GgaINT1020139 @ galGal4
Intron Retention
Gene
ENSGALG00000004548 | NUP188
Description
nucleoporin NUP188 homolog [Source:RefSeq peptide;Acc:NP_001025861]
Coordinates
chr17:5418241-5418812:+
Coord C1 exon
chr17:5418241-5418374
Coord A exon
chr17:5418375-5418705
Coord C2 exon
chr17:5418706-5418812
Length
331 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGT
5' ss Score
8.35
3' ss Seq
TTTGACTGTGTTCCCTTCAGGTG
3' ss Score
11.88
Exon sequences
Seq C1 exon
TGATGAGTCGCAAGGCCAAGGCCAGCTGCTGATACAAACTGTGAAGCTGGCGTTCTCAGTCACCAATAATGTCATACGATTGAAACCCCCCTCTAGTGTGGTATCTCCACTAGAACAGGCACTTACTCAGCATG
Seq A exon
GTATGTATTCCTCCATGGGGACAGCCTGGGAAGCTGTGTTTTTTTTGTTACTTAGAAACAGTCGTGTGTCTCACCACAGAGAGTATGTCAGTTATTGAAATGTCCAAAATATGCTTTCTAGTGATAGGAGAAGGCTAATTCTCCCTCCTGTAAGGCATTCTAGCAGGTGGTAACCCTGTTCATGGCAGAGGGGTTGGATCTAGGTGATCTTTAGGGTCCCATCATGCTTCATTTTTTTTGGAGGGCTTACCTAATTCTCACCTTCTGCTATGGAAGGCATTCTTTATGAAATAGCTGCTCTTATCTTTGATTTTGACTGTGTTCCCTTCAG
Seq C2 exon
GTGCTCATGGAAACAATCTTATTGCGGTCTTGGCCAAATACATCTACCACAAGCATGACCCTGCACTCCCACGCCTGGCCATCCAGCTGCTCAAGAGACTGGCTACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004548:ENSGALT00000039668:24
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(4.9=100)
A:
NA
C2:
PF104874=Nup188=FE(3.8=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:
CAAGGCCAGCTGCTGATACAA
R:
TAGCCAGTCTCTTGAGCAGCT
Band lengths:
223-554
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]