GgaINT1020129 @ galGal4
Intron Retention
Gene
ENSGALG00000004548 | NUP188
Description
nucleoporin NUP188 homolog [Source:RefSeq peptide;Acc:NP_001025861]
Coordinates
chr17:5414145-5414542:+
Coord C1 exon
chr17:5414145-5414271
Coord A exon
chr17:5414272-5414386
Coord C2 exon
chr17:5414387-5414542
Length
115 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGG
5' ss Score
10.48
3' ss Seq
CTTGCTTCTTCACTATTTAGGAC
3' ss Score
10.03
Exon sequences
Seq C1 exon
GTGTACAGTTTCCTGGATAAAATGTCCTTCTACATTGAACTCTACAAGCATAAACCTCCTGATGTGATCTCTCATGAAGATGGCACCCTGTGGCGAAGGCAGGCTCCAAAGCTCCTCTATCCTCTCG
Seq A exon
GTAAGGAAACTGCATTGTATCTTTTCTTATTCAAGTGCTTTGGGGATTTTAATTCTTTACCTGGCTTCTAACTTGTGGGGAGATTGATGGATTTACTTGCTTCTTCACTATTTAG
Seq C2 exon
GACTAGGTCAAACAAATTTGCGGATACCTCAGGGAACAGTGGGCCAAGTGATGCTGGATGATCGGGCTTATTTAGTACGATGGGAGTACTCCTACAGCAGCTGGACACTGTTTACCTGTGAGATTGAAATGCTGCTCCATGTTGTATCCACAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004548:ENSGALT00000039668:15
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:
PF104874=Nup188=FE(4.6=100)
A:
NA
C2:
PF104874=Nup188=FE(5.7=100)
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:
TGTACAGTTTCCTGGATAAAATGTCC
R:
GGTAAACAGTGTCCAGCTGCT
Band lengths:
242-357
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]