MmuINT0040590 @ mm9
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108875554-108875741:+
Coord C1 exon
chr9:108875554-108875622
Coord A exon
chr9:108875623-108875696
Coord C2 exon
chr9:108875697-108875741
Length
74 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
CTGACGTCTCATCTAAACAGGGG
3' ss Score
9.1
Exon sequences
Seq C1 exon
GTGGCCATTGAAGAGCCAGGCCCTGGACTGGCTAGAGAGCAAGGACCTCCTGGACTCAAGGGTGCCAAG
Seq A exon
GTCAGTGTGGGGTCAACCTGTGACTCAAGCCTTACCACGCCCCTCGGGCCTGACCTGACGTCTCATCTAAACAG
Seq C2 exon
GGGGAGCCAGGCAGTGATGGTGACCCTGGACCTAAAGGAGACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-Col7a1:NM_007738:76
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(10.3=30.4),PF0139113=Collagen=PU(25.7=78.3)
A:
NA
C2:
PF0139113=Collagen=FE(20.0=100)
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:
GTGGCCATTGAAGAGCCAGG
R:
TGTCTCCTTTAGGTCCAGGGT
Band lengths:
112-186
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: