HsaALTA0002023-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61945424-61946791:+
Coord C1 exon
chr20:61945424-61945553
Coord A exon
chr20:61946753-61946755
Coord C2 exon
chr20:61946756-61946791
Length
3 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CTGACCCTGTCTCCTCTCAGCAG
3' ss Score
8.26
Exon sequences
Seq C1 exon
GTCTCTGTGCCAGGAGCCAGGAGCCACGTGACACTGCCCGACCTGCAGGCAGCCACGAAGTACAGGGTCCTGGTCTCAGCTATCTATGCAGCAGGCAGGAGTGAGGCTGTGTCTGCCACGGGCCAGACAG
Seq A exon
CAG
Seq C2 exon
CCTGCCCAGCCCTCCGCCCTGACGGCTCCCTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-19-22,19-21-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.182 A=NA C2=0.154
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(43.2=79.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
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:
CAGGGTCCTGGTCTCAGCTAT
R:
CTGGGAGGGAGCCGTCAG
Band lengths:
104-107
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)