HsaINT0025392 @ hg19
Intron Retention
Gene
ENSG00000197768 | C9orf173
Description
chromosome 9 open reading frame 173 [Source:HGNC Symbol;Acc:37285]
Coordinates
chr9:140146453-140146977:+
Coord C1 exon
chr9:140146453-140146587
Coord A exon
chr9:140146588-140146888
Coord C2 exon
chr9:140146889-140146977
Length
301 bp
Sequences
Splice sites
5' ss Seq
GAGGTGTGT
5' ss Score
6.14
3' ss Seq
TCTCCATCCTCCAACTACAGAGG
3' ss Score
6.44
Exon sequences
Seq C1 exon
TGCTGGAGCAACGCCCCCTGATCACAGCTGACCTGGAAGTCCCCAGCCCCACCAGGTACCAGGTGCCGAGCCCGTCCGTACGAGAGTCCTCCCCACACCCCCACTACAGCATCGGCTGCAAGCACCAGGGCCGAG
Seq A exon
GTGTGTGTCCCCTCCCTGAGGCCCAACCACCGGGCCTGTCCCTCACCCTGGGAATGGGGGCCTTTGCCTCTGTGCTGAAACCCCCACGGCCTGAGGGCCCCTCCACCCTTCCCTGCGTTCACCTCTAGGCTCAGCACCTGTAAGGAGGCCTGGAGAGAGGAGGGCTAGGGCTGGGGCATGGGTGGACATTGTGAAGACAAGGGTTCAGGGGCCGAGGGTGGGAACCGGGAGACAGGTTCGAGTGGGGACTGTCACCTGGGTGGGGCTCCCAGCCTTCTCTCTCTCCATCCTCCAACTACAG
Seq C2 exon
AGGGCGGTGGCCGCAGGGCATGGCAGACTTTGTGGTTCCAGAGCGAAAGCCCCTTCACGCAGAAAGCTGACTTCGACCAAGAGCAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197768-C9orf173:NM_001004353:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.775 A=NA C2=0.422
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAACGCCCCCTGATCAC
R:
TTGCTCTTGGTCGAAGTCAGC
Band lengths:
214-515
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)