MmuINT0040561 @ mm10
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108955629-108956055:+
Coord C1 exon
chr9:108955629-108955790
Coord A exon
chr9:108955791-108955891
Coord C2 exon
chr9:108955892-108956055
Length
101 bp
Sequences
Splice sites
5' ss Seq
CTTGTAAGT
5' ss Score
8
3' ss Seq
ACCCCCAACCCCATTCACAGCTG
3' ss Score
5.98
Exon sequences
Seq C1 exon
GAATCAAGAATGCCGACCCTGAGGAACTGAAGCGTGTGGCCTCACAGCCAACCAGCGATTTCTTCTTCTTCGTCAATGACTTCAGCATCTTGAGGACCCTGTTGCCTCTCATTTCCAGGAGGGTGTGCACAACTGCTGGTGGTGTGCCTGTGACCCTGCCTT
Seq A exon
GTAAGTTTCTGCCTGTTCTGGGTACCCTAACCCCAGCCTGGGAGTGCCGACCTATGCACTCCTTGCCCATGACCTGATACTACCCCCAACCCCATTCACAG
Seq C2 exon
CTGATGACACTCCGTCTGGGCCCCGGGACCTGGTGCTCTCTGAGCCAAGTAGCCAATCCTTGCGAGTACAATGGACAGCAGCCAGTGGCCCTGTGACTGGCTACAAGGTTCAGTACACACCTCTGACAGGGCTAGGGCAGCCACTGCCAAGTGAGCGACAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650:ENSMUST00000112070:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.182 A=NA C2=0.455
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(21.3=67.3)
A:
NA
C2:
PF0004116=fn3=PU(57.0=89.1)
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:
ACAGCCAACCAGCGATTTCTT
R:
CTAGCCCTGTCAGAGGTGTGT
Band lengths:
254-355
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