DreINT0107451 @ danRer10
Intron Retention
Gene
ENSDARG00000030022 | nup188
Description
nucleoporin 188 [Source:ZFIN;Acc:ZDB-GENE-030131-7184]
Coordinates
chr21:4411246-4411836:+
Coord C1 exon
chr21:4411246-4411371
Coord A exon
chr21:4411372-4411702
Coord C2 exon
chr21:4411703-4411836
Length
331 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAC
5' ss Score
7.82
3' ss Seq
GAATTTGTGTCTGTCTGCAGTGG
3' ss Score
7.99
Exon sequences
Seq C1 exon
TGCCCCGAGTCTGCAGTCGTTGTGTATCTACAGTCTGGCCAACACTGAGGCAGGACAGGCAGTGGTCAACATCATGGGTGTTGGAGTGGACACTATTAACATGGTGCTCGCAGCTCAGCCCAGCAG
Seq A exon
GTAAACACTGATTGAGTGTTTATTATAGGAGCATCAGCCTTCACATCCTCAGTTAAAAATAAGTAAAAGCATCATATAATTTAAAATGTTTTCTTACTATGAAATTTGCCTTAATTGCTGGAGCAAACAAACAAATTCTCTGCCGAACAAAGTGTAAATGTAATGTTATATCTTAAATCTAATTGTATATCTTTTTTTGGCTTCAGCAATGTGGGATACACTTGATTCTGTCAGCATTTGTTCTTTAAACCTAAAATTTGAAAGGCAAAAATGTATTTACCAAATGTGGTAAAGTACATAAATAATTCATTGAATTTGTGTCTGTCTGCAG
Seq C2 exon
TGGTGGTTCTGAAGGACCTGGTCAAGTTCTGATCCAGACAGTGAAACTGGCGTTTTCAGTCACTAACAATGTGATCCGACTCAAGCCTCAGTCTGATACGGCTTCACCTCTGGAGCAGGCTTTAACTCAGCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000030022:ENSDART00000043431:23
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=0.130
Domain overlap (PFAM):
C1:
PF104874=Nup188=FE(4.6=100)
A:
NA
C2:
PF104874=Nup188=FE(4.9=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:
CGAGTCTGCAGTCGTTGTGTA
R:
CGTGCTGAGTTAAAGCCTGCT
Band lengths:
255-586
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]