HsaEX0016470 @ hg38
Exon Skipping
Gene
ENSG00000188517 | COL25A1
Description
collagen type XXV alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:18603]
Coordinates
chr4:108834355-108840959:-
Coord C1 exon
chr4:108840867-108840959
Coord A exon
chr4:108838098-108838178
Coord C2 exon
chr4:108834355-108834390
Length
81 bp
Sequences
Splice sites
3' ss Seq
GCATTTGCTTTTGCATTTAGGGT
3' ss Score
8.91
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
Exon sequences
Seq C1 exon
GCTGTATCACCTTGAGCAGATTATGGACCCTCTCTGATCCTTTATTTACTCAACTGGGTAACTCACCTTACAGTGCTGTGATAACTTAATGAG
Seq A exon
GGTGAACCAGGGTTAAATGGTGTTAAAGGATTGAAGGGTGAACCAGGTCAAAAGGGTGACAGAGGACCCCTTGGTCTTCCA
Seq C2 exon
GGAGCATCTGGCTTAGACGGAAAGCCAGGATCCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188517-'62-57,'62-56,63-57
Average complexity
C3
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=1.000 C2=0.316
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(3.2=40.0)
A:
PF0139113=Collagen=PD(7.7=22.2),PF0139113=Collagen=FE(36.6=100)
C2:
PF0139113=Collagen=FE(15.5=100),PF0139113=Collagen=PU(7.8=41.7)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGTATCACCTTGAGCAGAT
R:
GGGATCCTGGCTTTCCGTCTA
Band lengths:
127-208
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development