HsaEX0016445 @ hg19
Exon Skipping
Gene
ENSG00000050767 | COL23A1
Description
collagen, type XXIII, alpha 1 [Source:HGNC Symbol;Acc:22990]
Coordinates
chr5:177690209-177695757:-
Coord C1 exon
chr5:177695731-177695757
Coord A exon
chr5:177694308-177694334
Coord C2 exon
chr5:177690209-177690325
Length
27 bp
Sequences
Splice sites
3' ss Seq
TCCCTGTCTTTTGTTCCCAGGGT
3' ss Score
10.71
5' ss Seq
CGGGTAAGA
5' ss Score
9.84
Exon sequences
Seq C1 exon
GGACTTCCAGGCCCGAAAGGGGAAAAG
Seq A exon
GGTGCACCAGGAGACTTTGGCCCCCGG
Seq C2 exon
GGAGACCAAGGACAAGATGGAGCTGCTGGGCCTCCGGGGCCCCCTGGACCTCCTGGGGCCCGGGGCCCTCCTGGCGACACTGGGAAAGATGGCCCCAGGGGAGCACAAGGCCCAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000050767_CASSETTE5
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=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(14.0=100),PF0139113=Collagen=FE(10.5=100)
A:
PF0139113=Collagen=PD(12.3=77.8),PF0139113=Collagen=FE(10.5=100)
C2:
PF0139113=Collagen=FE(45.8=100),PF0139113=Collagen=PU(27.4=43.6)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGACTTCCAGGCCCGAAAG
R:
CATCTTTCCCAGTGTCGCCAG
Band lengths:
118-145
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)