GgaINT0055153 @ galGal3
Intron Retention
Gene
ENSGALG00000004260 | PKP3
Description
NA
Coordinates
chr5:1582960-1583583:-
Coord C1 exon
chr5:1583379-1583583
Coord A exon
chr5:1583135-1583378
Coord C2 exon
chr5:1582960-1583134
Length
244 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGA
5' ss Score
7.41
3' ss Seq
GATCCCTTTCTTCCATACAGGGA
3' ss Score
9.51
Exon sequences
Seq C1 exon
GCTCGCAGCCTCCAGGCCATGCCCAAGCTGGTGAAGCTCTTTAACAGCCCTAACCAGGAGGTGCAGCGCCATGCAACAGGTGCCATGCGCAACCTCATCTACGACAATGCTGAGAACAAGCTGGCGCTGGTGGAGGAGAACGGCATCTATGAGCTCATGAGGACACTGCGGGAGTCCGATGATGAGCTCCGCAAGAATGTCACAG
Seq A exon
GTCAGAGATGGTCACAGGGTTGGACTGGGGTCCTCCTCCCACTGAGGTGGCATCTGGTTTCCCCAGCCTGTGAGTAAGGCCAGGGTGATACTGCGTGAGGACAACTCTGTGTTGTCAACACACACCTGGGTGGTGCCCCCAGCCATGAGCTGCCTCATAGCTGTGAGTGGCCAGCGTGAGGTGGGCCACGGTGGACATGCTCTCTAACTGTCCCCAGGACTGAGGATCCCTTTCTTCCATACAG
Seq C2 exon
GGATCCTATGGAATCTTTCCTCCAGTGACAACCTGAAGGATCGCTTGGCTCGAGACACACTGGAGCAGCTCACGGACCTGGTCCTGGTCCCCCTCTCTGGCCTGGGTGGCTCTGGTGTCATCCAGCAGAACCCCTCCGAGGCAGAGATCTTCTACAACTCCACAGGCTTCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004260:ENSGALT00000006774:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.087 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0051418=Arm=PD(80.5=47.8),PF0051418=Arm=PU(80.5=47.8)
A:
NA
C2:
PF0051418=Arm=PD(17.1=11.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGCAACCTCATCTACGACAA
R:
TGAGGAAGCCTGTGGAGTTGT
Band lengths:
293-537
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]