MmuINT0040551 @ mm9
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108867483-108867659:+
Coord C1 exon
chr9:108867483-108867542
Coord A exon
chr9:108867543-108867623
Coord C2 exon
chr9:108867624-108867659
Length
81 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
TCCCCATTCATCCTTTCCAGGGC
3' ss Score
10.97
Exon sequences
Seq C1 exon
GGTGACTGTGAGGATGGAGGTCCAGGCCTCCCAGGACAGCCTGGGCCCCCAGGGGAGCCG
Seq A exon
GTGAGTTAGTCTTCAACCATCAACTCCCCAACCATCAACGCTCAAACCTAAGTCTCTGAACTCCCCATTCATCCTTTCCAG
Seq C2 exon
GGCCTGCGGGGAGCTCCTGGAATGACTGGGCCCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-Col7a1:NM_007738:40
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(7.1=20.0),PF0139113=Collagen=PU(31.0=90.0)
A:
NA
C2:
PF0139113=Collagen=FE(19.0=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:
GGTGACTGTGAGGATGGAGGT
R:
TTTGGGCCCAGTCATTCCAGG
Band lengths:
96-177
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: