MmuALTD1003926-2/2 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:180992434-180993008:+
Coord C1 exon
chr2:180992434-180992573
Coord A exon
chr2:180992574-180992577
Coord C2 exon
chr2:180992853-180993008
Length
4 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGT
5' ss Score
8.82
3' ss Seq
AGTCCTTCCTCTCTCTGCAGTTG
3' ss Score
10.43
Exon sequences
Seq C1 exon
GGGACTTGGAGCAGGAGCTGATACTGACCACCAAGACCCCCAAGGCCACTGTGGGTGGCCTGAACCCTTCCAAGAGCTACACCTTGCAGATCTTTGAGCTCACTGACTCGGGGCCTATCCTGCTGGCACGAAGGGAGTTT
Seq A exon
GTGA
Seq C2 exon
TTGAGGATCTGAAGAGCCAATCTTTGGGCAGAGGCAGCCGGAGGCTGGCTGGAGCCACCCTGGAGCCTACCTCCTTGCCTCTGAGGGGCCCAGACTCTGAGAAAACATCTGAGCCCAGCATTGCCTTTACCTTAAGCAGGGACCTGCCCATTCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356-3-5,4-5-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.061 A=NA C2=0.440
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(50.6=79.6)
A:
NA
C2:
NO
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:
TGCTGGCACGAAGGGAGTTT
R:
CCTCAGAGGCAAGGAGGTAGG
Band lengths:
106-110
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