HsaEX0016247 @ hg19
Exon Skipping
Gene
ENSG00000060718 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:2186]
Coordinates
chr1:103356007-103363734:-
Coord C1 exon
chr1:103363681-103363734
Coord A exon
chr1:103360921-103361020
Coord C2 exon
chr1:103356007-103356060
Length
100 bp
Sequences
Splice sites
3' ss Seq
GGTCTCTTTTCCCCTTCTAGAAG
3' ss Score
9.28
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
Exon sequences
Seq C1 exon
GGAGAACAAGGTCTCCCTGGAGCTGCAGGCCAAGATGGACCACCTGGTCCTATG
Seq A exon
AAGCTGCCTGTAACTACCTACTGTATTGTTTCTACTGGTGAGATAAAGCTACCAAGACATTCCCCTTTTCCCCACCTTTTAAATACAACCTAGCTGTTCA
Seq C2 exon
GGACCTCCTGGCTTACCTGGTCTCAAAGGTGACCCTGGCTCCAAGGGTGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000060718_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=1.000 C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(24.6=100),PF0139113=Collagen=FE(22.4=100),PF0139113=Collagen=PU(6.3=27.8)
A:
PF0139113=Collagen=PD(0.1=0.0)
C2:
PF0139113=Collagen=PD(2.9=11.1),PF0139113=Collagen=FE(22.4=100),PF0139113=Collagen=FE(21.5=100)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
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:
GGAGAACAAGGTCTCCCTGGA
R:
CTTTTCACCCTTGGAGCCAGG
Band lengths:
108-208
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)