DreINT0016704 @ danRer10
Intron Retention
Gene
ENSDARG00000079438 | PKP3 (2 of 2)
Description
plakophilin 3 [Source:HGNC Symbol;Acc:HGNC:9025]
Coordinates
chr7:32670018-32672013:-
Coord C1 exon
chr7:32671818-32672013
Coord A exon
chr7:32670106-32671817
Coord C2 exon
chr7:32670018-32670105
Length
1712 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATA
5' ss Score
8.55
3' ss Seq
CTGCTCTTATTCTTTCTCAGTCC
3' ss Score
9.08
Exon sequences
Seq C1 exon
CTACCAAAGTAGTGAACGTTCTTGTGAACAAGCTGCCCAGTGATGGACATCAGAAAGAGCCGTCCAGTGAGGTGGTGGTGAACATCTGTGGGGTGCTCAACAATCTGGTTACTGGAAGCTCTCTGGCTGCCAGAGACATCACTTACTTTGATGGACTGCCCAAGCTGGTCAGCATTAAGAGTTCCCATGACAACAG
Seq A exon
GTAATAAAACAGCTGAAATGCTACGAAGAAATAAATTAAACCCTGGAAAGAATAAAGTCCATTTACAGTTGAAGTCAGAATTATTAGCCTTCCTAATTTATTAGCCCCAAAGTATATGTTTTCCCCAATTTGTGTTTAACGAAGAGAAGATTTTTTTCAACAATAGTTTTGATAGCTCATTTTTAATAACTGATTTATTTTATCTTTGCCATGATGACAGTACATTATATTTGACTAGTTATTTTTCAAGACACTTCTATACACCTTAAAGTGACATTTAAAGGCTTAACTAGGTTAATTAAGATATTTAGGCACGTTATTGTATAACGATGGTTTATTCTGTAGACAATCTAAAAAATATCTAGCTTAAAGGGGGCTAATAATTTTACCCTTAAAATGTTTTTTTTTTTAATTAATTTTTTTTCTTCATAAAAACTGCTTTTATTTGAACCAAAATAAAACAAATAAGCCTTTCAACAAAAGAAAAAATATAGGAAATACTGTGAAAATTCCCTTGCTTTGTTAAACATCATTTGGGAAACATTGGGGGAAAAAATCCACAGGAGGGTTAATAATTTTGATTTCAACTGTATGTGACGCTGGACCACACAAATATAACCAATTATGCCCAAATACATTAGAATATTAAATGAAGTTTTATGTTTATGTTAAATAAAGTTTTATGTTTTTTGTAGTACATTTGTTACTGTAAGAAATAAAATTTTAATTAGTAATGTGCATTGCTAAAAACTTAATCTGGACAGTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATTTATATATTTATATACACACACACAAACATGCATATACACATTAAATCAAAACTATGCAAAAACCTTTTTTTTGCCTTAATATTTAGGTGTATCTATAACTTATATCACATACATATATATTTTATATCTAAATAAATATAAATAAACATTTTCTCAAATATATGCATAATAGAGAATAAATATACACAGAACAGTCACGTATATTTTGTCAAAACAAACTTTTATTTTGGATGTGATACTATATGTAACATCACTCTGCTTTAAAATTATTAAATTTAATTATTTGTAAATGTAATAGGTTCTCAGTTCAAATATATGTAAAAAAAATGCTTCATTTTGGTTATTCTCAGACTGAATACTGCTAAAGAAATACAATTAGATTTACTGGAAAGTTTACTTTTTATAAAGGAAACACTGCATCAGTTTTAAATAAAATACAATATTTATTTTCATTTTATCATCTTAAAATTAAAACGTGTTTAAATGCAAGATTCACCTACTGTCATGAGGTTAAGAAATGTTGTCATTAAAGGATTGTGATCAAGGTTAGAAGCAATAAATAATTAAAACATTGTAGAACGAGCCTCATATTTGTCACAGGTGTATGATGCTGACAGCCCTATTACTTTTGAAGGTAAAAAAATATTGTTTCTTTAAAAAATAAACCCAACTGATATGATAAGAAATCATAAAAGTTTCTGAAACTGTTCATGCGCTCTTAATTGACCCATTTATCTGCACCTCACCTGCCTGCTGTTGTAATATAGTTTACAAGCTCTTTTATTATTTAGCTGTTTAATCAAGAGCACAATGTCCCAGTACGGCTTCTCAAGTTTCTCTGCTCTTATTCTTTCTCAG
Seq C2 exon
TCCTGGAAAGCTGAAAGCAGCGAGAGCCGCCTCCACCGTCCTGTCCAACATGTTTCAGTACAACAAACTTCACAGAGACTACAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079438:ENSDART00000113744:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.045 A=NA C2=0.133
Domain overlap (PFAM):
C1:
PF040639=DUF383=PD(1.4=6.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCAAAGTAGTGAACGTTCTTGTGA
R:
TTGTAGTCTCTGTGAAGTTTGTTGT
Band lengths:
278-1990
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]