GgaINT1020158 @ galGal4
Intron Retention
Gene
ENSGALG00000004548 | NUP188
Description
nucleoporin NUP188 homolog [Source:RefSeq peptide;Acc:NP_001025861]
Coordinates
chr17:5429145-5429469:+
Coord C1 exon
chr17:5429145-5429276
Coord A exon
chr17:5429277-5429398
Coord C2 exon
chr17:5429399-5429469
Length
122 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATA
5' ss Score
7.96
3' ss Seq
ATAGCTGTCTTTTTTTTCAGTTG
3' ss Score
8.97
Exon sequences
Seq C1 exon
TCACTGGACCTTGCTGAGTACAACGTGCTCTTTGTCTTGAGTTTCACCACACCAGCCTTTGATTCGGATGTCGCACCTTCCTTTGGGACCCTCCTTGCCACAGTCAATGTGGCCCTCAACATGCTGGGAGAG
Seq A exon
GTAATAGCCATCTCTGTTTGGGAAAGCACAGCTCTTGCAGTCATCTCAGGGAACTTATTCAATTAATATTTTGAAGAGTAGCTTCTGTATGTGCTGTGTCCAATAGCTGTCTTTTTTTTCAG
Seq C2 exon
TTGGATAAGAAGAAGGAACCTTTTCCTCAGGCTGCAGGGCTGAATATGCAAGAGGGAACCAAAACCCTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004548:ENSGALT00000039668:41
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=0.292
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:
GGACCTTGCTGAGTACAACGT
R:
GGGTTTTGGTTCCCTCTTGCA
Band lengths:
194-316
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]