HsaEX0016466 @ hg19
Exon Skipping
Gene
ENSG00000188517 | COL25A1
Description
collagen, type XXV, alpha 1 [Source:HGNC Symbol;Acc:18603]
Coordinates
chr4:109861695-109863424:-
Coord C1 exon
chr4:109863365-109863424
Coord A exon
chr4:109862522-109862593
Coord C2 exon
chr4:109861695-109861802
Length
72 bp
Sequences
Splice sites
3' ss Seq
GACCTCAACTGACTGATCAGATG
3' ss Score
2.5
5' ss Seq
AAGGTAGTG
5' ss Score
5.56
Exon sequences
Seq C1 exon
GGCCTGCCAGGCTTCCCCACAGTTGCTGCCCTGCACAGTAATCAGATCCTCACCGTCAAG
Seq A exon
ATGGTGTTTCCTAAAATCAATCATGGGTTTCTCTCTGCTGATCAGCAGCTCATTAAACGCCGCCTGATTAAG
Seq C2 exon
GGTGACCAAGGACAGGCAGGGCCTCCAGGACCCCCTGGCCCTCCAGGCCCAAGAGGGCCACCTGGGGACACAGGGAAAGATGGCCCCCGTGGAATGCCAGGAGTACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188517_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=0.991 C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(16.1=45.0),PF0139113=Collagen=PU(1.5=5.0)
A:
PF0139113=Collagen=FE(53.8=100),PF0139113=Collagen=PU(14.8=33.3)
C2:
PF0139113=Collagen=FE(16.9=100),PF0139113=Collagen=FE(13.6=100)
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGCTTCCCCACAGTTGC
R:
GTACTCCTGGCATTCCACGG
Band lengths:
159-231
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)