GgaINT0055152 @ galGal4
Intron Retention
Gene
ENSGALG00000004260 | PKP3
Description
plakophilin 3 [Source:HGNC Symbol;Acc:HGNC:9025]
Coordinates
chr5:1564724-1565192:-
Coord C1 exon
chr5:1565069-1565192
Coord A exon
chr5:1564929-1565068
Coord C2 exon
chr5:1564724-1564928
Length
140 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGC
5' ss Score
8.07
3' ss Seq
CAACCTGTTTCCCATTGTAGGCT
3' ss Score
10.08
Exon sequences
Seq C1 exon
GTTTGACGACATTGACCTGCCCTCAGCGGTGAAATACCTGATAGCCAGTGACCCCAACCTACAAGTCCTGGGTGCTGCCTACCTCCAGCACAAATGCTACAGTGACAGTAATGCCAAGAAGCAG
Seq A exon
GTGGGCACCAGAGGGGGGAGGGTCTCCTGAGCCCCTCCGGTATGGTGGGGCACACCTGGGAGGATGGAGGAAATGGAGGGAGCCTCAGATTCCCTGGGAAGTTGTCTTGGCCTCTCCACCCAACCTGTTTCCCATTGTAG
Seq C2 exon
GCTCGCAGCCTCCAGGCCATGCCCAAGCTGGTGAAGCTCTTTAACAGCCCTAACCAGGAGGTGCAGCGCCATGCAACAGGTGCCATGCGCAACCTCATCTACGACAATGCTGAGAACAAGCTGGCGCTGGTGGAGGAGAACGGCATCTATGAGCTCATGAGGACACTGCGGGAGTCCGATGATGAGCTCCGCAAGAATGTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004260:ENSGALT00000006774:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.048 A=NA C2=0.087
Domain overlap (PFAM):
C1:
PF0051418=Arm=PU(14.6=14.3)
A:
NA
C2:
PF0051418=Arm=PD(80.5=47.8),PF0051418=Arm=PU(80.5=47.8)
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:
TTTGACGACATTGACCTGCCC
R:
GCCAGCTTGTTCTCAGCATTG
Band lengths:
248-388
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]