HsaEX0016404 @ hg38
Exon Skipping
Gene
ENSG00000108821 | COL1A1
Description
collagen type I alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2197]
Coordinates
chr17:50194573-50195100:-
Coord C1 exon
chr17:50195047-50195100
Coord A exon
chr17:50194721-50194828
Coord C2 exon
chr17:50194573-50194626
Length
108 bp
Sequences
Splice sites
3' ss Seq
CTCCTCTCGGCCCTCTCCAGGGC
3' ss Score
8.31
5' ss Seq
CGTGTAAGT
5' ss Score
8.58
Exon sequences
Seq C1 exon
GGTGAACCTGGTGCTCCTGGCAGCAAAGGAGACACTGGTGCTAAGGGAGAGCCT
Seq A exon
GGCCCTGTTGGTGTTCAAGGACCCCCTGGCCCTGCTGGAGAGGAAGGAAAGCGAGGAGCTCGAGGTGAACCCGGACCCACTGGCCTGCCCGGACCCCCTGGCGAGCGT
Seq C2 exon
GGTGGACCTGGTAGCCGTGGTTTCCCTGGCGCAGATGGTGTTGCTGGTCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108821-'29-29,'29-27,31-29=AN
Average complexity
A_S
Mappability confidence:
89%=100=75%
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(22.7=100)
A:
PF0139113=Collagen=PD(30.7=63.9),PF0139113=Collagen=PU(23.4=41.7)
C2:
PF0139113=Collagen=FE(26.6=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGAACCTGGTGCTCCTG
R:
CTTGGGACCAGCAACACCATC
Band lengths:
108-216
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