HsaINT0126229 @ hg19
Intron Retention
Gene
ENSG00000057294 | PKP2
Description
plakophilin 2 [Source:HGNC Symbol;Acc:9024]
Coordinates
chr12:32974290-32975565:-
Coord C1 exon
chr12:32975401-32975565
Coord A exon
chr12:32974464-32975400
Coord C2 exon
chr12:32974290-32974463
Length
937 bp
Sequences
Splice sites
5' ss Seq
GAGGTATAT
5' ss Score
7.3
3' ss Seq
TTCCTTTTGTGTGTGGTCAGCAA
3' ss Score
4.99
Exon sequences
Seq C1 exon
GCCACGGAGAATTGTGTGTGCATTCTTCATAACCTCTCCTACCAGCTGGAGGCAGAGCTCCCAGAGAAATATTCCCAGAATATCTATATTCAAAACCGGAATATCCAGACTGACAACAACAAAAGTATTGGATGTTTTGGCAGTCGAAGCAGGAAAGTAAAAGAG
Seq A exon
GTATATTGGGAAGTTTTTGAAAGAATGAGAAAGGGAGAGAATGAGAGAGAGTGTGTGTTTGTGTATATGTGTATGTCTAAGTACTTGGTATATATCGGCACTATTTTAAGTTATTTTAATTCTTACATCAACCTTTTGAAGTGTGTATTATTAATACCCTCATTTACCAGTGAGGAAACAGAGACACAGTAAGATTAATTTTCCTGGAATAATTCAGCAAATAAGTGGAAGAGATTGAATACAATGCCAGGCAGTCTGGCTCCAGATTTTCATTGCTACCCATGAACCGTACTGCTTTATGCCTTATAGGTTAGGAAATAAGCTTAATGCAGCATAGCTAATTGTATATAAATTGTTTTTATTAAAGTCGGCCCTGATATTTGGCCTTGGGTATTCTAAAAACAAACTTTGGACATACTAAAAGCAAACCTCATAGGAAGGAATACATATTTATTTCCATACTGATATGAAAACTAAGAGAATGTAACCTCCCCTCCTTCTCTGAGTATCGTGGTATTTGTGGAAACCAGCTGGTAAATTTAGAACCCTGGTGCTATCCTGGACACTTTCACAAGACTCTGAGGGAACAGGCCTGTTTTTCTTATCTACAGGGTGGTTGTGACTAATTTAGCTTTTAGCTCAACAGCAGCCTGAAAACCATTCTAGAATGACCTATGCTTAATTCTCTGAATTTTCTCTCACTGGGAGAAATATCAAGTTAGGGGTGTGGAGTGTTATTAGGAAGAAATAATCATTATGGGCTAAAAGTTAAGTGATTAGAAATTATATATATTTGCTTTTAAAATTTCTATTTCAAGGGCTTCTTATGCAAATTATGAGCCTTTCTAGACAGTATTTCTGGTCTCCTGGTTTGAGTGTGAAATTATAGCCATCACCTGACATGCATTAATTCTGGATTCCTTTTGTGTGTGGTCAG
Seq C2 exon
CAATACCAGGACGTGCCGATGCCGGAGGAAAAGAGCAACCCCAAGGGCGTGGAGTGGCTGTGGCATTCCATTGTTATAAGGATGTATCTGTCCTTGATCGCCAAAAGTGTCCGCAACTACACACAAGAAGCATCCTTAGGAGCTCTGCAGAACCTCACGGCCGGAAGTGGACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000057294-PKP2:NM_004572:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.224
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0051418=Arm=WD(100=72.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCACGGAGAATTGTGTGTGCA
R:
TCCACTTCCGGCCGTGAG
Band lengths:
335-1272
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)