HsaINT0025493 @ hg19
Intron Retention
Gene
ENSG00000179058 | C9orf50
Description
chromosome 9 open reading frame 50 [Source:HGNC Symbol;Acc:23677]
Coordinates
chr9:132375386-132375876:-
Coord C1 exon
chr9:132375714-132375876
Coord A exon
chr9:132375531-132375713
Coord C2 exon
chr9:132375386-132375530
Length
183 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGG
5' ss Score
3.69
3' ss Seq
TGGGGTCCTGTCTCCCCCAGGTC
3' ss Score
11.24
Exon sequences
Seq C1 exon
TCCAACAGAGCGTCATTGTGAACCAGAAGGCCGCCCTGCCAGTGGCGTCCGAGCGGGTGTTTGGGAGTGTCGGAAAACGGCTGGAGAGTTTGCCCAAAGCCCTGTACCCTGGGGCCAAGGAGGAGACCCTGGCCAGCTCCTCGTGTTGGGACTGCGCTGGCCT
Seq A exon
GTGAGGCTCCAGGGAAGCGGATGGGACTCGTGGACATTGCCAGGGCCCTCCACCCCCCTTGCCTACAGACCTCCCCACCCAGCAGCAGGCGGGTTGCCAGTGTGGGTCCTCAAGGGCCCTGCCAGCCATGGGTGGGCCGGGGACTCAGAGTCCAGGAAGCTCATGGGGTCCTGTCTCCCCCAG
Seq C2 exon
GTCCACCCAGAAGACACAGGGCTACCTTTCTGAGGACACCTCCATGAACAGCAGCCTGCCCTTCTGTTCATGGAAGAAGGCCGCTGCTCAGAGGCCGCGAAGCAGCCTCCGAGCCTTCTTGGACCCGCACAGAAACCTGGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000179058-C9orf50:NM_199350:5
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=0.143
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
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:
GGTGTTTGGGAGTGTCGGAAA
R:
GTTTCTGTGCGGGTCCAAGAA
Band lengths:
244-427
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)