HsaINT0025311 @ hg19
Intron Retention
Gene
ENSG00000198917 | C9orf114
Description
chromosome 9 open reading frame 114 [Source:HGNC Symbol;Acc:26933]
Coordinates
chr9:131588819-131589470:-
Coord C1 exon
chr9:131589311-131589470
Coord A exon
chr9:131588909-131589310
Coord C2 exon
chr9:131588819-131588908
Length
402 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGG
5' ss Score
7.66
3' ss Seq
CCCCATCTCTCTCTCTCCAGGAC
3' ss Score
13.24
Exon sequences
Seq C1 exon
GGCGGCCCTACACACTGAGCGTAGCCCTGCCGGGCTCCATCCTGGACAATGCTCAGTCGCCGGAGCTTCGCACCTACTTGGCCGGTCAGATTGCCAGAGCCTGTGCCATCTTCTGTGTGGATGAGATCGTGGTGTTTGATGAGGAGGGCCAGGATGCCAA
Seq A exon
GTAAGGGGCCATCCCACAGGGTGCCAGGGTTCAGGGAGAGGGAGGGGCTGCCGGGATGGGCCGAGGCTTCACCATGGCCCCGTCCACATGCCTGGCTCTTCCCTCGTGCCCTGCCTGAAATATTCCCTGTGTAATCCTTAGTGGGTAGAGTTGCCAGGTGGGGGTGATGACTACAGAGGTGGGATTGGGAGCCAGAAGGCCTAAACCTGTATCTCAGCTGTCACCCCGGCTGGAGTGCATGCAGTGGCATGGTCATGGCTCACTGCAGCCTCTACTTGCTGCACTCAGATGATCCTCCCACCTTAGCCTCCTGAGTAGCTGGGATTATACGCGTGCACTTGTAGACAGGAGCTCTTGAAGGGGCCACAGCTGGATCCTGAGCCCCCATCTCTCTCTCTCCAG
Seq C2 exon
GACTGTGGAGGGGGAATTCACAGGAGTTGGGAAGAAGGGGCAGGCGTGCGTACAGCTGGCCCGGATCCTGCAGTACCTGGAGTGTCCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198917-C9orf114:NM_016390:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.162
Domain overlap (PFAM):
C1:
PF0259812=Methyltrn_RNA_3=PU(16.8=90.7)
A:
NA
C2:
PF0259812=Methyltrn_RNA_3=FE(10.3=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:
GGCGGCCCTACACACTGAG
R:
AGGTACTGCAGGATCCGGG
Band lengths:
238-640
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)