HsaINT0130409 @ hg19
Intron Retention
Gene
ENSG00000118898 | PPL
Description
periplakin [Source:HGNC Symbol;Acc:9273]
Coordinates
chr16:4949224-4950872:-
Coord C1 exon
chr16:4950831-4950872
Coord A exon
chr16:4949386-4950830
Coord C2 exon
chr16:4949224-4949385
Length
1445 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
CCTTGCCCCGGCCCCTTCAGGCA
3' ss Score
7.46
Exon sequences
Seq C1 exon
GAGCAGAACAGCGAACTCCGGGCCAAGTACCAGAAACTGCTG
Seq A exon
GTGAGGAGCTCCCTGGGGGAAAGGCCTCATGGGGAGAGGAGAGGATGGGAAGCTTGGAGTCGGGGGGACAAGGATGTATTGTTTTAAAAATGACATAGGCAGCTGGGCATGGTGGCTCACGCCTAGCACTTTGGGAGGCAGAGGCAGGAGGATCACTTGAGCCCACGAGTTTGAGACCAACCTGGGCAACATAGTGAGACTCCAGCTCTACAAAACATTTAAAAATTAGCTGGGCTTGGTGGCATGCCTGTGGTCCCAGCTACTTGGGAGGCTGAAGTGGGAGGATCGCTTGAGCCCAGGAGGTGGAGGCTGCAATGAGCTGTGATCGTGCCACTCCACTCCAGCCTGGGAAACAGAGCAAAACCCTGCCTTTAAAAAAAAAAAAAAAAAAAAAAGGCGTGCAGTAAACGTTTCAATCAGGAGAGGGGTTGAGGCGGGAAGAGAGGTGCCCCAGCCTTTTCCTGAGCGGCTGCAAGGTCTGCCCTGGTTGTTCAGGGAAAACCCTAACAGGCCCCAGGGGTACAGCCTGTCCTGCTCATTTCTTTATTATCTGCTGTGTGCCAAGTATGATGCCACTTGCTTTCTATACAAAAGCTTTCCATTTTCCTTCCCAAACCTTTAAAGAATGCATTCTTTTAAAAATTGCATAAGTGTTATGCAAACGCTTCCTTGTTGCCAATGTTTCAGACAGAGAATACAGAGGCAGCATTGTGTCGCTATAAGGAGCCATGCTTCCTCTGCTCCTTAGTGTTAGTGGTGACACCTTGAGCGAGTTACTTAGCCTCCGGGAGCCTCAGTTTCCTCATCTGAGAAATGGAGCTCCTACATGTTCCTGTCTCATAGGGTCGCTTTGAGGATGAAATGAGTCAATGTTGCAGAAGTTCATCAGGCGTGGAGGGCCCCACGTACCAAAATGCAAACATCCCTCCTTTCCCTTGCACACCCGCTTCTCAGACGTACAGTGGTGCTTTCCTTCCAGCCCTCTATAAGACGATCATGATACAGATAAAAGTAGAAGCTATAGTTACTGATATTTGTTGAGCACCAACTATATGCCAGTCTCTGTACGCTGTGAGGTCAGGACTGTCATCTTCCCCATTTACAGATGGGCGAACTAAGCCTTCACAAAAATGTCAGTTCCGTAAGGGTTTTGTGTGTTTCGTTTGCTGTATCCCCAGTGTCTGGAGCCATGTCCAGCATGTAGTAGATGCTCAGTAAACATTTACTGAATGAATGAATGAATGAATGAATGAGTTTCAGGGGTTCAGGTGACTTGTCTAAGGGGGACTGGCCTGGACGTGGCTAAGCTGGGCTTGTCCTCAGGCCACCCATAGCTGGGCTTGTCCTCAGGCCAGCCATAGCTGGGCCCTGCAGGAGGTAGGGAAGGAAGCGAGCAGTGGCAGCGGGCTGAGGACGCAGCCCTTTCCTTGCCCCGGCCCCTTCAG
Seq C2 exon
GCAGCATCACAGGCCCGGCAGCAGCACCTGAGTTCGCTGCAGGACTACATGCAGCGCTGCACCAATGAGCTGTACTGGCTGGACCAGCAGGCCAAGGGCCGCATGCAGTACGACTGGAGTGACCGCAACCTCGACTACCCCAGCCGCCGGCGCCAGTATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000118898-PPL:NM_002705:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.571 A=NA C2=0.037
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0043516=Spectrin=PU(41.3=79.6)
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:
GAGCAGAACAGCGAACTCCG
R:
GGCTGGGGTAGTCGAGGTT
Band lengths:
187-1632
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)