HsaEX0016502 @ hg38
Exon Skipping
Gene
ENSG00000196739 | COL27A1
Description
collagen type XXVII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:22986]
Coordinates
chr9:114183022-114196012:+
Coord C1 exon
chr9:114183022-114183075
Coord A exon
chr9:114194404-114194457
Coord C2 exon
chr9:114195959-114196012
Length
54 bp
Sequences
Splice sites
3' ss Seq
TGGAATTGTTTTTGTTTCAGGGA
3' ss Score
9.15
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
Exon sequences
Seq C1 exon
GGTCCTCCTGGGCCTTATGGAAATCCAGGTCTCCCCGGCCCTCCTGGAGCCAAA
Seq A exon
GGACAGAAAGGGGACCCAGGGCTCTCACCAGGAAAGGCCCACGATGGGGCAAAG
Seq C2 exon
GGTGACATGGGCTTGCCTGGGCTCTCCGGGAATCCAGGACCTCCGGGACGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196739_MULTIEX4-1/4=C1-2
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(27.4=100),PF0139113=Collagen=PU(12.6=61.1)
A:
PF0139113=Collagen=PD(19.4=66.7),PF0139113=Collagen=PU(13.6=50.0)
C2:
PF0139113=Collagen=PD(17.7=61.1),PF0139113=Collagen=PU(21.9=77.8)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCTCCTGGGCCTTATGGAA
R:
GGTCCTGGATTCCCGGAGAG
Band lengths:
94-148
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development