MmuINT0120846 @ mm9
Intron Retention
Gene
ENSMUSG00000026785 | Pkn3
Description
protein kinase N3 [Source:MGI Symbol;Acc:MGI:2388285]
Coordinates
chr2:29935054-29935591:+
Coord C1 exon
chr2:29935054-29935282
Coord A exon
chr2:29935283-29935445
Coord C2 exon
chr2:29935446-29935591
Length
163 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGC
5' ss Score
8.69
3' ss Seq
ACTCTAGCCTTGTGTTGCAGAGC
3' ss Score
5.86
Exon sequences
Seq C1 exon
CCTGGGACTGGCCAGAGAGCCCCCAAGGATGAGAAAGAGATGGTCCGCCGAGCCATCCAGAAGGAGCTGAAGATCAAGGAGGGCATGGAGAACATGCGGCGCGTGGCCACAGACCGACGCCACCTGGGTCATGTGCAGCAACTGCTTAGGGCCTCCAACCGCCGCCTGGAGCAGCTGCATGGCGAGCTTCGGGAGCTGCATGCCCAAGTTCTGCTGCCAGCCTCAGCCG
Seq A exon
GTGAGCGAGGAGTCTGAATAAACCTGGGAACGGGAGACTCACGAACACAATCCTGGCCTTGGCTTTGACCACCCTATATCATCCACATGTTGTCTATACGGAAGGGAAGGGAAAAAGGCAAGCGCTGCTTCCCCGGGGTCTGAACTCTAGCCTTGTGTTGCAG
Seq C2 exon
AGCCAGTGACCTCGGAACCCCAGCCGCGGGCGGAGCAGTCCAGGGCTCGGCTCTCGGAGGCTTTACATAGGCAGCTGCAGGTAGAGCTAAAGGTAAAGCAGGGGGCTGAGAATATGATTCACACGTGTGCCAGCGGCACCCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026785-Pkn3:NM_153805:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.939 A=NA C2=0.732
Domain overlap (PFAM):
C1:
PF0218511=HR1=WD(100=88.3)
A:
NA
C2:
PF0218511=HR1=PD(0.1=0.0),PF0218511=HR1=PU(43.8=65.3)
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:
AGCTGAAGATCAAGGAGGGCA
R:
TGCAGCTGCCTATGTAAAGCC
Band lengths:
244-407
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: