HsaINT0130402 @ hg19
Intron Retention
Gene
ENSG00000118898 | PPL
Description
periplakin [Source:HGNC Symbol;Acc:9273]
Coordinates
chr16:4938103-4939062:-
Coord C1 exon
chr16:4938979-4939062
Coord A exon
chr16:4938220-4938978
Coord C2 exon
chr16:4938103-4938219
Length
759 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
CATGTCTCTCCCTCATGCAGGAC
3' ss Score
11.52
Exon sequences
Seq C1 exon
AACCTGCTAGATGAGATAGCAAGTAGGGAGCAGGAAGTACAGAAGATCTGTGCCAATTCCCAGCAGTACCAGCAAGCTGTAAAG
Seq A exon
GTGAGCCGGGAAACTTCCGCCCAAAGCACAAACAGCAGGGGTCTTATTCCACCGTGCCCTGGTCAGAGAAGCAGCAAGCACCGGCCCTGGCACATGGGGGTGGAGCTGGCCATCCGAGGCACTGCCGGCTGCTGTGCAAACTGGCACAGGCTTTTGGGAAAACAGCATGGTACTAGACATGGAATGCTGTAAAAGGGTTTTATACTCTGAAGCAGTAAACACTTTGGGGGAATTTATCCTTAAGGAAAAAGTACAAAAAAAAAAATGCAGGATAAACAACATTGTTGCAACAGCACTATTTACAATAGCAAAACTAGTACGCTGGAAAGGACTGGTGTCCAGTGGAAGGGGAAAGCTGCGTGAATCAGCACACATCCACCTGATGGATTATAAAGTCAGCAAGCTGGTAAACATGAGAAGAGGTGGTGGCAAGGTGAGACAGGGTTATGGTACGATGTTAAAAGCAGCAGCAGAATGTGAAAATCTCTAGGCATGTAGAAAGGCTGGGAGGGGAATTCAGGGGGCACTTCTTGTCTCATATGTTACTGAGTGATGGAGCTATGTACTGCTGAGATATCAGTAATTCTCAAAACCTCCTGGAAATCACTGCAGGGTGCAGCTGTGAGGAAGACCCACGCAGATTATAAAACCAGCACATGGCACAGGGCAGGTCTGGGTCAGCCTGAAGGGGTACAGGAACATGTCTGTCTCTTCTCAGCTGTTTTAATCTCCCCTCTGCCATGTCTCTCCCTCATGCAG
Seq C2 exon
GACTATGAGTTAGAAGCAGAAAAACTAAGGTCTCTTCTCGACTTGGAGAATGGAAGGAGAAGCCACGTGAGCAAGAGAGCCAGGCTCCAATCTCCTGCCACCAAAGTGAAGGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000118898-PPL:NM_002705:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.071 A=NA C2=0.346
Domain overlap (PFAM):
C1:
PF0026115=Tropomyosin=FE(18.0=100)
A:
NA
C2:
PF0026115=Tropomyosin=PD(10.7=41.0)
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:
TGAGATAGCAAGTAGGGAGCAGG
R:
CTCTTCCTTCACTTTGGTGGCA
Band lengths:
190-949
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)