HsaEX0016468 @ hg38
Exon Skipping
Gene
ENSG00000188517 | COL25A1
Description
collagen type XXV alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:18603]
Coordinates
chr4:108859656-108863387:-
Coord C1 exon
chr4:108863319-108863387
Coord A exon
chr4:108860927-108860971
Coord C2 exon
chr4:108859656-108859733
Length
45 bp
Sequences
Splice sites
3' ss Seq
TCTCTTTCCAACGGGAAAAGGGG
3' ss Score
-0.45
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
Exon sequences
Seq C1 exon
GGTGAACGGGGGGAAGCAGGGCCTCCTGGAAGAGGTGAGCGAGGGGAACCTGGAGCCCCCGGACCAAAG
Seq A exon
GGGGATCGTGGAGAAAAAGGGGACTCTGGAGCTCAGGGACCAAGG
Seq C2 exon
GGTCCACCTGGTCAAAAAGGGGATCAAGGAGCCACTGAGATCATAGACTACAACGGCAACCTCCACGAAGCCTTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188517_MULTIEX4-3/3=C1-C2
Average complexity
C1
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=0.921 C2=0.961
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(16.1=43.5),PF0139113=Collagen=PU(22.8=56.5)
A:
PF0139113=Collagen=FE(24.6=100)
C2:
PF0139113=Collagen=PD(22.4=50.0),PF0139113=Collagen=PU(5.0=11.5)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCTGGAAGAGGTGAGCGAG
R:
TGTAAGGCTTCGTGGAGGTTG
Band lengths:
124-169
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