GgaINT0055156 @ galGal4
Intron Retention
Gene
ENSGALG00000004260 | PKP3
Description
plakophilin 3 [Source:HGNC Symbol;Acc:HGNC:9025]
Coordinates
chr5:1562942-1563632:-
Coord C1 exon
chr5:1563465-1563632
Coord A exon
chr5:1563128-1563464
Coord C2 exon
chr5:1562942-1563127
Length
337 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGC
5' ss Score
5.66
3' ss Seq
TGCTCCCCTTGTCCCCGCAGCAC
3' ss Score
11.11
Exon sequences
Seq C1 exon
AGCGTGGAGAATGCTGTCTGTGTCCTGCGCAACCTCTCCTACCGCCTCTACGATGAAATGCCCCCCTCCTCCCTCCAACGCCTGGAGGGCCACCGTAGGAACAACGGTGGAACCATGACAGGGGAGCTGGTGGGCTGCTTCAGCCCCCAGAGCAAGAAGGCTCGAGAG
Seq A exon
GTCAGCAGGTGGTGGTGGGGGACCGTGGCATTTTTGTGCTGTGACAGCTGCATCACCTGGGGTGTGGAAGGATGTGAAAGCAGCTGGTGAAACGTGGTGATTGTGTGTGGAGGTGGACACCAGCCTTGGCTGCTGGGTGGGACACGTGGGTGAACTCAGACCGTGAATCAGGTGCTACCTGCATGTAGCGATGGGTGCAAACCCCCCCACGCTGAGGGGAGTGACACAGCTGGGTTGACGTGTCCACTTCTTGCCAAGCTGGAGGTGCCCACAGCAAGAGGACGACACAGAGGGACTGTTCTCTCTGGGTCTGACGCTGCTCCCCTTGTCCCCGCAG
Seq C2 exon
CACTATCTGAATGCAGACATCGTCACTTTCACGGAGGTGTCCAAGGATCCCAAGGGCATGGAGTGGCTCTGGAACCCACAGATTGTGGGCATCTACAACCGGCTGCTGCAGCGCTGCGAGCTCAACAAGCACACCACCGAGGCGGCCTCGGGTGCCTTGCAGAACATCACTGCTGGGGATCGCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004260:ENSGALT00000006774:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.304 A=NA C2=0.048
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
AGAATGCTGTCTGTGTCCTGC
R:
CGATCCCCAGCAGTGATGTTC
Band lengths:
343-680
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]