DreINT0115101 @ danRer10
Intron Retention
Gene
ENSDARG00000045331 | pkp4
Description
plakophilin 4 [Source:ZFIN;Acc:ZDB-GENE-120411-14]
Coordinates
chr6:11997705-11998193:-
Coord C1 exon
chr6:11998035-11998193
Coord A exon
chr6:11997916-11998034
Coord C2 exon
chr6:11997705-11997915
Length
119 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
GCTCCTGCTCTCTCACTCAGGGT
3' ss Score
9.16
Exon sequences
Seq C1 exon
GCCTGCAAACCTCTTACAGTCAAAATAGCCAGTTAGGCCAGGACACACGCTCCCCTGACTGCCATGTCACGCCAATCTATGAAGACAGAACCTTCCAGAACCCTCTGTACCAGAGTCCAACGCACGGCTCCCAAAGCGCTGCCTCCAGAAACAATACAG
Seq A exon
GTATGTGCTGAATGTCCTTCACGCACTGCGGCTGTCTTTGCAAACTCTGAGAATGAGCTCTGACATTTCCTCAATGTTAATCTTAACAATGACTGTCCTGCTCCTGCTCTCTCACTCAG
Seq C2 exon
GGTTTGGTACTTTACAAAGGACCACGAGTCAGTGTAGCACTCTGAGGTACCAGCGAGGGTTATTCTCTATGGGCTCCATGGCAACGCACTCTGACACCTATCGTCCTGGACATTATCGCCAAGCCGATTCGAACTACTCCAGACACTCAGCTGCCCTTGACAACGCCGTCACTCGCTCGCCTTCCATAGACAGTGTTCACAAAGATCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000045331:ENSDART00000155685:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.676
Domain overlap (PFAM):
C1:
NO
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:
CTGTACCAGAGTCCAACGCAC
R:
CACTGTCTATGGAAGGCGAGC
Band lengths:
250-369
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]