MmuALTD0003422-2/2 @ mm9
Alternative 5'ss
Gene
ENSMUSG00000045672 | Col27a1
Description
collagen, type XXVII, alpha 1 [Source:MGI Symbol;Acc:MGI:2672118]
Coordinates
chr4:62915323-62915775:+
Coord C1 exon
chr4:62915323-62915372
Coord A exon
chr4:62915373-62915376
Coord C2 exon
chr4:62915731-62915775
Length
4 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCAG
5' ss Score
4.95
3' ss Seq
CCCCCATATTTCTGTTTCAGGGG
3' ss Score
11.5
Exon sequences
Seq C1 exon
GGGCAGCCAGGACCTGAGGGCAGTCCAGGGGCCAAAGGTTACCCTGGCAG
Seq A exon
GCAG
Seq C2 exon
GGGTTCCCTGGACCTGTAGGAGACCCTGGCCCCAAAGGCAGCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045672-10-11,11-11-2/2
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=FE(25.8=100),PF0139113=Collagen=FE(18.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(6.1=26.7),PF0139113=Collagen=FE(15.1=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGCAGCCAGGACCTGAG
R:
TTTGGGGCCAGGGTCTCCTA
Band lengths:
86-90
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: