MmuINT0120798 @ mm10
Intron Retention
Gene
ENSMUSG00000057672 | Pkn1
Description
protein kinase N1 [Source:MGI Symbol;Acc:MGI:108022]
Coordinates
chr8:83673302-83673556:-
Coord C1 exon
chr8:83673481-83673556
Coord A exon
chr8:83673394-83673480
Coord C2 exon
chr8:83673302-83673393
Length
87 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACT
5' ss Score
6.64
3' ss Seq
CTGTGCCTACTGTGTTCCAGGTG
3' ss Score
11.11
Exon sequences
Seq C1 exon
CCCCTTGAGAAAGTCGCCCCTGACACTTGAGGACTTCAAGTTCCTGGCCGTGCTTGGCCGGGGTCACTTTGGAAAG
Seq A exon
GTGACTTGGGGGAGGACTTAGGGGCTCGGAGTTTTACCCCAAGGGCCTAGACTGTCCACTAAAGCCCCTGTGCCTACTGTGTTCCAG
Seq C2 exon
GTGCTGCTGTCTGAATTCCGCTCCAGTGGGGAGCTCTTTGCCATCAAAGCCTTGAAGAAAGGTGACATTGTAGCCCGAGATGAGGTTGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057672:ENSMUST00000005616:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.087 A=NA C2=0.032
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=PU(24.5=50.0)
A:
NA
C2:
PF0006920=Pkinase=FE(11.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTTGAGAAAGTCGCCCCT
R:
CTCTCAACCTCATCTCGGGCT
Band lengths:
167-254
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types