HsaEX0016459 @ hg19
Exon Skipping
Gene
ENSG00000188517 | COL25A1
Description
collagen, type XXV, alpha 1 [Source:HGNC Symbol;Acc:18603]
Coordinates
chr4:109861695-109895549:-
Coord C1 exon
chr4:109895523-109895549
Coord A exon
chr4:109863365-109863424
Coord C2 exon
chr4:109861695-109861802
Length
60 bp
Sequences
Splice sites
3' ss Seq
GTGCTGTGCTATGTCCATAGGGC
3' ss Score
10.4
5' ss Seq
AAGGTTTGT
5' ss Score
7.81
Exon sequences
Seq C1 exon
GGAGAACAAGGTGATCAGGGACCTAGG
Seq A exon
GGCCTGCCAGGCTTCCCCACAGTTGCTGCCCTGCACAGTAATCAGATCCTCACCGTCAAG
Seq C2 exon
GGTGACCAAGGACAGGCAGGGCCTCCAGGACCCCCTGGCCCTCCAGGCCCAAGAGGGCCACCTGGGGACACAGGGAAAGATGGCCCCCGTGGAATGCCAGGAGTACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188517-'11-14,'11-12,12-14
Average complexity
ME(12_12-13_13[100=92])
Mappability confidence:
78%=75=80%
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=1.000 C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=PU(1.5=4.2)
A:
PF0139113=Collagen=PD(16.1=45.0),PF0139113=Collagen=PU(1.5=5.0)
C2:
PF0139113=Collagen=FE(16.9=100),PF0139113=Collagen=FE(13.6=100)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAACAAGGTGATCAGGGACCT
R:
GGTACTCCTGGCATTCCACG
Band lengths:
132-192
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)