HsaALTA0002023-2/3 @ hg38
Alternative 3'ss
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63314072-63315439:+
Coord C1 exon
chr20:63314072-63314201
Coord A exon
chr20:63315401-63315403
Coord C2 exon
chr20:63315404-63315439
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
ENSG00000101203-19-26,19-25,19-24-2/3
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
Mouse
(mm9)
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