HsaINT0116947 @ hg19
Intron Retention
Gene
ENSG00000095319 | NUP188
Description
nucleoporin 188kDa [Source:HGNC Symbol;Acc:17859]
Coordinates
chr9:131768518-131769374:+
Coord C1 exon
chr9:131768518-131768647
Coord A exon
chr9:131768648-131768780
Coord C2 exon
chr9:131768781-131769374
Length
133 bp
Sequences
Splice sites
5' ss Seq
TTGGTACGG
5' ss Score
6.56
3' ss Seq
AGCCACTTTTTTTCTTGTAGAGC
3' ss Score
7.23
Exon sequences
Seq C1 exon
GTCCCTCCTGATGTTTACCATGGAAAACTGCTTCTACCTGCTCATCTCTCAGGCGATGCGGTACCTTAGGGACCCGGCTGTGCACCCCCGGGACAAACAGCGGATGAAGCAGGAGCTCAGCTCTGAGTTG
Seq A exon
GTACGGATGGATAGGGATACGGAGGGCTGGACCAATAGGGCCAGAGCCCTGTGGGGTCCTGCCTGGCAACCCCCAAGGGTCAGAACAGTAGCCAGATGTGCTGAGCCTCACCAAGCCACTTTTTTTCTTGTAG
Seq C2 exon
AGCACGCTGCTGTCCAGCCTCTCGCGCTACTTCCGCCGGGGAGCCCCCAGCTCCCCTGCCACTGGTGTCCTCCCCTCGCCGCAGGGCAAGTCCACCTCTCTCTCCAAAGCCAGCCCTGAGAGTCAGGAGCCTCTGATCCAGTTGGTGCAGGCGTTTGTCCGGCATATGCAAAGATAGGGCAGTGCTGTTCTGCCCACCTACCCCTCTCCACCAGCCTACACTGCACCCTGGCTGGCAGGGGTGCTGCTGGCTGCTAGGGCCTATACAATGGAGGGCACCTCCTGTCACCCCCCTCCCGGAGTAGCCACGACTCCAGCCACCACCCACTGACGTTATTTTTATACTAGATGAAGAGGTCAACAGCAGGCATGGGGAGCCGAGTCTTCTGTGCTCAGGTCCTCACGCTGCAGACGCCCCCTAGAGGAACTTTCCTTCCTTTCCAGCATTCCCCACAGCACTGCCGGCCAGGGGAGAGGCGGCAGCCCAGCAGAGGGCTCTATGCACGGGTTTCAAACCTGTTTTCCACACTCTGTCTTTGCAGTTTTGGTAATTCTGTGGTCTATTTATACAGATATTAAAATCTTGTTTATAGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000095319-NUP188:NM_015354:43
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.295 A=NA C2=0.414
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:
TACCTGCTCATCTCTCAGGCG
R:
CTGCACCAACTGGATCAGAGG
Band lengths:
246-379
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)