DreINT0107457 @ danRer10
Intron Retention
Gene
ENSDARG00000030022 | nup188
Description
nucleoporin 188 [Source:ZFIN;Acc:ZDB-GENE-030131-7184]
Coordinates
chr21:4419075-4420630:+
Coord C1 exon
chr21:4419075-4419142
Coord A exon
chr21:4419143-4420434
Coord C2 exon
chr21:4420435-4420630
Length
1292 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGA
5' ss Score
10.03
3' ss Seq
TAATATTGTTTGTTTGTCAGTGG
3' ss Score
4.93
Exon sequences
Seq C1 exon
CCGTGTGTCCTGGAGTCTTGTGCATTTGTGATGAAGATTATCGCTCTTGAGATCTACTATGTTGTCAG
Seq A exon
GTACGATACACACAGACATGCATATGCTAATGCACTGTCAAATTAAAATTATTTGAAAAAGACTGGCTGGAAATACCCCAAACAACTGTTTTAAAGTAAGGCAAGGCAAGGCAAGTTTATTTATATAGCACATTTCATACACAGTGGCAATTCAAAGTGCTTTAGGAACATAAAATGCAGACAATAAAAATTATTAAAAGCAGATAAAAACAAATTAAAATGAGTTAAAATAGGTTATACAAGGATGAAAAAGAAAACAAAAAACGTAATAGTGCGATCTGTCGGACGCAGCACAGTGCTCATTTAGTAAAGGCACAGCTAAACAGATGTGTTTTCAGTCTCGATTTGAATGTGCCTAATGTTGGAGCACATCTGATCATTTCTGGAAGCTGATTCCAGCAGTGAGGAGCATAGTGGCTGAAGGCAGATTCACCCTGCTTTGACTGAACCCTTCGAATTTCTAGTTTATAAGATCCTAAAGATCTGAGTGATCTGTTAGGTTTGTATTCAGTGAGCATATCTGTAATGTATTTAGGTCCTAGGCCATTTAGTGATTTATAGACCAGTAATACTTTAAAATCTATTCTGAATGTAACTGGCAGCCAGTGTAAAGACCTGAGGACAGGTGTGATGTGCTCTGATTTCCTGCTTCTGGTCAGAATTCTGGCTGCAGCATTCTGGATGAGCTGCAAGTGTCTGACTGTCTTTTTGGGAAGGCCAGTGAGGAGTCCATTACAGTAATCCACCCTACTGCTGATAAAAGCATGAACAAGTTTCTCTAAGTCTTCACTGGAAACAAAGCATCTGATTCTTGCTATGTTTTTGAGATGATAGTATGCTGATTTACTGACTGCTTTGACATGACTATTGAAACTCAGATCTGACTCCAGAGTCACACCAAGATTCTTGACCTTATTTTTTGTCGTTTGACCTTTAGAGCCTTTTTTTATAAAGTTTCATACATCTGATGAACAAAAAAAACATGATATTTTGGAAAAATCTGAACAGTTGGCTTTCATTTTAACTGTGAAGAGCACAGACAAAGCCTTGCATTGTTTATGCGAAGGGATTTCTTTTATATGTGCAAGTTATTTCAATTTGTTTTTATATATTTATTTAGTTTTTTGAAAACTACCATTTTGAAATGGATAGAAATGGAAAAGACGAGTGCAGAAATACAACTGTGCAATATGAAATGTATATATATATCATAGGGACAAAATAAAAAGTGTTGTTTTATATTATGGTCTATTGTTTATTTCATGGTGTTAATAATATTGTTTGTTTGTCAG
Seq C2 exon
TGGTGTGTTGGAACCGTCTCTGAAAGCAGCTCTGGAGAGTTTCAGCAGTAAGCGGCGCTATGAGTTCTGGTCAGACTACGTGCGGGAGTTGGTGTGTGTGGCGTGTGATGGTGAAGAGGAGGGTCTGCGCTCTCTGTCTGAGTCTCAGATGCTTATCTCAGCCTGGAGGACGCTATTAATACTCTCCACCAGTCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000030022:ENSDART00000043431:29
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTGTGTCCTGGAGTCTTGTG
R:
TGACTGGTGGAGAGTATTAATAGCG
Band lengths:
262-1554
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]