RnoINT0104217 @ rn6
Intron Retention
Gene
ENSRNOG00000025185 | Nup188
Description
nucleoporin 188 [Source:RGD Symbol;Acc:1306022]
Coordinates
chr3:8906006-8906720:+
Coord C1 exon
chr3:8906006-8906143
Coord A exon
chr3:8906144-8906645
Coord C2 exon
chr3:8906646-8906720
Length
502 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGC
5' ss Score
8.07
3' ss Seq
CTGTCCCTCCTGTGTCCCAGGTG
3' ss Score
10.31
Exon sequences
Seq C1 exon
TGTCTCAATGCCGTGAGGACAGTACAGAGTCTAGCCTGCCTGGAGGAGGCAGATCACACTGTGGGCTTCATCCTACAACTGTCCCACTTCAGGAAGGAGTGGCACTTCCACCTGCCTCAGCTCATGCGTGATGTTCAG
Seq A exon
GTGGGCCTCGCACACGGCTTCTTAGAGGGTGTGGGCAGATGAGGGGCAGGGAGTCAGTGGACATCCTCAGGGAACTGTAGGCTGTCTCTGAACGTGGGCTTCTTGCTTGGGGCTGCTTACTTAGGTTAGATCTTCCTCCATAGTGAAGTGAGACTGGACGAGAACTTGGGCTCAATGAGGTAGACTTAGGTTCAGAACCCTCAGGAGAAGGCCTGAAGCTGGAGGAGCCCACAGGCTTTAGGGCTGTGGCCATGGCTATTGTCTCTATGACATTGGCCAGTCCCATCACCTCTGTCCCTTCTTCAGTGTGGAAACAGTAGTGATCCCCACCTGACTGATGTCTGAGGACTGTCATATGCCAGCAGTGCAGGGAAGCACTCCAGGCCTGAGCCCTGCTGGTTAGAGCATCAGTCAATGAGAGGGGAGACGTGCTGGCATCGCAGGGGGACATGTGTTCATAGGGTGGCCTCCATGAGTTTTTTCTGTCCCTCCTGTGTCCCAG
Seq C2 exon
GTGAACCTGGGTTACTTGTGCCAGGCCTGCACTTCCCTCCTACACAGTCGCAAGATGCTGCAGCACTACCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025185:ENSRNOT00000030996:30
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:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGACAGTACAGAGTCTAGCCTG
R:
CTGTAGGTAGTGCTGCAGC
Band lengths:
198-700
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]