HsaEX0016517 @ hg38
Exon Skipping
Gene
ENSG00000139219 | COL2A1
Description
collagen type II alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2200]
Coordinates
chr12:47979511-47980661:-
Coord C1 exon
chr12:47980554-47980661
Coord A exon
chr12:47980009-47980062
Coord C2 exon
chr12:47979511-47979564
Length
54 bp
Sequences
Splice sites
3' ss Seq
TCTCCCTCTTTCCTTTCCAGGGT
3' ss Score
13.31
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
Exon sequences
Seq C1 exon
GGTGCTGATGGCCAGCCTGGGGCCAAGGGTGAGCAAGGAGAGGCCGGCCAGAAAGGCGATGCTGGTGCCCCTGGTCCTCAGGGCCCCTCTGGAGCACCTGGGCCTCAG
Seq A exon
GGTCCTACTGGAGTGACTGGTCCTAAAGGAGCCCGAGGTGCCCAAGGCCCCCCG
Seq C2 exon
GGAGCCACTGGATTCCCTGGAGCTGCTGGCCGCGTTGGACCCCCAGGCTCCAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139219-'48-50,'48-49,49-50=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(29.0=55.6),PF0139113=Collagen=PU(36.4=66.7)
A:
PF0139113=Collagen=FE(25.8=100)
C2:
PF0139113=Collagen=FE(22.7=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:
CCAAGGGTGAGCAAGGAGAGG
R:
GAGCCTGGGGGTCCAACG
Band lengths:
136-190
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