DreINT0107465 @ danRer10
Intron Retention
Gene
ENSDARG00000030022 | nup188
Description
nucleoporin 188 [Source:ZFIN;Acc:ZDB-GENE-030131-7184]
Coordinates
chr21:4428366-4429217:+
Coord C1 exon
chr21:4428366-4428458
Coord A exon
chr21:4428459-4429064
Coord C2 exon
chr21:4429065-4429217
Length
606 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTT
5' ss Score
8.17
3' ss Seq
TTTCTCTGTGTGTGTGTCAGGCG
3' ss Score
9.25
Exon sequences
Seq C1 exon
GGGGCAGCAGCAGTGGCAGGAGCAGGAGTGATTCAGAGCATCTGTCTTCCTCTACTCAGTGTGTACGAGGGTCCAGCAAACGGAGCCAATCAG
Seq A exon
GTACTTCTGAGCATCTACAGCCCCATCAGTGTTTCTGACTGTTTACAGAAGCTGCATCCCAAATCGCATGCTTATGCACTATTCTACTGCATTTTATAGTATAAATGGTGTAAGTAGTGTGTTCACACTGGAAAGTCTAAAAATAATAAGTGCACTTTAATTACCCGGATGATGCACTCATTCAGCCGCTAAAATGAAGTGTGGAATGATGAACACTTCACGCACTCAACAGTCGCCGCTTTGCTCCCGTAGCAGGAGGGGCGGAGCTATCGGGCGCACATGTTGGATAACTTTATTTATTTTGGATGGTGAAAGCAAAGTTCTCCAACGAGAGTAATTATAGCGCCTCCCGATGGTGAATGCGGTTATACTCATGGCAGGTATTATTTGATAATTCAGTCGTTTATTTCACTGATTAGTCAACCATCAAACATCATCAGGGAAATGGTTTGAATTTCTGCTTAGTAAAAAAACATTATTGTTCCTATTAGGACGACACTATATACATATACTATCCTGTTGAGTGAGTAAGTGCATAGTGTATAGTGTGCCATTTGAGACGCAGCTAGACTCTCATGTGCTGCTGTTTCTCTGTGTGTGTGTCAG
Seq C2 exon
GCGTTTGTGCGCAAGTGTCAGGACGCCCCCTCCTGGCCTGGAGTTTACAGACTGAGTTTATCTCTGATGGAAAGCCTGCTCAAAACTCTCCGCTACAACTTCATCAATGAAGCGCTCGACTTCGTGGGTGTGCATCAGGAGCGCATCCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000030022:ENSDART00000043431:36
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:
CAGTGGCAGGAGCAGGAGT
R:
GATGCGCTCCTGATGCACAC
Band lengths:
230-836
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]