HsaINT0126125 @ hg19
Intron Retention
Gene
ENSG00000123143 | PKN1
Description
protein kinase N1 [Source:HGNC Symbol;Acc:9405]
Coordinates
chr19:14580975-14581494:+
Coord C1 exon
chr19:14580975-14581117
Coord A exon
chr19:14581118-14581386
Coord C2 exon
chr19:14581387-14581494
Length
269 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
CCGGGCCTCCCTCTCCCCAGTCC
3' ss Score
9.29
Exon sequences
Seq C1 exon
GGATGGGCTATGGGGACCGGACCAGCACATTCTGTGGGACCCCGGAGTTCCTGGCCCCTGAGGTGCTGACGGACACGTCGTACACGCGAGCTGTGGACTGGTGGGGACTGGGTGTGCTGCTCTACGAGATGCTGGTTGGCGAG
Seq A exon
GTGAGACCCCGCCCCTGTGTGTCTCGGATCTCATTGGAACCTGCGCGTGCCCAGGGTGGGATCCAAGTCTGCCTCCACCATGTGTTGTGTGATTGAGGGCTGCTGGCTCTGCTTCCCTGGCCTCAGTTTCCACATCTATAAAATGGGGCATTTCCCTGCCCAAGTAAGCCAGCACCCAAGAGCTGCAGCAGAGTGTGGGGCTCAGGCCGGGCTGGGTTTGGAGCAGCCAGAGGAGGGGCCTCGTTCACCCCGGGCCTCCCTCTCCCCAG
Seq C2 exon
TCCCCATTCCCAGGGGATGATGAGGAGGAGGTCTTCGACAGCATCGTCAACGACGAGGTTCGCTACCCCCGCTTCCTGTCGGCCGAAGCCATCGGCATCATGAGAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000123143-PKN1:NM_002741:19
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=0.028
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=FE(18.1=100)
A:
NA
C2:
PF0006920=Pkinase=FE(13.5=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:
GACCGGACCAGCACATTCTG
R:
CCTTCTCATGATGCCGATGG
Band lengths:
237-506
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)