RnoINT0104198 @ rn6
Intron Retention
Gene
ENSRNOG00000025185 | Nup188
Description
nucleoporin 188 [Source:RGD Symbol;Acc:1306022]
Coordinates
chr3:8890395-8890687:+
Coord C1 exon
chr3:8890395-8890515
Coord A exon
chr3:8890516-8890620
Coord C2 exon
chr3:8890621-8890687
Length
105 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGG
5' ss Score
9.31
3' ss Seq
ATGTCTTTTCTGGAGTCTAGGTT
3' ss Score
3.47
Exon sequences
Seq C1 exon
GGACAGCTCGGTAGTACCCAGAGCCAAGGCCTGGTGCCCTGCGTGATGTTCGTGTTGAAGGAGGTGCTTCCCAGCTATCACAAATGGCGCTACAGCTCTCACGGCGTGCGGGAGCTCATAG
Seq A exon
GTAAGGACAGCACACACCCCAGAAGGTCTGCTCCCTGGAGGCCTTCCCCTCTCTTCTTTGAGGCAGGTCATTAACACATCATCACATGTCTTTTCTGGAGTCTAG
Seq C2 exon
GTTGCCTGATTCTGGAGCTGATTCATGCAATACTGAACCTGTGCCAAGAGACAGAGCTGCATAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025185:ENSRNOT00000030996:13
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=0.000
Domain overlap (PFAM):
C1:
PF104874=Nup188=FE(5.5=100),PF118943=DUF3414=FE(8.0=100)
A:
NA
C2:
PF104874=Nup188=FE(3.0=100),PF118943=DUF3414=FE(4.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGACAGCTCGGTAGTACCCAG
R:
GCTATGCAGCTCTGTCTCTTGG
Band lengths:
186-291
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]