exon
chr9:108977821-108977856
Coord A exon
chr9:108977857-108977952
Coord C2 exon
chr9:108977953-108978012
Length
96 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TTATTCCGGTTGAACTCTAGGGA
3' ss Score
7.13
Exon sequences
Seq C1 exon
GGAGCACCTGGCGCCTCTGGACTCAAAGGAGACAAG
Seq A exon
GTAGGTGGCATGCTGCTGGCTTTCCTATGCCTCACTGAGCTCCTATAATCCTCTGTCCTCTACTGAGTCCCCTTACTTATTCCGGTTGAACTCTAG
Seq C2 exon
GGAGACCCGGGAGCAGGACTGCCGGGGCCCCGAGGTGAGCGTGGTGAGCCAGGTGTCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650:ENSMUST00000112070:97
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(18.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(8.3=25.0),PF0139113=Collagen=PU(25.0=75.0)
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:
TGGCGCCTCTGGACTCAAAG
R:
CGGACACCTGGCTCACCA
Band lengths:
87-183
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