MmuINT0040544 @ mm9
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108866266-108866529:+
Coord C1 exon
chr9:108866266-108866301
Coord A exon
chr9:108866302-108866457
Coord C2 exon
chr9:108866458-108866529
Length
156 bp
Sequences
Splice sites
5' ss Seq
CCGGTAGGT
5' ss Score
9.39
3' ss Seq
CTGCTTTCTGCCCCACACAGGGT
3' ss Score
8.37
Exon sequences
Seq C1 exon
GGAGAACGAGGGCCTCAAGGTCCAAAGGGGGAGCCG
Seq A exon
GTAGGTGAAAGGGAAATGGGGCCAGGATATTCCCTGGAGGAGTGGAGTGCCCCAGGCCAAACCCTGTACAAGACCTGAAGCATGCTAAGAACTGGAACACCATGAAGGGTGTCTCCCACCTCCCCTACCCTGAGAACTGCTTTCTGCCCCACACAG
Seq C2 exon
GGTGAGCCTGGGCAAATCACTGGCGGTGGAGGGCCAGGGTTTCCTGGAAAGAAAGGGGACCCTGGACCTTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-Col7a1:NM_007738:34
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=FE(17.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(11.3=29.2),PF0139113=Collagen=PU(29.3=70.8)
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:
GAGAACGAGGGCCTCAAGGTC
R:
GAAGGTCCAGGGTCCCCTTTC
Band lengths:
106-262
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: