HsaALTA0001380-2/2 @ hg38
Alternative 3'ss
Gene
ENSG00000160345 | C9orf116
Description
chromosome 9 open reading frame 116 [Source:HGNC Symbol;Acc:HGNC:28435]
Coordinates
chr9:135495469-135498663:-
Coord C1 exon
chr9:135498585-135498663
Coord A exon
chr9:135495570-135495615
Coord C2 exon
chr9:135495469-135495569
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
ENSG00000160345-4-9,4-8-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref, Alt. Stop)
No structure available
Features
Disorder rate (Iupred):
C1=0.296 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
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
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