HsaEX0016444 @ hg19
Exon Skipping
Gene
ENSG00000050767 | COL23A1
Description
collagen, type XXIII, alpha 1 [Source:HGNC Symbol;Acc:22990]
Coordinates
chr5:177688723-177690325:-
Coord C1 exon
chr5:177690209-177690325
Coord A exon
chr5:177689218-177689253
Coord C2 exon
chr5:177688723-177688749
Length
36 bp
Sequences
Splice sites
3' ss Seq
GTCCCCTCACACTTCCGCAGGGC
3' ss Score
8.88
5' ss Seq
ATGGTCAGT
5' ss Score
6.57
Exon sequences
Seq C1 exon
GGAGACCAAGGACAAGATGGAGCTGCTGGGCCTCCGGGGCCCCCTGGACCTCCTGGGGCCCGGGGCCCTCCTGGCGACACTGGGAAAGATGGCCCCAGGGGAGCACAAGGCCCAGCG
Seq A exon
GGCCCCAAAGGAGAGCCCGGACAAGACGGCGAGATG
Seq C2 exon
GGCCCAAAGGGACCCCCAGGGCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000050767_CASSETTE4
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(45.8=100),PF0139113=Collagen=PU(27.4=43.6)
A:
PF0139113=Collagen=PD(12.0=83.3),PF0139113=Collagen=FE(17.7=100)
C2:
PF0139113=Collagen=FE(12.9=100)
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:
GACAAGATGGAGCTGCTGGG
R:
CCTGGGGGTCCCTTTGGG
Band lengths:
127-163
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)