HsaEX0016440 @ hg19
Exon Skipping
Gene
ENSG00000050767 | COL23A1
Description
collagen, type XXIII, alpha 1 [Source:HGNC Symbol;Acc:22990]
Coordinates
chr5:177666142-177669129:-
Coord C1 exon
chr5:177669043-177669129
Coord A exon
chr5:177667462-177667539
Coord C2 exon
chr5:177666142-177666180
Length
78 bp
Sequences
Splice sites
3' ss Seq
CCTTGTCTCCTTTGAAACAGGAG
3' ss Score
8.45
5' ss Seq
GCGGTAGGC
5' ss Score
7.2
Exon sequences
Seq C1 exon
GGAGAACGAGGGGTCCCCGGCCGGAAAGGAGTGAAGGGCCAGAAGGGCGAGCCGGGACCACCAGGCCTGGACCAGCCGTGTCCCGTG
Seq A exon
GAGAATCCCACGTGCGGAGGCCGGAGAGGGGCACCAGGCTGGCGGGGCCCTGCGAGGGGCAATGGGCCATGCCCTGCG
Seq C2 exon
GGCCCCGACGGGCTGCCTGTGCCTGGCTGCTGGCATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000050767-'32-32,'32-31,33-32
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=1.000 C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(41.3=89.7)
A:
NO
C2:
PF0139113=Collagen=PD(5.7=30.8)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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:
GGAGAACGAGGGGTCCCC
R:
CTTATGCCAGCAGCCAGGC
Band lengths:
126-204
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)