MmuINT0040504 @ mm10
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108979214-108979530:+
Coord C1 exon
chr9:108979214-108979285
Coord A exon
chr9:108979286-108979494
Coord C2 exon
chr9:108979495-108979530
Length
209 bp
Sequences
Splice sites
5' ss Seq
AAGGCAAGT
5' ss Score
3.24
3' ss Seq
CCTCAATCTGTTTCCCATAGGGA
3' ss Score
8.89
Exon sequences
Seq C1 exon
GGTTCCAAAGGAGAGCCAGGTGACAAAGGCTCAGCTGGATCGATTGGAGTTCGAGGACTCACAGGACCCAAG
Seq A exon
GCAAGTTCCACCCCAGGCTTAGTCACTCACGCTCACACCTGCCTTGGGGATTTCTTATGTTAAAGGGATATTGGTTTCCTTGGTCATGTGTGTTCACACAGGCTCTATGTGCAGACTGGGCCCTGGTTTAACTGGGTCACCAAATGATTGCATGTGCCAGCTTAAGGCACCGTTACACTGAAGGACTTACCTCAATCTGTTTCCCATAG
Seq C2 exon
GGAGAGCCAGGTGCTGCAGGGATCCCCGGTGAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650:ENSMUST00000112070:104
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=PD(31.6=75.0),PF0139113=Collagen=PU(23.9=70.8)
A:
NA
C2:
PF0139113=Collagen=FE(15.5=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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