HsaALTD0001552-2/2 @ hg38
Alternative 5'ss
Gene
ENSG00000196739 | COL27A1
Description
collagen type XXVII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:22986]
Coordinates
chr9:114252593-114252932:+
Coord C1 exon
chr9:114252593-114252646
Coord A exon
chr9:114252647-114252653
Coord C2 exon
chr9:114252879-114252932
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
ENSG00000196739-54-56,55-56-2/2
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:
PF0139113=Collagen=PD(5.4=22.2)
A:
NA
C2:
PF0139113=Collagen=FE(28.8=100),PF0139113=Collagen=PU(16.7=72.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
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