HsaALTA0001380-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000160345 | C9orf116
Description
chromosome 9 open reading frame 116 [Source:HGNC Symbol;Acc:28435]
Coordinates
chr9:138387315-138390509:-
Coord C1 exon
chr9:138390431-138390509
Coord A exon
chr9:138387416-138387461
Coord C2 exon
chr9:138387315-138387415
Length
46 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
TGTTCCTTTATCTCTTATAGAAA
3' ss Score
9.72
Exon sequences
Seq C1 exon
GACCCAGAAGGCTGTCTCCGTGTACAGGACCAGTAACCAGGCTTACGGGAGCAGAGCCCCCACCGTGCACGAGATGCCT
Seq A exon
AAAGTATTTTATCCAAATTCGAATAAATTTTCCCAACAACTTGCAG
Seq C2 exon
CGGGTGGAATGTTCCGGAACAATACTCTCAATGTTTACCTGGAGAAAAGCATCGTGACTGGCCCCGATAACTGCATCACCTCCTGTGACCGGCTCAACTTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000160345-3-7,3-6-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.250 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF148921=DUF4490=FE(33.8=100)
A:
NA
C2:
PF148921=DUF4490=PD(2.6=10.5)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAAGGCTGTCTCCGTGTACA
R:
GGCCAGTCACGATGCTTTTCT
Band lengths:
137-183
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)