DreINT0107452 @ danRer10
Intron Retention
Gene
ENSDARG00000030022 | nup188
Description
nucleoporin 188 [Source:ZFIN;Acc:ZDB-GENE-030131-7184]
Coordinates
chr21:4411703-4413644:+
Coord C1 exon
chr21:4411703-4411836
Coord A exon
chr21:4411837-4413537
Coord C2 exon
chr21:4413538-4413644
Length
1701 bp
Sequences
Splice sites
5' ss Seq
ACGGTTAGT
5' ss Score
7.37
3' ss Seq
CTGTATTGTTTGTCTTGCAGGGG
3' ss Score
10.51
Exon sequences
Seq C1 exon
TGGTGGTTCTGAAGGACCTGGTCAAGTTCTGATCCAGACAGTGAAACTGGCGTTTTCAGTCACTAACAATGTGATCCGACTCAAGCCTCAGTCTGATACGGCTTCACCTCTGGAGCAGGCTTTAACTCAGCACG
Seq A exon
GTTAGTACACACATTTCATGGTAAATGCACCATATCACAGCATTCGCACAGGGTTTACTTTAGGGCTGGGATGATGAATCAATGCACTGTCAATGGAGAAATGATTCAGCATTAATTCTGAGATTTTCTGAAAGCATTGCGATTCTCTTTTGGAAAGGAAAGGTTTAGGTGAGCGCCCTCTGCTGTTAAACTAGTCTAGAACGCCCACTGCTGTTAAAAAACTAGTCTAGAGCACGAGCTGCTGTTACAAACAAGCCTAGAGCACTGTCTACTATTTAAAAACTAGCCTAAAGCAGCCTCTGCTGTCAAAAATAAGGTTAGAGCGCCCTCTGCTGTTAAAACTAGCCTAAAGCGCCCTCTGCTGTTAAAAACTAGCCTAGAGCGCCCTCTGTGCTTACAAACTAGCCTTGAGTGCTTTCTGCTATTAAAAACTAGCCTAGAGAGCCTTCTGCTGTCAAAAACTAGCCTAGAGTGCCCTCTGCACTTACAAACTAGCCTAGAGCGCACTCTGCTGTTAAAAACTAGCCTAGTGCGCGCTCTGCTGTCAAAAACTAGCCTAGAGCGCCCTCTGCTGTTAAAAACTAGCCTACTGCGCGCTCTGCTGTCAAAAACTAGCCTAGAGCGCCCTCTGCTGTTAAAAATTAGCCTAGAGCACGCTCTGCTCTCAAAAACTAGCTTAGATTGGCATCCGTTGTTAAAAATTAGCTTAGAGCGAGCTCTGCTATAAAAACTGGCCTAGAGTGCCTTCTGCTGTTAAAAACTAGCTTAGATTGCCATCTGTTGTTAAAAATTTGACTAGAGCACAGTCTGCTGTTAAGATGGCCTAGAGCGCCATCTGCTGTTAAAAACTATTCTAGAGCACCATGTTGTTAAAAATTAGCCTATAGCGCCCTCTGCTGTTAAAAACTGGCCTAGATCGCCTTCTGCTGTTAAAAACTGGCCTAGAGCGGCCTCTGCTGTTTAAAACTAGTCTAGAGCGCCCTCTGCTATTAAAAACTGGCCTAGATTGCCCTCTGCTGTTAAAATCTAGCATAGAGCACCATCTGCTGTTAAAAACTATTCTAGAGCACCATGTTGTTAAAAATTAGCCTATAGCGCCCTCTGCTGTTAAAAACTGGCCTAGAGCGCCCTCTGCTGTTAAAACCTGGCCTAGAGCGCCCTCTGATGTTAAAAACTAGTCTAGAGCGCCATCTGCTGATAAAAAATGGCATAGAGTGCCATCTGTTGTTAAAAACTGGCCTAGAGCGCCTTCTGCTGTTAAAAAATGGCATAGTGCCATCTGCTGTTAAAAATTAGCCTAGAACGCCCTCTGCTGTTAAAAACTAGCCTAGAGCGCCCTGTGCTATTAAAAACAGGCCTAGAGCGCCCTCTGCTAGTAAAAACTAGTCTAGAGCACCATCTGTTGTTAAAAACTAGCCTAGAGCGCCCTCTGCTATTAAAAACTGACCTAGAGTGCCCTCTGCTGTTAAAAACTAATCTAGAGCGCAGACTACTGGTAAAAATTAGCCTAGAGTGCCATCTGTTGTTAAAATCTAACATCAGAATTAATTCCAGAAAGACTTGCAGTGCATTCAGAAAATCTAAAAAACAATTATCGAATCGCTTTACATTGATTTATTGTGCCAGCCCTAGATTGCTCAGAATAACAAACGCCTGATCTTTCTTGTAGATTTTTATGCAGCTGTATTGTTTGTCTTGCAG
Seq C2 exon
GGGGTCATGGAAATAACCTGATTGCTGTGCTGGCGAAGTATATTTATCATAAACACGACCCAGCGCTGCCTCGACTGGCCATACAGCTGCTGAAGAGACTCGCCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000030022:ENSDART00000043431:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.130 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF104874=Nup188=FE(4.9=100)
A:
NA
C2:
PF104874=Nup188=FE(3.8=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:
TGGTGGTTCTGAAGGACCTGG
R:
GTGGCGAGTCTCTTCAGCAG
Band lengths:
240-1941
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]