MmuINT0040578 @ mm9
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108873498-108873639:+
Coord C1 exon
chr9:108873498-108873533
Coord A exon
chr9:108873534-108873603
Coord C2 exon
chr9:108873604-108873639
Length
70 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
AAAAGCCGTATCTCCCTTAGGGA
3' ss Score
6.59
Exon sequences
Seq C1 exon
GGAGACCCTGGAGACCCTGGAGAAGATGGAAGGAAG
Seq A exon
GTAAGCCCCTCTCTCGGAGGATGCTGTGGCCTCAGATTGGACCACGTCTAAAAAGCCGTATCTCCCTTAG
Seq C2 exon
GGAGAAAAGGGAGATTCGGGTGCCCCTGGAAGAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-Col7a1:NM_007738:65
Average complexity
IR-S
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(11.2=83.3),PF0139113=Collagen=FE(14.1=100)
A:
NA
C2:
PF0139113=Collagen=FE(14.1=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:
GGAGACCCTGGAGACCCTG
R:
GGCACCCGAATCTCCCTTTTC
Band lengths:
60-130
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: