HsaEX0016343 @ hg19
Exon Skipping
Gene
ENSG00000084636 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:2193]
Coordinates
chr1:32145233-32145702:-
Coord C1 exon
chr1:32145643-32145702
Coord A exon
chr1:32145405-32145452
Coord C2 exon
chr1:32145233-32145286
Length
48 bp
Sequences
Splice sites
3' ss Seq
CGACCCCCACTCCCACCCAGGGT
3' ss Score
5.19
5' ss Seq
CAGGTGTGT
5' ss Score
6.99
Exon sequences
Seq C1 exon
GGTGAGCCAGGGGAGTGCTCCTGCCCCTCTCAAGGAGACCTCATCTTCTCTGGCATGCCG
Seq A exon
GGTGCTCCGGGACTTTGGATGGGCAGCTCCTGGCAGCCGGGCCCGCAG
Seq C2 exon
GGTCCACCAGGTATTCCCGGACCACCAGGCCCCCCTGGAGTACCTGGGCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000084636_CASSETTE2
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=1.000 C2=0.914
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(20.4=50.0),PF0139113=Collagen=PU(20.0=50.0)
A:
PF0139113=Collagen=PD(7.3=25.0),PF0139113=Collagen=FE(23.8=100)
C2:
PF0139113=Collagen=FE(27.0=100)
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGCCAGGGGAGTGCTC
R:
CTGCAGCCCAGGTACTCCAG
Band lengths:
112-160
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Genotype-Tissue Expression Project (GTEx)
- 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)