HsaEX0016520 @ hg38
Exon Skipping
Gene
ENSG00000139219 | COL2A1
Description
collagen type II alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2200]
Coordinates
chr12:47977102-47977653:-
Coord C1 exon
chr12:47977600-47977653
Coord A exon
chr12:47977320-47977427
Coord C2 exon
chr12:47977102-47977155
Length
108 bp
Sequences
Splice sites
3' ss Seq
TGAGACCTCTCTCCTGACAGGGT
3' ss Score
8.92
5' ss Seq
GCTGTAAGT
5' ss Score
8.56
Exon sequences
Seq C1 exon
GGAAGCCCCGGTGCTGATGGCCCCCCTGGCAGAGATGGCGCTGCTGGAGTCAAG
Seq A exon
GGTGATCGTGGTGAGACTGGTGCTGTGGGAGCTCCTGGAGCCCCTGGGCCCCCTGGCTCCCCTGGCCCCGCTGGTCCAACTGGCAAGCAAGGAGACAGAGGAGAAGCT
Seq C2 exon
GGTGCACAAGGCCCCATGGGACCCTCAGGACCAGCTGGAGCCCGGGGAATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139219-'54-57,'54-56,55-57
Average complexity
S
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(19.5=100),PF0139113=Collagen=PU(16.5=77.8)
A:
PF0139113=Collagen=PD(16.1=38.9),PF0139113=Collagen=FE(41.2=100)
C2:
PF0139113=Collagen=FE(20.0=100),PF0139113=Collagen=PU(13.4=61.1)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGCCCCGGTGCTGATG
R:
CTGGATTCCCCGGGCTCC
Band lengths:
107-215
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development