RnoINT0104212 @ rn6
Intron Retention
Gene
ENSRNOG00000025185 | Nup188
Description
nucleoporin 188 [Source:RGD Symbol;Acc:1306022]
Coordinates
chr3:8902457-8904726:+
Coord C1 exon
chr3:8902457-8902638
Coord A exon
chr3:8902639-8904525
Coord C2 exon
chr3:8904526-8904726
Length
1887 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGG
5' ss Score
5.5
3' ss Seq
GTTGCCCTGACTACCAGCAGGTA
3' ss Score
4.67
Exon sequences
Seq C1 exon
TAAGCGAAATCCCCCAGTACTCCCAGCTGGTGCTGAATGTCTGCGAGACCCTCCAGGAAGAGGTGATTGCACTCTTTGACCAGACCCGCCACAGCCTGGCATCAGGCAGTGCTGCCGAAGACAAAGACAGCATGGAAACAGATGACTGCCCTCGGCCCCGGCACAAGGACCAGCGTGACGGG
Seq A exon
GTGAGGGAAGGTGGGAACCTGAGGAACCCAGAGCCCCGGGGGCTCAGGGCTTTGAGGGAAGCACTTGGAGAGGCGTGGCTTCCAGCCATGTCAGCATTATCAGGCAGGCATCGTGGGCCAGGGAGATTGGACCACGAAGAGTGTGAGCGGTTTCAGGTCAGCATCTTCTGTGTAAGCCCCGGCTGGTGTGAGCAAAGTAAAGTGAGGGCGGGGTGGGCTGCTTTAGAGGGCAGACACAGGCTCCTTAACCTCAGGACTCAGGAAGAGGTAACGGATACAGTGTGGAACAGTCTTTCCTTTGGTGGGGGCAGGACTGAAGAAGGTTTCTCCATAACAGCCCTGGCTTCCTGGGACTTGCTTTATGGGCCAGGCTGACCTACAACCTACAGAGGTCTGTTGCCCTTTGTCCTCTTGCCTCTGTCTTCTCCGCCCAATAGCCGGGATTAAAGGCACACTCGACCACGCCTGCCTAGAACCATGGTTTTAAGCTGGGTATCACGACCGCTAGGTTATTTGGTCACTACCAGCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGGTAGAGTCCTACTTTGTAGCCCAGGCTAGCCTCTTAACTTCCTGCCTCAGCCTCCTGAGTGCTAGAGTTACAGGTGTGTACACTAGTTCTCAAGAGAATTTCAGGTATGTTTTACATGGGGTGAAAGCAGGTACTATTAGAGGGAAACAGGAAGTGTGCTGATGCTGGGGAGTCTTAGTGCCTTGGTATGGGCAGTAGTCACAACTAAGTGTGTGTTATTCTTGAAGTAGAGTCTCTCCTGAGCCAGGCGCTCATGGTTCTCAGGCAGACTAAAACCTAGGAAGTCTACTGAGTGTTGGCATGCATCAAAGCTGGAGAACTCCTGCCTTGTTATGTGGCTACTAGTACCAAACTCCAGTCCTTAGGCATGGATAGCATGTACTAACATGTGTTTTGTCTGCATATGTGTTAGTGTACACACACGCACACACACACATGCATGCACACACACGCACGCGCACAGTACATGCTCTGGAACTGGAGTTAGATAGTTATATGTCACGGGGAGTTCTGTTCTGGTTCTATTTGCTGATCAGAGCTCCACCCCTAGCTGTGTTACTATTGCCAACTGTGGCTCCTGAGGAAAGGGGCCGTTTCTTTAAGGGTGTGACCCCTGCTCAGTGGACTGTGCTCCAGGGTCCAGCAACACAATGGACTCACTGTGTTTCTTGCTGGTAGTTTTTTTGTTTTGTTTTGGACAGGGTCTGACTATGTAGCCTTGGCTGGTCTGGGCCACACTTTTGTAGACCAGGTTGGCCCCAAACAGAAATCTGACTGCCTCTTCCTCCCCGAGCTGAGATTAAGGCGTGTACTAACATTCCAAGATTAAGAAAGTAAGTCAGGTGGGTAGAGAGGTGGAGGTGGGTCTGAGAGAAGTTGGTGGGATAAATATAACCAAAATGAATATGAAATTCTCAAATAATAAATTATTTTTAAAATTAGCATGTAACAGGCTATGGTGACACACACCTTTAATCCCAGCATTCAGGAGGTGAGTTTGAGGCAGGCCTTGTCTACAGAGTGAGTTCTGGACAGTGAGGAGTACACACAGAAATCTTGTCTCTGACACACAAACAAGCAGAGGGGTATAAAACGCTGGTGTTTGAATAGAGCCTAAGGTTGCAGATGGAGGCCCCTCCGACTGCCAGTGTAGAGTGGGGTGGACTTGCCATGCCTGCCTGAAGAGATGGCACAGCTGCACAGACAAGAAGCCCAGTGGCCCAGTCACACTCCTGAGAGGAGCCCTGGAGGCCAGGCCCAGCACTCTCCCCTCCCCTCCCGCTACTGCCTTTCCACCTTTCCCAGTCGTTGCCCTGACTACCAGCAG
Seq C2 exon
GTATGTGTCCTGGGACTGCATCTGGCAAAGGAGCTCTGTGAGGTGGATGAGGATGGGGACTCGTGGCTGCAGGTGACCCGAAGGCTCCCCATTCTGCCCACGCTGCTCACCACCCTGGAGGTGAGCCTCCGCATGAAGCAGAACCTGCATTTTACTGAGGCTGCGCTGCACCTGCTCCTCACCCTGGCTCGCACCCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025185:ENSRNOT00000030996:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.328 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:
CGAAATCCCCCAGTACTCCCA
R:
CGCAGCCTCAGTAAAATGCAG
Band lengths:
343-2230
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]