GgaINT1020150 @ galGal4
Intron Retention
Gene
ENSGALG00000004548 | NUP188
Description
nucleoporin NUP188 homolog [Source:RefSeq peptide;Acc:NP_001025861]
Coordinates
chr17:5424499-5425217:+
Coord C1 exon
chr17:5424499-5424680
Coord A exon
chr17:5424681-5425016
Coord C2 exon
chr17:5425017-5425217
Length
336 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAAG
5' ss Score
3.53
3' ss Seq
TGCCCTGTTCTCCCTTCCAGGTT
3' ss Score
13.69
Exon sequences
Seq C1 exon
TGAATGAGATCCCTCAGTACTCCCAGCTGGTGCTGAGTGTGTGTGAAACTCTCCAGGATGAGGTCATTGCACTCTTTGATCAGACTCGACATAGCCTGACCTTGGGGGATGCCACAGATGACAAGGACAGCATGGAAACAGATGATGCCTCCCGAGTTAAACACAAGGACCAGCGAGATGGG
Seq A exon
GTAAAGGGCCAAAAAAATCTGTGTATGTTGGGGACCCCCTTTCCTGCCTGCTGCCTCCAAAGGAAGCTTTGGCACTTCTTGCATGGGAATTGCTCCATGGTATTTCGGCGTATGTCAGCCTGGGAAGTTGGGTGTTGCTGTCTCTCAGATCTGTCCTAAGAAACATTGTCACAATTTATATGAGAGCCAGGAAGTACATAGAGTATAATGTGACACCAGCCAACTTAATTTGTGATTCTGAGAATGAGTGAACTTCAGATCATCACATGAAATGCTTTCAAGATTGATTTCTTTCTTTGCATACATGTCAAGCATATGCCCTGTTCTCCCTTCCAG
Seq C2 exon
GTTTGTGTTTTGGGTCTGCATCTCGCAAAAGAGCTCTGTGAAGTTGATGATGATGGAGACTACTGGCTGCAGATTACTAGGAAAGTCCCTGTGCTTCCTACCATCTTTACTGCTTTGGAGATCAGCCTGAGAGTTAAACAAAACCTTCACTTCACAGAGGCCTCGTTACATCTGCTGCTGACCTTAGCAAGGACGCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004548:ENSGALT00000039668:34
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.279 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:
ATCCCTCAGTACTCCCAGCTG
R:
AGCAGATGTAACGAGGCCTCT
Band lengths:
350-686
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]