HsaEX0016301 @ hg19
Exon Skipping
Gene
ENSG00000197467 | COL13A1
Description
collagen, type XIII, alpha 1 [Source:HGNC Symbol;Acc:2190]
Coordinates
chr10:71637795-71647247:+
Coord C1 exon
chr10:71637795-71637821
Coord A exon
chr10:71640259-71640309
Coord C2 exon
chr10:71647212-71647247
Length
51 bp
Sequences
Splice sites
3' ss Seq
CCCTTCCTCTCTCCCCGCAGGGG
3' ss Score
14.96
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
Exon sequences
Seq C1 exon
GGAGTAAAGGGCCAACCAGGCGAGAAG
Seq A exon
GGGTCCCCCGGAGACGCTGGGCTGTCCATCATTGGTCCCCGCGGCCCCCCT
Seq C2 exon
GGTCAACCAGGAACTAGAGGTTTCCCTGGATTTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197467-'7-10,'7-9,9-10
Average complexity
C2
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=1.000 C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(15.4=100)
A:
PF0139113=Collagen=PD(17.4=47.1),PF0139113=Collagen=PU(9.8=35.3)
C2:
PF0139113=Collagen=FE(25.0=100),PF0139113=Collagen=FE(17.5=100)
Other Inclusion Isoforms:
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGTAAAGGGCCAACCAGG
R:
GGAAACCTCTAGTTCCTGGTTGAC
Band lengths:
52-103
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)