MmuINT0040528 @ mm10
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108954330-108955354:+
Coord C1 exon
chr9:108954330-108954510
Coord A exon
chr9:108954511-108955194
Coord C2 exon
chr9:108955195-108955354
Length
684 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
ACCCCGTTTCCTCCCCTCAGGAC
3' ss Score
12.49
Exon sequences
Seq C1 exon
TGACCTGCACACGCCTTTATGCTGCTGACATCGTGTTCTTACTCGATGGCTCGTCGTCCATTGGCCGCAGCAACTTTCGAGAAGTGCGAGGATTCCTGGAGGGGCTGGTGCTGCCTTTCTCAGGAGCAGCCAGTGCACAGGGCGTCCGGTTTGCCACAGTGCAGTACAGTGATGATCCACA
Seq A exon
GTGAGTAGTCGACGTGGGGTCAGGACTGTAGGCCCCAAGACCCCTTAACAGGAAGGAGTCTAGAAATAGGCTTTGGAGAGCCCAGAAAGGCCCTCGCCAACACCTCTTCTGGAGAGAGGTGGGGATAACTTGGAAGAGTGTTCTTGTCCTAAAACACCTCTCAGTCAGTGTCCTGGGGTTGTGGTGGGGTGGGGGTGGGGTGGACAGGATGATTCTGCTTCCTGATCTGCATAGAGAGAGAGAGTCCAGGAGCTCCAGGCGTTGGGCTCCTGGTGGAGTCTGCATGTTTGGGCTCTGCCAGCTCTTCAGCCCTCTGTTCATCAGAAATGCTTTGTCTGGCCAGTGACCACTGTCCTGAAACTGAGCCCTTCCTCCTACAATTATTTAATCAGATATCCTGCCCACACACACCACCACCACCACCACCACCACCCCCGCCCCAGGCTAGGGACCTAGAGGGTTCCAGGCCTGTTGAGGCTCAGTGACATTGCTATGTCAAGCAGCATCTGAGGAGGCTGCTAACGTGGACACTTCCGCGGTAGAGGGCTGGGGGGGGGTGGGGTCTCAGAACCAAGGGTGCTTGCCTCAGAGCTCACTCATCTCAGTGGCCTCATCTCAGAGGCAGGGCTGGAAGAGATCATGACCCCCCCCCCCGCCTTGTGTTACCCCGTTTCCTCCCCTCAG
Seq C2 exon
GACAGAATTTGGTCTGGATACACTTGGCTCTGGGAGTGACACCATCCGAGCCATCCGTGAGCTCAGCTATAAAGGTGGTAACACTCGCACGGGGGCCGCTCTTCACCACGTTTCTGACCGTGTCTTCCTGCCTCGTCTAACACGTCCTGGTGTCCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650:ENSMUST00000112070:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(29.3=83.6)
A:
NA
C2:
PF0009223=VWA=FE(30.5=100)
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:
TGACCTGCACACGCCTTTATG
R:
GGGACACCAGGACGTGTTAGA
Band lengths:
337-1021
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