MmuALTA0004425-1/2 @ mm10
Alternative 3'ss
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:181000893-181001343:+
Coord C1 exon
chr2:181000893-181001041
Coord A exon
NA
Coord C2 exon
chr2:181001227-181001343
Length
0 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
TCCACAGATCTCTGTACCAGGCA
3' ss Score
4.48
Exon sequences
Seq C1 exon
CTGCAGCAAGCAGAAGCCCCCCATCCAGCCTGGCCTTGTCCTCGGAGACCCCCAACAGCCTGCAGGTCAACTGGACACCACCAAGTGGCCATGTCCTCCATTACCGGCTCAACTACACACTGGCCTCAGGCTCTGGACCAGAGAAATCG
Seq A exon
NA
Seq C2 exon
GCACCAGGAGCCATGCCGTGCTTCGTGATCTGATGTCTGCCACGAAGTACAGGGTCCTGGTCTCAGCTGTCTACAGAGCAGGGGAGAGCATGGCAGTGTCTGCCACATACCGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356-23-28,23-27-1/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence exclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.330 A=NA C2=0.041
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(54.3=88.0)
A:
NA
C2:
PF0004116=fn3=PD(43.2=79.5)
Main Inclusion Isoform:
NA
Other Inclusion 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:
GCTCAACTACACACTGGCCTC
R:
AGACCAGGACCCTGTACTTCG
Band lengths:
106-119
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