HsaINT0025605 @ hg19
Intron Retention
Gene
ENSG00000165698 | C9orf9
Description
chromosome 9 open reading frame 9 [Source:HGNC Symbol;Acc:1367]
Coordinates
chr9:135762756-135763824:+
Coord C1 exon
chr9:135762756-135762958
Coord A exon
chr9:135762959-135763676
Coord C2 exon
chr9:135763677-135763824
Length
718 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
GGCCCCCTGCCGTCCTGCAGATA
3' ss Score
9.47
Exon sequences
Seq C1 exon
GTGCAGAGCTACATGGAACACTACTGCAACAGCTCCACAGACCGGCGGGTTCTGCTCATGTTCCTGGACATCTGTTCAGAGCTGAATAAGCTCTGCCAGCACTTTGAGGCCGTGCACTCTGGCACCCCAGTCACCAACAACCTCCTGGAGAAATGCAAAACCCTCGTTAGCCAAAGCAACGACTTAAGCAGCCTCAGAGCAAA
Seq A exon
GTAAGTCCCTCTGATGCTGCTCTTGAGGCCCCGTGTGTGCCTGTGGGGAGGCCTCTGTCCTGCTTCTTTCCTGTTGCCTGGATCATGGTGCTCCTATTAGACCACCCCGGGCAGGAAATCCCAGTCTCCACTCATTTATTGGAATGACTCGGATTCAACAAAACCTTTTCTTTACAACCATCGTAGACATGGCAGGACACCAGGTGTCTCACGGGTGTTAGCACCAGGCAGGTGGAGAAGGGGGTGTAGAGCCCAGAGCAGTTGCCCCCAGAAGCCCACAGAGATCCTCACTGACATGCAAAGAAGTGGACACCAGAGCCGCCTCCCAGGGGCAGCAGCACTGGCACTGAGGGCTCCTCATCCTGACAGCCCGGGAGCCTGCAGCACAGTGGGCCAGAGCCTGGGGAAGCTCTGTAGATACCAGGGTGAGAAGAGCCAGAGGGATGAGCCAGCCAGTTCCTCACCCCTAACCCAGGTTTCTACGGACCATGGGGCAGTGGTTTGCATCTCCTGTCTTTCACACCAGAATTACCTGGGGCTTGTGGCACCCCAGGCCTGGTCTGCCAGAATCTCTGGGGACAGAGCGCCTCAGCGTGCTGTGTGTCCAGTTCTAAAGCCTCCCCAGGTGACTCTGCTGTGCCTGAGGTGTGGCAGCTGCTTGCCACGGCATGGCAAGTCCCGGGAGCATGGGTTCACCTGGCCCCCTGCCGTCCTGCAG
Seq C2 exon
ATACCCTCATGATGTGGTGAACCACCTCAGCTGTGACGAGGCCCGGAACCACTACGGCGGCGTGGTCAGCCTCATCCCCCTCATCCTAGACTTAATGAAAGAATGGATCGCCCACTCCGAGAAGTTGCCGCGCAAGGTGCTGCAGCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165698-C9orf9:NM_018956:3
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=0.272
Domain overlap (PFAM):
C1:
PF151201=DUF4561=FE(39.0=100)
A:
NA
C2:
PF151201=DUF4561=PD(32.6=51.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAACACTACTGCAACAGCT
R:
CCTTGCGCGGCAACTTCTC
Band lengths:
327-1045
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)