HsaINT0130393 @ hg19
Intron Retention
Gene
ENSG00000118898 | PPL
Description
periplakin [Source:HGNC Symbol;Acc:9273]
Coordinates
chr16:4945262-4945717:-
Coord C1 exon
chr16:4945595-4945717
Coord A exon
chr16:4945409-4945594
Coord C2 exon
chr16:4945262-4945408
Length
186 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGC
5' ss Score
4.72
3' ss Seq
CCTGACCCCGTTCTCTCCAGGAC
3' ss Score
10
Exon sequences
Seq C1 exon
TTTCACGAAGACGTGAAGGACGCTCAGGAGCTGCTGCGCAAGGTGGACTCGGACCTGAACCAGAAGTATGGCCCTGACTTCAAGGACCGGTACCAGATTGAGCTGCTGCTGCGGGAGCTGGAT
Seq A exon
GTGAGCGATGGCCCAGGACCCCTGCTGGCCCGGGGGGCGGGGGACCCCTCTACACCATGCCTGCCCTCAGCCCTGTACAGGCCCCTCCACAGCACCCCACCTGCTGAATCCAGCCCCTGCTCTGCGTCCTCCCACCAGGGGGAAGGCTGTTGGTCTCACCTGGGCCCCTGACCCCGTTCTCTCCAG
Seq C2 exon
GACCAGGAGAAGGTGCTGGACAAGTATGAGGACGTGGTGCAGGGGCTGCAGAAGCGAGGCCAGCAGGTGGTGCCCCTCAAGTACCGCCGGGAGACTCCGCTCAAGCCCATCCCCGTGGAGGCACTCTGTGACTTTGAGGGGGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000118898-PPL:NM_002705:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.024 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(50.6=100)
A:
NA
C2:
PF0043516=Spectrin=PD(40.5=65.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTGAAGGACGCTCAGGAG
R:
CCCTCAAAGTCACAGAGTGCC
Band lengths:
252-438
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)