HsaINT0025493 @ hg38
Intron Retention
Gene
ENSG00000179058 | C9orf50
Description
chromosome 9 open reading frame 50 [Source:HGNC Symbol;Acc:HGNC:23677]
Coordinates
chr9:129613107-129613597:-
Coord C1 exon
chr9:129613435-129613597
Coord A exon
chr9:129613252-129613434
Coord C2 exon
chr9:129613107-129613251
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:ENST00000372478:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.133
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
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