DreINT0016710 @ danRer10
Intron Retention
Gene
ENSDARG00000079438 | PKP3 (2 of 2)
Description
plakophilin 3 [Source:HGNC Symbol;Acc:HGNC:9025]
Coordinates
chr7:32678105-32678953:-
Coord C1 exon
chr7:32678779-32678953
Coord A exon
chr7:32678223-32678778
Coord C2 exon
chr7:32678105-32678222
Length
556 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTG
5' ss Score
9.04
3' ss Seq
ACCAACCCCTATATTGGAAGGAA
3' ss Score
1.93
Exon sequences
Seq C1 exon
GTATTTTGTGGAACCTATCATCTAAAGATAGTCTGAAGGAGAGGTTGGCCAGAGAGAGTTTGGCTGAGCTGACAGAGAGAGTGCTGGTGCCTCTGTCTGGAGGAGGAGATGCTGGAGTCATTCAACAGAGCGCGTCTGAGGCTGATATATTCTTCAACACCACAGGCTGCCTCAG
Seq A exon
GTACTGCTCTCACATGCCTTCAGTTTCAGATTCCTGCATGCATACCTATGCAAATGCATGCACAGCACGGTCAAAAATTAACAAAAACATGGAGCAAATATGTCAAACATTGTAGTAAGGCATTTAAATTGTGCAAACATTTTAACAAAAAACAATCATACATTAAATTACAAGTTGTATATTTCATGATGTATAAGAGCTAGGAATAATGTTGTGCATTATGTCACAAAAGGATCCAAAAGTAATGCTCATTAAAAAAAAATGAAAAGAGTTTTGGGACGACAGTCTGGCTTACAGTTGCCAGGTTGGCATTGCAAATAAAAATAATAATTAATGCAAATAAAAAGAAAAAGTTTTAAACAGATACACCATATATAAACACATGTCATTGTGTACTATTATAAATGTGTTTATGGCTTGTAGTCTCTGTTTTTGCCAATTATACTAGATAAAGTGTACGTTACAGATTGGATTTTTCAATAGAAGGATTTACCTGCAATAAATTTTTAAACATTTCTGCTTGAAAACATCTTGTTACCAACCCCTATATTGGAAG
Seq C2 exon
GAACCTGAGCTCGGTGAATGAAAGGACCAGGCAGCAGATGCGGGAAACTCGAGGGCTAGTGGACTCTCTGGTGGGATACATTCAAAACTCCCTGCAGGAGGGCAAAGGAGAGAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079438:ENSDART00000113744:6
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=0.250
Domain overlap (PFAM):
C1:
PF0051418=Arm=PD(17.1=11.9),PF040639=DUF383=FE(20.4=100)
A:
NA
C2:
PF040639=DUF383=FE(13.7=100)
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:
TGTGGAACCTATCATCTAAAGATAGT
R:
TTGTTCTCTCCTTTGCCCTCC
Band lengths:
286-842
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]