HsaALTA0001379-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000198917 | C9orf114
Description
chromosome 9 open reading frame 114 [Source:HGNC Symbol;Acc:26933]
Coordinates
chr9:131586075-131586453:-
Coord C1 exon
chr9:131586351-131586453
Coord A exon
chr9:131586143-131586173
Coord C2 exon
chr9:131586075-131586142
Length
31 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGT
5' ss Score
6.99
3' ss Seq
CCCCCTCTTACATGGGCCAGGCA
3' ss Score
3.38
Exon sequences
Seq C1 exon
GTGCTGTGTTTGCTGAGGCCCCCTTCCAAGATGGGTATGACCTGACCATCGGGACGTCAGAGCGCGGCTCAGATGTGGCCTCTGCCCAGCTTCCCAACTTCAG
Seq A exon
GCATGCTCTTGTGGTGTTCGGGGGCCTCCAG
Seq C2 exon
GGTCTGGAAGCTGGAGCGGATGCTGACCCCAACCTGGAGGTGGCTGAACCCAGTGTCCTCTTTGACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198917-16-19,16-18-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.036 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF0259812=Methyltrn_RNA_3=FE(11.6=100)
A:
NA
C2:
PF0259812=Methyltrn_RNA_3=FE(16.8=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCCCCTTCCAAGATGGGTAT
R:
CTCCAGGTTGGGGTCAGCATC
Band lengths:
125-156
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)