HsaALTD0001552-2/2 @ hg19
Alternative 5'ss
Gene
ENSG00000196739 | COL27A1
Description
collagen, type XXVII, alpha 1 [Source:HGNC Symbol;Acc:22986]
Coordinates
chr9:117014873-117015212:+
Coord C1 exon
chr9:117014873-117014926
Coord A exon
chr9:117014927-117014933
Coord C2 exon
chr9:117015159-117015212
Length
7 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGT
5' ss Score
8.57
3' ss Seq
TGTCTTCTCTGTCTTGGCAGGGT
3' ss Score
10.39
Exon sequences
Seq C1 exon
GGTGATCGTGGCATGATGGGACCCCCAGGCGTGCCTGGACCCAAGGGGTCGATG
Seq A exon
GTAAGGA
Seq C2 exon
GGTCATCCTGGAATGCCAGGTGGTATGGGGACCCCTGGAGAGCCTGGACCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196739-36-36,37-36-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(25.8=94.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGATCGTGGCATGATGGGAC
R:
CAGGCTCTCCAGGGGTCC
Band lengths:
99-106
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- 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)