MmuALTD0003438-2/2 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108977953-108978162:+
Coord C1 exon
chr9:108977953-108977986
Coord A exon
chr9:108977987-108978012
Coord C2 exon
chr9:108978118-108978162
Length
26 bp
Sequences
Splice sites
5' ss Seq
CGGGTATGT
5' ss Score
8.79
3' ss Seq
TAATGTCATCCATCATTCAGGGT
3' ss Score
6.28
Exon sequences
Seq C1 exon
GGAGACCCGGGAGCAGGACTGCCGGGGCCCCGAG
Seq A exon
GTGAGCGTGGTGAGCCAGGTGTCCGG
Seq C2 exon
GGTGAAGATGGCCACCCTGGCCAGGAAGGACCTCGTGGACTTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-111-122,112-122-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(8.3=25.0),PF0139113=Collagen=PU(25.0=75.0)
A:
NA
C2:
PF0139113=Collagen=FE(23.3=100)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGACCCGGGAGCAGGAC
R:
CACAAGTCCACGAGGTCCTTC
Band lengths:
78-104
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types