MmuALTD1003928-1/3 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:181013390-181013923:+
Coord C1 exon
chr2:181013390-181013443
Coord A exon
NA
Coord C2 exon
chr2:181013870-181013923
Length
0 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTG
5' ss Score
8.56
3' ss Seq
TCCCCTTCTTTGTTCACCAGGGC
3' ss Score
10.16
Exon sequences
Seq C1 exon
GGCCTCTCTGGCCAGCAAGGCATCCCTGGGAAAACTGGCCTACAGGGACCAAAG
Seq A exon
NA
Seq C2 exon
GGCATGAGAGGACTGGAGGGACCTGCTGGCCTGCCAGGACCACCTGGCCCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356-39-48,40-48,41-48-1/3
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(32.1=100)
A:
NA
C2:
PF0139113=Collagen=PD(17.0=50.0),PF0139113=Collagen=PU(28.8=94.4)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCTCTGGCCAGCAAGG
R:
CAGCAGGTCCCTCCAGTCC
Band lengths:
80-105
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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