DreINT0107463 @ danRer10
Intron Retention
Gene
ENSDARG00000030022 | nup188
Description
nucleoporin 188 [Source:ZFIN;Acc:ZDB-GENE-030131-7184]
Coordinates
chr21:4426775-4427565:+
Coord C1 exon
chr21:4426775-4426944
Coord A exon
chr21:4426945-4427364
Coord C2 exon
chr21:4427365-4427565
Length
420 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGT
5' ss Score
7.96
3' ss Seq
TCTCTCTCTCTCTGTGTCAGGTG
3' ss Score
11.65
Exon sequences
Seq C1 exon
GAGGAGAGATTTCCCAGCTGCCCCAGCTGCTGCTGTGTGTGTGTGAGATGGTTCAGGATGAAGCCCTCGCATTGATTGACAGCACACGTCATATGATCCAGAGAGGTGATGTTCAGGAGGACAGTATGGAGACCGACAGTCCACATGTCCAGAAAGACCAGCAAGACTCT
Seq A exon
GTAAGTGTCATAGTTCACCCAAAAATTTTTTATTCTGTTTTAGGGATTGTTGCAACTGACCAATCAGAATCGAGTATTCCAGACAGCCATGTAATATGTGTTAACAATACAGCATAATAATGTCTAAATACATGAAATAAAAGAGCTTTATTGGCATGACTTGTAAAGTATTGCCGTAGGATTGCAGATTACATAAACAATGAATAAAATTGTAAAGTCATTATATAATAAATACACACACACACACAAATAAACACAATTACACTTTTGATAAACATAAAAACAAATAAGAAAATACTACACAAAATAGGAAATTGAATTAAAATACAATACACAGCTGTAGATTCATTCAGATGCTTTGTAATAATGTTTCTGACTAGTTTTGTCCACTGTCTCTCTGTCTCTCTCTCTCTGTGTCAG
Seq C2 exon
GTGTGTGTTCTGGCCCTTCATCTGTCTAAAGAGTTGTGTCGGGCTGATGAAGACGGTGAGCAGTGGCTGCAGGTGGTCCGGAAGCTGCCGGTTCTGCCATCAGTTCTCAGTGCTCTAGAACTCAGTCTGCGCTCCAAACAGAACCTGTACTTCACTGAGGCAGCGCTTCATCTGCTACTCACACTCGCCAGGACACCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000030022:ENSDART00000043431:34
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.263 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:
GAGGAGAGATTTCCCAGCTGC
R:
TGTGAGTAGCAGATGAAGCGC
Band lengths:
353-773
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]