HsaINT0025393 @ hg19
Intron Retention
Gene
ENSG00000197768 | C9orf173
Description
chromosome 9 open reading frame 173 [Source:HGNC Symbol;Acc:37285]
Coordinates
chr9:140146889-140147417:+
Coord C1 exon
chr9:140146889-140146977
Coord A exon
chr9:140146978-140147113
Coord C2 exon
chr9:140147114-140147417
Length
136 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGG
5' ss Score
4.94
3' ss Seq
CGTCTCCTACCCCCTCGCAGTGG
3' ss Score
8.32
Exon sequences
Seq C1 exon
AGGGCGGTGGCCGCAGGGCATGGCAGACTTTGTGGTTCCAGAGCGAAAGCCCCTTCACGCAGAAAGCTGACTTCGACCAAGAGCAAAAG
Seq A exon
GTTGGGGGCTGGGCAGGAAGGGGGCGGGGAGTCCACGCAGGCAGGGGGCTGGGGGTTCCAGTGGGGCCAAAGGGGGGCTGGCTGAGGGTCCGTGGGGAGCACCCTGCCCTGCAGCCCGTCTCCTACCCCCTCGCAG
Seq C2 exon
TGGCCCTCGCCAGCCCACTACCAGCTGCTCAGCCGGCCCGCCTTCCCCGCCTTCAGCTTCAGAGGCTGCCACTCCGCTTCCAAGACACCTGAAGGCCACACCCACCTAGGGCTGCCTGGGGCTAGGGGGCTGGGCCTCAGGGTGCAGCCCCAGTCCCTGCTTCAGGCCTCTTTGCAGGCACCTGGCAAGAGATGCCCTGGCCCCAACACCTACAATATCCTTCCTGGGAGCCGCCTGCAGAGCCCCCGCTCGCCGGCCTTCTCGATGAGCCGCTCCCCTGCGTTCACCTCCTGGCTCAGCACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197768-C9orf173:NM_001004353:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.422 A=NA C2=0.542
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:
GCTGACTTCGACCAAGAGCAA
R:
CGGCTCCCAGGAAGGATATTG
Band lengths:
257-393
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)