HsaINT0025322 @ hg19
Intron Retention
Gene
ENSG00000160401 | C9orf117
Description
chromosome 9 open reading frame 117 [Source:HGNC Symbol;Acc:27843]
Coordinates
chr9:130473508-130474229:+
Coord C1 exon
chr9:130473508-130473775
Coord A exon
chr9:130473776-130474098
Coord C2 exon
chr9:130474099-130474229
Length
323 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTGC
5' ss Score
6.3
3' ss Seq
CCACCTGTCCGCACCCGCAGATC
3' ss Score
11
Exon sequences
Seq C1 exon
ACTGAGGAAAGAGATCATCCAGCGCGTGAACCTCGTGGCCAATGAGTTCCACAAGGTGACCACGAACCGGATGTGGGAGACAACCAAGCGGGCCATCAAAGAGAACAACGGCATTACCCTGCAGATGGCCAGGGTCTCCCAGCAAGGCATGAAGCTGCTGCAGGAGAATGAGCAGCTCAAGGGAAGACAGAACAATCTGTGCAAACAGCTGGAGCTGCTGGAGAACACCCAGAAGGTCATGGCCAGGCACAAAAGAGGCCACCAGAAG
Seq A exon
GTGTGCCTGCAGGCCTCAGCACAGGGCATTTGGCATGCAAGGCAGGAGGCCGCCCTGGGGGCCCTGCAGGGGTAGAGTCAGGGGCAGTCAAGTCAGGAGGGAGGGAGGCAGCAGAGAGAGGACTGGGCCTCCTGTGGGGGCTGCAGGGTGCTGGGCCTAGCTCCGGATTGTATTTATTTAAAGCCCCCATAACTTATGGAAGCAGAGTCCAGCCCTGGAGAGCTCACTGGCCGCTCTGCATAGGGGAACACGGGAGGCCTGGCTGTGTCTGCAGCTGGGGGACAGGGCAGGCTGAGGGCATGGCCACCTGTCCGCACCCGCAG
Seq C2 exon
ATCATCCTCATGCTGACTAAGAAGTGCCAGGAGCAGCAGCAGGACACCAAGGAGGCCGAGGAGCTGCGCCTCCTGCTGAGCCAGTTGGAGCAGAGATCCCTGCAGCTGCAGGTGGATAACCAGGCACTGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000160401-C9orf117:NM_001012502:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.067 A=NA C2=0.023
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAGAGATCATCCAGCGCGTG
R:
ATCTCTGCTCCAACTGGCTCA
Band lengths:
358-681
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)