MmuINT0040548 @ mm9
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108867203-108867408:+
Coord C1 exon
chr9:108867203-108867256
Coord A exon
chr9:108867257-108867345
Coord C2 exon
chr9:108867346-108867408
Length
89 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGG
5' ss Score
9.35
3' ss Seq
GTTTGTTTACTTCCTTCAAGGGG
3' ss Score
6.19
Exon sequences
Seq C1 exon
GGTCCCCCGGGACCAGGCATTGGTGCCAGTGAACAGGGTGACCCTGGACTTCCG
Seq A exon
GTGAGGGGCCTTGGGGTTCTGCTGGGGGGCGGTGGCTGAGTGTTGGCCTTCCTAGTTTTTTGCTTATGGGTTTGTTTACTTCCTTCAAG
Seq C2 exon
GGGCTTCCTGGAAGCCCTGGACCCCAAGGCCCAGCTGGCCGACCTGGAGAGAAGGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-Col7a1:NM_007738:38
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(6.9=22.2),PF0139113=Collagen=FE(30.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(35.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCGGGACCAGGCATTG
R:
TTTCTCCCTTCTCTCCAGGTCG
Band lengths:
111-200
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: