HsaEX0016500 @ hg19
Exon Skipping
Gene
ENSG00000196739 | COL27A1
Description
collagen, type XXVII, alpha 1 [Source:HGNC Symbol;Acc:22986]
Coordinates
chr9:117029784-117033061:+
Coord C1 exon
chr9:117029784-117029837
Coord A exon
chr9:117031521-117031574
Coord C2 exon
chr9:117033008-117033061
Length
54 bp
Sequences
Splice sites
3' ss Seq
TTTTGTTCGGCTTCTCCTAGGGT
3' ss Score
7.64
5' ss Seq
CGGGTAAGT
5' ss Score
10.75
Exon sequences
Seq C1 exon
GGGCCGCCTGGTGCAGTGGGAGAACCGGGCCTTCCTGGGGAAGCCGGGATGAAG
Seq A exon
GGTGACCTTGGACCCCTGGGCACTCCTGGGGAGCAGGGCCTCATTGGGCAACGG
Seq C2 exon
GGAGAGCCAGGCCTTGAGGGTGACAGTGGCCCCATGGGACCTGATGGGCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196739_MULTIEX3-2/2=1-C2
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.991 A=0.912 C2=0.955
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(20.5=100)
A:
PF0139113=Collagen=FE(20.5=100),PF0139113=Collagen=PU(19.2=83.3)
C2:
PF0139113=Collagen=PD(12.0=55.6),PF0139113=Collagen=FE(21.8=100)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGTGCAGTGGGAGAACC
R:
CTTCAGCCCATCAGGTCCCAT
Band lengths:
101-155
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)