MmuALTD0003438-2/2 @ mm9
Alternative 5'ss
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108879998-108880207:+
Coord C1 exon
chr9:108879998-108880031
Coord A exon
chr9:108880032-108880057
Coord C2 exon
chr9:108880163-108880207
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
ENSMUSG00000025650-102-105,103-105-2/2
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
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
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
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: