HsaEX0016461 @ hg38
Exon Skipping
Gene
ENSG00000188517 | COL25A1
Description
collagen type XXV alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:18603]
Coordinates
chr4:108852236-108859733:-
Coord C1 exon
chr4:108859656-108859733
Coord A exon
chr4:108852902-108852925
Coord C2 exon
chr4:108852236-108852280
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_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.961 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(24.1=100)
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
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