RnoINT0104204 @ rn6
Intron Retention
Gene
ENSRNOG00000025185 | Nup188
Description
nucleoporin 188 [Source:RGD Symbol;Acc:1306022]
Coordinates
chr3:8896385-8897680:+
Coord C1 exon
chr3:8896385-8896554
Coord A exon
chr3:8896555-8897610
Coord C2 exon
chr3:8897611-8897680
Length
1056 bp
Sequences
Splice sites
5' ss Seq
CAAGTATGT
5' ss Score
7.44
3' ss Seq
AACACGTGTTTTTATCCTAGACC
3' ss Score
7.15
Exon sequences
Seq C1 exon
GAATTCAGCCTTGGCGTGTGGAGTTGTCTCCATGTGGTGCTGGAGCTGATCGACTCCCAGCAGCAGGATCGATACTGGTGCCCACCTCTGCTGCACCGTGCAGCCATCGCCTTCCTTCACGCCCTGTGGCAGGACCGTAGGGACAGTGCCATGCTCGTCCTCAGAACCAA
Seq A exon
GTATGTCCCCTTGGGTGCTAGCTGATGCATGAGCTTGCCTGATCTTGTCTATAAAATGAAGTAGGTTTCTTGTGAGTTCACCAGATTATGCATGGAATACTTACTTAGCACACAGTTCAGTACCAGGGTCTCTTAGATGTCTTTTTCTTTCTTTTATTCTTTTTATTCATTTATTTGCTTTTTGGGTACAGGGTCACAAGTAGGATTGGGTGACCTGGAGCATGCTATGTAGACCTGCAGCCCTCTGCTTCCCACTTGCAGAGATTAAAGGTTTTGATCACCACACCTGGCTAGGGTTTTTGTGTTTTGCTTTTTTAAAGTTATTTTTATTTTATATTCATTGGTGTTTTACCTGTATGTACGTCTGTGTGTGGGCATCAGATCCCCTGGAACTGGAGTTACAGACAGATGTGAAGTAACTAACATGTGGTTGCTGGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCCGTGCTCTTAACCGCTGAGCCATCTCTCCAGCTCTTGTTTTCATTTTTTAAATAGTTAAAAAACAAAGGGTAGTTTTGTGGTTGTTTCGTTTTGTTTTTTAGGTTTTTCTGTGGGTTGTAAGCACATGTCACAGAGCTAAGTGTGGACATAGGACAACATGTCTGGCTTCTATGATGTGGGTCCTGGGAACTGAACTCAGATCATCAGTGTTGGCGGTTGTCTCTTGCACTCTTATTTTATTCTCTCTTTTTTGTTGTTTGTTTGTTTGGTTGGTTGGTTGGTTGGTTTGGTTTTGGGTTTTTTGAGGTGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGAGTGGGCTGGCCTCTGCCTCTTCCTCTCACGTGCTGGGATGAAAGACTTGTGCAGCTACTGCCTGGCTCCCAATTGCACTTGTTAAGTGGAAGATGCAGTTTTATTTATGGACTTTTTATGTTTACATAAGAATAATTGATTTATGAGAAACATTTTAGGTTTGGGATATTAAAGCATGAAAAAATACCAGCATGGGGGACCAGAGGCATCTCAACACGTGTTTTTATCCTAG
Seq C2 exon
ACCCAGGTTTTGGGAGAATTTAACGAGTCCGCTGTTTGGAACTCTCTCTCCTCCTTCAGAGACATCTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025185:ENSRNOT00000030996:19
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:
PF118943=DUF3414=FE(11.2=100)
A:
NA
C2:
PF118943=DUF3414=FE(4.6=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:
GAATTCAGCCTTGGCGTGTGG
R:
TCTGAAGGAGGAGAGAGAGTTCC
Band lengths:
230-1286
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]