HsaINT0025390 @ hg19
Intron Retention
Gene
ENSG00000197768 | C9orf173
Description
chromosome 9 open reading frame 173 [Source:HGNC Symbol;Acc:37285]
Coordinates
chr9:140145730-140146347:+
Coord C1 exon
chr9:140145730-140145848
Coord A exon
chr9:140145849-140146189
Coord C2 exon
chr9:140146190-140146347
Length
341 bp
Sequences
Splice sites
5' ss Seq
CCAGTAACT
5' ss Score
1.17
3' ss Seq
GCTGCTGGTCTCCCTTGCAGGCC
3' ss Score
10.05
Exon sequences
Seq C1 exon
GAGACTCTGATGATGAATTCTGACCAGAAGGCAGTGAAATTCCTGGCAAATTTTTACATCAATGGAGGCAAACACTGGACCCATGGTCACCTGAGGCAGACACAACCAGAGCCCACCCA
Seq A exon
GTAACTGGCGGAGAGGGGGAGAAGGGGCGGGCCAGCTGGGAGTGGCCAGGGGGCTGAGGGACAGTGTGGGGGGCAGGTTGCTGGGCAGGCGGCTGGGGGACTGAGGGACAGTGTGGGGACAGGCTGTGGGGCAGGCGGCTGGGAGCGGCCAGGGGCTGAGGGACAGTAGAGGGGACAGGCGGCTGGGAGCGGCCAGGGGCTGAGGGACAGTGTGGGGACAGGCTGTGGGGCACGTGGCTGGGAGCAGCCGGGGGCTGAGGGACAATAGAGGGGACAGGCTGTGGGGCATGTGGCTGGGAGCGGCCGGGGGCTGAGACAGTGGCTGCTGGTCTCCCTTGCAG
Seq C2 exon
GCCCAAGGCATCTGTGCTGTTGTTGGGCCCGGAGCCGGGGATGGCCTGGGATGAGACACAGCCCCCAAAGATGAAGGAGATCCCAGTTGGCCTCAGGTTACAGACGGGCACCCCCCAGGAGTCCCTGCCCACCTACACCCAGACCCTGAGGGAACTAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197768-C9orf173:NM_001004353:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.405 A=NA C2=0.914
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
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:
ACTCTGATGATGAATTCTGACCAGA
R:
ATAGTTCCCTCAGGGTCTGGG
Band lengths:
274-615
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)