HsaINT0025313 @ hg19
Intron Retention
Gene
ENSG00000198917 | C9orf114
Description
chromosome 9 open reading frame 114 [Source:HGNC Symbol;Acc:26933]
Coordinates
chr9:131588301-131588712:-
Coord C1 exon
chr9:131588663-131588712
Coord A exon
chr9:131588432-131588662
Coord C2 exon
chr9:131588301-131588431
Length
231 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACG
5' ss Score
10.52
3' ss Seq
TCCCGGCTCTGCCTCCACAGGGC
3' ss Score
10.84
Exon sequences
Seq C1 exon
GTACCTGAGGAAGGCGTTCTTCCCCAAGCACCAGGATCTACAGTTTGCAG
Seq A exon
GTAACGCTGTATGGGCCCGCCCCCCCATTTCCCCTGGATCATGCCACAGACACTGAGACCACCCAGTCCTACCCTGCGCTGTCCAGGTGGGAAAGCAGGCCTGGGAGAGCAAGACCTGTGTCTGATGCCAAGACGCAGGTCTGTGGCAGAGCCGGTACTCCGCTCCAGGGTCCCCACTGCACCCTGTGTGCCCTAGCACTTCCCAGACTCTTCCCGGCTCTGCCTCCACAG
Seq C2 exon
GGCTCCTGAACCCCCTGGACAGCCCCCACCACATGCGTCAGGATGAGGAATCCGAGTTCCGAGAGGGCATCGTGGTGGATCGGCCCACCCGGCCAGGCCACGGCTCCTTTGTCAACTGTGGCATGAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198917-C9orf114:NM_016390:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.489
Domain overlap (PFAM):
C1:
PF0259812=Methyltrn_RNA_3=FE(5.8=100)
A:
NA
C2:
PF0259812=Methyltrn_RNA_3=FE(14.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGGCGTTCTTCCCCAAGC
R:
CTTTTTCATGCCACAGTTGACA
Band lengths:
172-403
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)