MmuALTD1003928-2/3 @ 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
chr2:181013444-181013468
Coord C2 exon
chr2:181013870-181013923
Length
25 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TCCCCTTCTTTGTTCACCAGGGC
3' ss Score
10.16
Exon sequences
Seq C1 exon
GGCCTCTCTGGCCAGCAAGGCATCCCTGGGAAAACTGGCCTACAGGGACCAAAG
Seq A exon
GTACTGGCTCCAGGCCCAGTGGGTG
Seq C2 exon
GGCATGAGAGGACTGGAGGGACCTGCTGGCCTGCCAGGACCACCTGGCCCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356-39-48,40-48,41-48-2/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
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 Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
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:
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