HsaEX0016474 @ hg19
Exon Skipping
Gene
ENSG00000188517 | COL25A1
Description
collagen, type XXV, alpha 1 [Source:HGNC Symbol;Acc:18603]
Coordinates
chr4:109745330-109748344:-
Coord C1 exon
chr4:109748291-109748344
Coord A exon
chr4:109746352-109746378
Coord C2 exon
chr4:109745330-109745383
Length
27 bp
Sequences
Splice sites
3' ss Seq
CTACTATGGTTCTTTGGCAGGGG
3' ss Score
6.51
5' ss Seq
GATGTAAGT
5' ss Score
9.11
Exon sequences
Seq C1 exon
GGTGAAAAAGGAGCTATGGGAGAGCCTGGACCAAGAGGGCCCTATGGGCTGCCT
Seq A exon
GGGAAAGATGGAGAGCCTGGTCTTGAT
Seq C2 exon
GGCTTCCCTGGTCCACGGGGTGAGAAGGGTGATCTAGGAGAAAAGGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188517_MULTIEX2-5/8=4-6
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=0.802
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(20.2=100),PF0139113=Collagen=PU(18.9=77.8)
A:
PF0139113=Collagen=PD(12.3=55.6),PF0139113=Collagen=FE(23.6=100)
C2:
PF0139113=Collagen=PD(15.5=72.2),PF0139113=Collagen=FE(23.0=100)
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:
GGTGAAAAAGGAGCTATGGGAGA
R:
TCTCCCTTTTCTCCTAGATCACCC
Band lengths:
104-131
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)