DreINT0107467 @ danRer10
Intron Retention
Gene
ENSDARG00000030022 | nup188
Description
nucleoporin 188 [Source:ZFIN;Acc:ZDB-GENE-030131-7184]
Coordinates
chr21:4431055-4432191:+
Coord C1 exon
chr21:4431055-4431192
Coord A exon
chr21:4431193-4432116
Coord C2 exon
chr21:4432117-4432191
Length
924 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
CAGCAGTGTTTGTGTTTCAGGTG
3' ss Score
7.96
Exon sequences
Seq C1 exon
TGTCTGAATGCGGTACGGACGGTTCAGTCTCTGGCGTGTCTGGATGAAGCTGATCACACCGTGGGTTTTCTGCTCCAGCTCTCCAACTTCTGTAAAGAGTGGCAGTTTCATCTGCCACAGCTACTCAGAGACGTACAG
Seq A exon
GTACAGAAAGCACACACTCATTAACACTACATCAGACATAACCACACACCATATACAGTAGAAGTCAGAGTTATTCGCCCCTCCGTTTATTTTTCCGCAATTTCTGTTTAATAGAGCCGATTTTTTTTCAACACATTTATAAACGTAATAGTTTTAATGACTCATTTCTAATAACTGATTTATTCTATCTTTGCCATGATGACAGTAAATAATATTTGACTAGATATTTTTCAATCACTTCTATACAGCTTAAAGTGTCATTTAAAGGTTAATTAGGTTAATTAGGGTAACTAGACAGGTTAGGGTAATTAGGCAAGTTATTGTAAAATGATGGTTTGTTCTGTGGACTATAGATAAAAATATATAGTTTAAAGAGGCTAATAATTTTGACCTTAAAATCGACCTTAAAAAATTAAAAACTGCTTTTATTCCAGCTGAAATAAAACCAATCAGACTTTCTCCAGACGAAAAAATATTGTCAGACATACTGTGAAAATTTCCTTGCTCTGTTAAACATCATTTGTGAAAAATAAAAAAAAAATAATAATTCAAAAGGGAGCCAAACACATTTTTTTATTTCTTGTGCATATAAACCATTTGATTTTTATTTTGTATAAATCTAAATATTTTATTCCAATTTTGTTTACTTGAGTTTTACAGTTATACACACACTTTTAAGTTTTATATAAATGTGTAATAAACTTGAATGTATTTAGATTTTAAACAGACAGATATATTTATATGCATACATTTTTTATTAAATAACTACATAATGTTTTGTATATTTAAGTTTTTTAATATGTAATTATCTAATATAATTAAAAAATATTGTACAAATCATATGAAGTTCTGAAAGTATGAAGTATTTCGACAGGTTTTTTTTCCATCCCTATTGTTAAGCTGACAGCAGTGTTTGTGTTTCAG
Seq C2 exon
GTGAATCTGTGTTATCTGTGTCAGACGTGTACATACCTCCTGCACAGCAAGAAGATGCTGCACCATTACCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000030022:ENSDART00000043431:38
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:
TACGGACGGTTCAGTCTCTGG
R:
GCAGGTAATGGTGCAGCATCT
Band lengths:
198-1122
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]