HsaEX6066215 @ hg38
Exon Skipping
Gene
ENSG00000139219 | COL2A1
Description
collagen type II alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2200]
Coordinates
chr12:47981776-47982609:-
Coord C1 exon
chr12:47982502-47982609
Coord A exon
chr12:47982107-47982160
Coord C2 exon
chr12:47981776-47981829
Length
54 bp
Sequences
Splice sites
3' ss Seq
CTGGTTTTCTCTTCCCTCAGGGT
3' ss Score
11.14
5' ss Seq
CGAGTAAGT
5' ss Score
10.15
Exon sequences
Seq C1 exon
GGTGCATCTGGCCCAGCAGGCCCCCCTGGGGCTCAGGGCCCTCCAGGTCTTCAGGGAATGCCTGGCGAGAGGGGAGCAGCTGGTATCGCTGGGCCCAAAGGCGACAGG
Seq A exon
GGTGACGTTGGTGAGAAAGGCCCTGAGGGAGCCCCTGGAAAGGATGGTGGACGA
Seq C2 exon
GGCCTGACAGGTCCCATTGGCCCCCCTGGCCCAGCTGGTGCTAATGGCGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139219-'42-45,'42-44,43-45=AN
Average complexity
A_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=PD(23.6=47.2),PF0139113=Collagen=FE(53.8=100),PF0139113=Collagen=PU(40.8=80.6)
A:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(23.9=100)
C2:
PF0139113=Collagen=FE(23.9=100),PF0139113=Collagen=PU(15.9=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:
CCCTCCAGGTCTTCAGGGAAT
R:
CTTCTCGCCATTAGCACCAGC
Band lengths:
124-178
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains