HsaINT0116938 @ hg19
Intron Retention
Gene
ENSG00000095319 | NUP188
Description
nucleoporin 188kDa [Source:HGNC Symbol;Acc:17859]
Coordinates
chr9:131763808-131764255:+
Coord C1 exon
chr9:131763808-131764008
Coord A exon
chr9:131764009-131764162
Coord C2 exon
chr9:131764163-131764255
Length
154 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CTGTCTTTCCCTCCTCCCAGGGA
3' ss Score
12.23
Exon sequences
Seq C1 exon
GTGTGTGTCCTGGGCCTGCACCTGGCCAAGGAGCTGTGTGAGGTAGACGAGGATGGTGACTCCTGGCTGCAGGTAACCCGCAGGCTCCCCATCCTACCCACCCTCCTCACCACTCTAGAGGTGAGCCTTCGCATGAAGCAGAACCTGCATTTCACTGAGGCCACATTGCATCTGCTCCTCACCCTGGCTCGCACTCAGCAG
Seq A exon
GTAGGAGGCCAGCCCGAAGGCAGGAGGGAGCGTCCTTGCTTGCCTGGGTGGGTTCTGACAATCCCAGAAGCTGTGATCTAGCCTGAGAGCCCTACCTACCCTAGGCAGGGCAGGGGCAGGCTCCATCTCATTTCCTGTCTTTCCCTCCTCCCAG
Seq C2 exon
GGAGCCACAGCAGTGGCTGGAGCTGGCATCACCCAGAGCATTTGTTTGCCCCTTCTGAGTGTGTACCAGCTGAGCACCAACGGCACAGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000095319-NUP188:NM_015354:35
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=0.000
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGTGTGAGGTAGACGAGGA
R:
GTGCTCAGCTGGTACACACTC
Band lengths:
246-400
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)