HsaALTD0001547-2/2 @ hg19
Alternative 5'ss
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61959431-61959850:+
Coord C1 exon
chr20:61959431-61959479
Coord A exon
chr20:61959480-61959497
Coord C2 exon
chr20:61959683-61959850
Length
18 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
GACACCCCTCCTCCCCACAGCAC
3' ss Score
9.96
Exon sequences
Seq C1 exon
GGCGAGCCGCAGTCCCTTGCCACCCTCTACCAGCTTGTGAGCCAGGCCT
Seq A exon
GTGAGTCTGCCATTCAGA
Seq C2 exon
CACACGTGTCAAAGTTCGACTCCTTCCACGAGAACACCAGGCCCCCCATGCCCATCTTGGAGCAGAAGCTGGAGCCGGGCACTGAGCCCCTGGGGTCCCCTGGCACCCGCAGCAAGGCCCTGGTTCCTGGAGAATGGGGGCGTGGTGGCCGCCACCTTGAGGGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-36-42,37-42-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.832 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(6.8=23.5)
A:
NA
C2:
NO
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:
AGTCCCTTGCCACCCTCTAC
R:
TTCTGCTCCAAGATGGGCATG
Band lengths:
106-124
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)