MmuINT0040526 @ mm10
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108959936-108960311:+
Coord C1 exon
chr9:108959936-108960061
Coord A exon
chr9:108960062-108960164
Coord C2 exon
chr9:108960165-108960311
Length
103 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
CTCTCTGCCGGCCTGTCCAGGTG
3' ss Score
9.04
Exon sequences
Seq C1 exon
CTCCTGAGCCTGTGGGCAGTGTGTCGAAACTGCAAATCCTTAATGCTTCCAGTGATGTTCTACGGGTCACTTGGGTAGGAGTCCCTGGGGCCACATCCTATAAACTGGCGTGGGGACGTAGTGAAG
Seq A exon
GTAAGGCTCCAGGTTTCCATCCTTGTCCTTCCTGGCTACAAGTGCCCTCTCTGCTAAGCTCCCCACAGCCCCCCTAACTTTTACTCTCTGCCGGCCTGTCCAG
Seq C2 exon
GTGGCCCTATGAAACACCGGATACTCCCAGGAAACAAAGAGTCTGCAGAGATACGGGATCTCGAAGGAGGAGTCAGCTACTCCGTGAGAGTGACGGCGCTTGTTGGAGACCGAGAGGGTGCACCGGTGTCCATTGTCATCACCACAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650:ENSMUST00000112070:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.023 A=NA C2=0.340
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(46.8=86.0)
A:
NA
C2:
PF0004116=fn3=PD(51.9=82.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGTGTGTCGAAACTGCAAA
R:
GGTGATGACAATGGACACCGG
Band lengths:
254-357
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