HsaEX0016461 @ hg19
Exon Skipping
Gene
ENSG00000188517 | COL25A1
Description
collagen, type XXV, alpha 1 [Source:HGNC Symbol;Acc:18603]
Coordinates
chr4:109773392-109780889:-
Coord C1 exon
chr4:109780812-109780889
Coord A exon
chr4:109774058-109774081
Coord C2 exon
chr4:109773392-109773436
Length
24 bp
Sequences
Splice sites
3' ss Seq
TCAACACATTTTCCCAACAGAGG
3' ss Score
7.52
5' ss Seq
ACGGTAACT
5' ss Score
7.53
Exon sequences
Seq C1 exon
GGTCCACCTGGTCAAAAAGGGGATCAAGGAGCCACTGAGATCATAGACTACAACGGCAACCTCCACGAAGCCTTACAG
Seq A exon
AGGATTACCACCTTAACTGTCACG
Seq C2 exon
GGTCCCCCTGGACCTCCTGGACCTCAAGGACTACAAGGGCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188517-'30-33,'30-31,33-33
Average complexity
S
Mappability confidence:
91%=100=80%
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(22.4=50.0),PF0139113=Collagen=PU(5.0=11.5)
A:
PF0139113=Collagen=PU(1.7=12.5)
C2:
PF0139113=Collagen=FE(23.3=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:
GTCCACCTGGTCAAAAAGGGG
R:
GGCCCTTGTAGTCCTTGAGGT
Band lengths:
118-142
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)