MmuINT0040529 @ mm10
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108960514-108961098:+
Coord C1 exon
chr9:108960514-108960636
Coord A exon
chr9:108960637-108960951
Coord C2 exon
chr9:108960952-108961098
Length
315 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGA
5' ss Score
6.65
3' ss Seq
TACATTCATACTTCTCTCAGGTG
3' ss Score
7.34
Exon sequences
Seq C1 exon
CGCCTGCGACCCCAGCACTTCTGGAGACTCTTCAAGTTGTGCAGAGCGGGGAGCACTCCTTGAGGCTGCGATGGGAACCAGTACCCGGAGCACCAGGCTTCCGCCTGCACTGGCAACCTGAGG
Seq A exon
GTGAGAGACACTGGAGGAGGGAGTTGGGACCAATTAAGGGAGAGGGCCTCTGGGCAAAGTTGCTGAAAGGAGTGGGCAGCCAGGTCTGCAGAATCAAAAGCATCAGGGGGCTTAATCCACAAGGTGGGTGGGCGTAGTCAGCCTTGAGGAGATGCATCTGGTGAACAGGCTAAAGACGAATGAGAAAGATTGTTGGGAGAATGGATGTGATGGGTCAGCGTGGTTGGTGAGAGTCAGTGAGATGGGGACCGCCACCCCTGTTATCAGTCACCACCCCCTGCATATTCTTGGCCCTTACATTCATACTTCTCTCAG
Seq C2 exon
GTGGCCAGGAACAGTCCCTGACCTTGGGACCTGAGTCTAACAGCTACAACCTGGTTGGTCTGGAGCCAGCAACAAAGTACCAAGTATGGCTGACTGTCCTGGGCCAGACTGGAGAAGGTCCCCCTAGGAAGGTGACTGCATACACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650:ENSMUST00000112070:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.286 A=NA C2=0.540
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(45.6=85.7)
A:
NA
C2:
PF0004116=fn3=PD(53.2=84.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCGACCCCAGCACTTCT
R:
CAGTGTATGCAGTCACCTTCCT
Band lengths:
266-581
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