HsaEX0016473 @ hg38
Exon Skipping
Gene
ENSG00000188517 | COL25A1
Description
collagen type XXV alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:18603]
Coordinates
chr4:108825196-108832433:-
Coord C1 exon
chr4:108832380-108832433
Coord A exon
chr4:108827135-108827188
Coord C2 exon
chr4:108825196-108825222
Length
54 bp
Sequences
Splice sites
3' ss Seq
CTTTCTACTTTTCATTTTAGGGT
3' ss Score
11.71
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
Exon sequences
Seq C1 exon
GGTACAGATGGTCCTATGGGACCCCATGGCCCTGCAGGTCCCAAAGGAGAAAGA
Seq A exon
GGTGAAAAAGGAGCTATGGGAGAGCCTGGACCAAGAGGGCCCTATGGGCTGCCT
Seq C2 exon
GGGAAAGATGGAGAGCCTGGTCTTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188517-'66-62,'66-61,67-62
Average complexity
C1
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.808 A=1.000 C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(21.8=100),PF0139113=Collagen=PU(25.8=94.4)
A:
PF0139113=Collagen=FE(20.2=100),PF0139113=Collagen=PU(18.9=77.8)
C2:
PF0139113=Collagen=FE(9.5=100),PF0139113=Collagen=FE(10.8=100)
Main Skipping Isoform:
NA
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:
GGTACAGATGGTCCTATGGGA
R:
TCAAGACCAGGCTCTCCATCT
Band lengths:
80-134
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