HsaINT0116925 @ hg19
Intron Retention
Gene
ENSG00000095319 | NUP188
Description
nucleoporin 188kDa [Source:HGNC Symbol;Acc:17859]
Coordinates
chr9:131749868-131750465:+
Coord C1 exon
chr9:131749868-131749996
Coord A exon
chr9:131749997-131750325
Coord C2 exon
chr9:131750326-131750465
Length
329 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGG
5' ss Score
8.76
3' ss Seq
GTTTCCATTTGGCACCCTAGTGA
3' ss Score
3.87
Exon sequences
Seq C1 exon
TCATACTCCCAGCCTGCAGTTTCTCTGCATCTGCAGCCTGGCATACACAGAAGCAGGACAGACAGTTATCAATATCATGGGCATTGGCGTGGACACCATTGACATGGTGATGGCTGCTCAGCCTCGAAG
Seq A exon
GTAGGGCTCCTTCTCCACGTTCCCTTTGTCTGTCTTTATTGTGCCTGCATGTTACTAATAACTCCAGTTTAAGTTAACTTGCAGTAGCTTTTAGAAGACGACATTGTTCTTCCTAGGACATAGCCTTTACATACCCTAGTGGCTGCTGTATAGATTGGCGTATAGCAAAGGGAGTTGATTACTCCTCCTCTCTCCTAGTTTGGACTGGGGCCTCTAACAGAAGCTGTTGAACTCTGGGATTATTGTTGGAATCTAATTCATGAGAGCACATATATTGCGAATGAAGTCATACTGTCTGAATCATCTTTGGTTTCCATTTGGCACCCTAG
Seq C2 exon
TGATGGGGCAGAGGGCCAGGGGCAGGGCCAGCTGCTGATCAAGACAGTGAAACTGGCATTCTCCGTCACCAACAATGTTATTCGGCTGAAACCTCCTTCTAATGTGGTGTCCCCCCTGGAACAGGCTCTCTCACAACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000095319-NUP188:NM_015354:23
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:
PF104874=Nup188=FE(4.7=100),PF118943=DUF3414=FE(8.7=100)
A:
NA
C2:
PF104874=Nup188=FE(5.1=100),PF118943=DUF3414=FE(9.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACTCCCAGCCTGCAGTTTCT
R:
GTTGTGAGAGAGCCTGTTCCA
Band lengths:
263-592
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)