GgaINT0126043 @ galGal3
Intron Retention
Gene
ENSGALG00000004548 | NUP188
Description
NA
Coordinates
chr17:5971566-5971979:+
Coord C1 exon
chr17:5971566-5971686
Coord A exon
chr17:5971687-5971912
Coord C2 exon
chr17:5971913-5971979
Length
226 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGG
5' ss Score
8.92
3' ss Seq
CCATTTCGTCTGTGTTTCAGGAT
3' ss Score
10.26
Exon sequences
Seq C1 exon
GGACAACTTGGTAGCACCCAGAGCCAAGGGCTTGTGCCCTGCATTGTGTTTGTCCTGAAGGAGATGTTACCAAATTACCACAAATGGCGTTACAACTCTCATGGAGTGAGGGAGAAAATTG
Seq A exon
GTAAGGGCATTGAGAGGGTAGACAGGTGAGGTCGAAAAGGTTCGCCTGTCTTGGGGAGAATGCATAAATTTTTCCCATTTATTAATCAGATCTTTTCTGGCAGACATTTAGGATTTGCTTTGTGCATCTGCTAATTTTGCTAGATGCTGAGATTTGGTTGAAAATATTAGGGACTGGGTAACAGGTCTTCCTGAGAACTGAGCGGTCCATTTCGTCTGTGTTTCAG
Seq C2 exon
GATGCCTCATTCTACAATTGATTCATGCAATACTGAATTTATGCCCTGAAATGGATCCTCGCAGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004548:ENSGALT00000039668:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF104874=Nup188=FE(4.4=100)
A:
NA
C2:
PF104874=Nup188=FE(2.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGACAACTTGGTAGCACCCAG
R:
CTACTGCGAGGATCCATTTCAGG
Band lengths:
188-414
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]