HsaEX0016472 @ hg38
Exon Skipping
Gene
ENSG00000188517 | COL25A1
Description
collagen type XXV alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:18603]
Coordinates
chr4:108827135-108841721:-
Coord C1 exon
chr4:108841695-108841721
Coord A exon
chr4:108832380-108832433
Coord C2 exon
chr4:108827135-108827188
Length
54 bp
Sequences
Splice sites
3' ss Seq
TCATATTATCTTTTTTTTAGGGT
3' ss Score
10.65
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
Exon sequences
Seq C1 exon
GGACCTCATGGACTTCCTGGACCAAAG
Seq A exon
GGTACAGATGGTCCTATGGGACCCCATGGCCCTGCAGGTCCCAAAGGAGAAAGA
Seq C2 exon
GGTGAAAAAGGAGCTATGGGAGAGCCTGGACCAAGAGGGCCCTATGGGCTGCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188517_MULTIEX2-4/10=C1-5
Average complexity
C2
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.807 A=0.808 C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(10.3=100),PF0139113=Collagen=FE(11.3=100)
A:
PF0139113=Collagen=FE(21.8=100),PF0139113=Collagen=PU(25.8=94.4)
C2:
PF0139113=Collagen=FE(20.2=100),PF0139113=Collagen=PU(18.9=77.8)
Main Skipping Isoform:
ENST00000399127fB12756
Other Inclusion Isoforms:
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:
GGACCTCATGGACTTCCTGGA
R:
CCCATAGGGCCCTCTTGGTC
Band lengths:
75-129
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