HsaEX0016437 @ hg19
Exon Skipping
Gene
ENSG00000050767 | COL23A1
Description
collagen, type XXIII, alpha 1 [Source:HGNC Symbol;Acc:22990]
Coordinates
chr5:177674527-177675255:-
Coord C1 exon
chr5:177675193-177675255
Coord A exon
chr5:177674776-177674832
Coord C2 exon
chr5:177674527-177674553
Length
57 bp
Sequences
Splice sites
3' ss Seq
CTGTCTCTCACCCTCCCTAGGCT
3' ss Score
11.22
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
Exon sequences
Seq C1 exon
GGCGCTGACGGCCTCAAGGGGGAGAAGGGGGAGTCGGCGTCTGACAGCCTACAGGAGAGCCTG
Seq A exon
GCTCAGCTCATAGTGGAGCCAGGGCCCCCTGGCCCCCCTGGCCCCCCAGGCCCGATG
Seq C2 exon
GGCCTCCAGGGAATCCAGGGTCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000050767-'25-25,'25-24,26-25
Average complexity
C1
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=PD(27.1=76.2)
A:
PF0139113=Collagen=PU(21.0=68.4)
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACGGCCTCAAGGGGGAG
R:
CTTGGGACCCTGGATTCCCT
Band lengths:
84-141
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)