GgaINT0124752 @ galGal3
Intron Retention
Gene
ENSGALG00000004689 | PKN3
Description
NA
Coordinates
chr17:5852376-5853168:+
Coord C1 exon
chr17:5852376-5852571
Coord A exon
chr17:5852572-5852976
Coord C2 exon
chr17:5852977-5853168
Length
405 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
ACTCTCCTAAAATTCTTCAGGAA
3' ss Score
7.8
Exon sequences
Seq C1 exon
GCTCAGGGTCGTTTGCAAGAGTCCTCTCAGAAGATTGACCTGCTGCGCTTGTCCTTGGAATGTCAGCTTAGTGGGCTTTCTCCAGATCACCCGAAACGAGCACTCATCAAGCAGGAATTAGTAAATACCTCTTCCCTGGGAGCACAGCATGGCATTATCCAACCCACTTCAGTCATCAAACCTACAGCCCTTACAG
Seq A exon
GTAAGTAAATCCTGTGTGGCATGTTGTTGTGGAGAAGATGAAATTAAAAATGAGTTGCATTTCTTTTGATTGTTGTAATGCCTCTTATGTGGACATTTGATCTTCTGTGAATGAGACTCATATCTTCTAGGCTACTAAAAGCTTTCTGATCATATGAGTTAATAGCTGATTAATATATTAAATATCTTTCATCTATTAAATAGGCTTTTGGACTTGTTGATCTCTGTGTGTTCCTTCCAACTGAGCTGTTCTACACGATGTCATTCTAACCTGGGGTAGAGTTAAGCTATATCAGCCAAAGAATAATGAATCTGAGAAATTCTTGGACTCTTATGAGGATAGATTAACTGGAATCGCTGTTGTCTTTTATGGAATAACATTCTTTACTCTCCTAAAATTCTTCAG
Seq C2 exon
GAACGTTGGAAGTGAGACTGATGGGGTGTCAGGATCTATTGGAAAATGTTCCTGGCCGTTCCCGAATGGCTGGTTCTTCTCCTGTCTGCGGCAGCCCAAGTGACTTGAAGTCCTTTTCCCTAACAAGAGTTGGCCTGGGTATCCATGGCCGTAGCGTTGCAGGAAAGTACCTGCGAAATGAAGAGCTATGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004689:ENSGALT00000007470:6
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=0.077
Domain overlap (PFAM):
C1:
PF0218511=HR1=PD(43.1=47.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGAAGATTGACCTGCTGCG
R:
CAGGTACTTTCCTGCAACGCT
Band lengths:
343-748
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]