HsaEX0016516 @ hg38
Exon Skipping
Gene
ENSG00000139219 | COL2A1
Description
collagen type II alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2200]
Coordinates
chr12:47980009-47980968:-
Coord C1 exon
chr12:47980915-47980968
Coord A exon
chr12:47980554-47980661
Coord C2 exon
chr12:47980009-47980062
Length
108 bp
Sequences
Splice sites
3' ss Seq
CTTCCTCCTTCCCATTATAGGGT
3' ss Score
12.17
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
Exon sequences
Seq C1 exon
GGTGAACGTGGAGAGACTGGGCCCCCCGGACCAGCGGGATTTGCTGGGCCTCCT
Seq A exon
GGTGCTGATGGCCAGCCTGGGGCCAAGGGTGAGCAAGGAGAGGCCGGCCAGAAAGGCGATGCTGGTGCCCCTGGTCCTCAGGGCCCCTCTGGAGCACCTGGGCCTCAG
Seq C2 exon
GGTCCTACTGGAGTGACTGGTCCTAAAGGAGCCCGAGGTGCCCAAGGCCCCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139219-'47-49,'47-48,48-49=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=FE(24.6=100)
A:
PF0139113=Collagen=PD(29.0=55.6),PF0139113=Collagen=PU(36.4=66.7)
C2:
PF0139113=Collagen=FE(25.8=100)
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:
GGTGAACGTGGAGAGACTGGG
R:
CTCGGGCTCCTTTAGGACCAG
Band lengths:
91-199
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