HsaINT0130400 @ hg19
Intron Retention
Gene
ENSG00000118898 | PPL
Description
periplakin [Source:HGNC Symbol;Acc:9273]
Coordinates
chr16:4940185-4940922:-
Coord C1 exon
chr16:4940729-4940922
Coord A exon
chr16:4940336-4940728
Coord C2 exon
chr16:4940185-4940335
Length
393 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TGAACGCTTTGCCTTGACAGGGC
3' ss Score
7.36
Exon sequences
Seq C1 exon
GCCATGGCCTGTGAGTTACAGGCCCAGAAGTCCCTCCTGGGTGAGGTGGAGCAGAACTTGCAGGCGGCCAAGCAGTGCTCGAGCACACTGGCCAGCCGCTTCCAGGAGCACTGTCCGGACCTGGAGCGCCAGGAGGCCGAGGTGCACAAGCTGGGCCAGCGTTTCAACAACCTGCGCCAGCAGGTGGAACGCAG
Seq A exon
GTGAGGGTGCGGTGGGTGGTGGCCATTTTTGTTTTCTGAGAATGCGATCTAATTCCCTCTAAGCAATGCTTTAGCCGTGTCCCACAGATTTTGCTGTTTTTCTTTTTGGTGAGTTCGTCAGATTCTCTGACGGCCCTGTGGTCTCTCTTTTGAGTCATGCTTACCTGGGTCCTGTAATCCACAATGGGCATCTCTGCAAGTCAATGTATATGGACCCACCTGGTTCTCCACAGTCCAACCTGACGTTCCCTAATGACCACCCACCCTGTGTGGGAGATACTTGGGGTATTTCTGGTTGTTACATTTGGTTGTTTCCCACTTTAAAAAAAAAAATGAGGGCTCGGTGAGGCATCTGTTTGCTGTGGCTGAGGCCTGAACGCTTTGCCTTGACAG
Seq C2 exon
GGCGCAGAGCCTACAGAGCGCCAAGGCAGCCTACGAGCACTTCCACCGCGGCCATGACCACGTGCTGCAGTTCCTAGTCAGCATCCCCAGTTACGAGCCCCAGGAGACAGACAGCCTCAGCCAGATGGAGACCAAGCTGAAGAACCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000118898-PPL:NM_002705:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.138 A=NA C2=0.314
Domain overlap (PFAM):
C1:
PF0026115=Tropomyosin=PU(36.0=83.1)
A:
NA
C2:
PF0026115=Tropomyosin=FE(33.3=100)
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:
GCCATGGCCTGTGAGTTACA
R:
CTGGTTCTTCAGCTTGGTCTCC
Band lengths:
342-735
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)