HsaEX0016464 @ hg19
Exon Skipping
Gene
ENSG00000188517 | COL25A1
Description
collagen, type XXV, alpha 1 [Source:HGNC Symbol;Acc:18603]
Coordinates
chr4:109790244-109810412:-
Coord C1 exon
chr4:109810377-109810412
Coord A exon
chr4:109805334-109805378
Coord C2 exon
chr4:109790244-109790306
Length
45 bp
Sequences
Splice sites
3' ss Seq
TATATGATTTTCCTGTGTAGGGT
3' ss Score
9.2
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
Exon sequences
Seq C1 exon
GGAGAACCTGGGGAATCTGGTCGTCCAGGGCAAAAG
Seq A exon
GGTGAACCAGGGCTTCCTGGGCTTCCTGGACTTCCGGGGATAAAG
Seq C2 exon
GGAGAACCAGGTTTCATTGGTCCTCAAGGAGAACCAGGCTTACCAGGTTTACCAGGAACAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188517_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=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(13.3=80.0),PF0139113=Collagen=FE(21.9=100)
A:
PF0139113=Collagen=FE(14.6=100),PF0139113=Collagen=FE(21.9=100)
C2:
PF0139113=Collagen=PD(17.2=47.8),PF0139113=Collagen=PU(22.8=56.5)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGAACCTGGGGAATCTGGT
R:
CCTGGTAAACCTGGTAAGCCTG
Band lengths:
92-137
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)