MmuINT0120832 @ mm9
Intron Retention
Gene
ENSMUSG00000004591 | Pkn2
Description
protein kinase N2 [Source:MGI Symbol;Acc:MGI:109211]
Coordinates
chr3:142483501-142484668:-
Coord C1 exon
chr3:142484483-142484668
Coord A exon
chr3:142483611-142484482
Coord C2 exon
chr3:142483501-142483610
Length
872 bp
Sequences
Splice sites
5' ss Seq
CCAGTTCAG
5' ss Score
-14.74
3' ss Seq
ACTTAAAATTGTAATTACAGATG
3' ss Score
4.71
Exon sequences
Seq C1 exon
GTACTTTGGAAGTTCGTCTTATGGGGTGCCAAGATATCCTAGAGAATGTACCTGGACGGTCAAAAGCAACGTCGGTAGCACTACCTGGGTGGAGTCCAAGTGACAACAGATCGTCTTTTATGAGCAGAACCAGCAAGAGTAAAAGTGGGAGTAGTCGCAACCTCCTGAAAACGGATGACTTGTCCA
Seq A exon
GTTCAGTAACCATACTTTTAAAGTCTTGCCACACATTCGAAGGGCCTTCTCATGGGAACAGGCAAAATGGGAAGTGTCCACACAGGACCAAAGAGCTCAATTGCCATTATTTTACATTTTTAAAATTTATAGTAGGAAAAAAACAAACAAAACGTATTTTACTTTATTAAAAATGAATGAAACTACATGATAAATAAAAACATTTGAAAGAATGAAACCCTGAATATCACTCTTTTTACCAAAATGAAGAGCTGTAGACACTGAGATTTTTCCTCCTGGTAGATTCCATCTTGGTTGTTTTAATGGTTTGGTGACCAGTAAAAACTGAACTTGTTAGTGAATGAGATATGTGCTGGGATAGACAGCATTTGAGATGGGCTGCAGTCGGTGTTGGGAAAAGCAAGAGTAAGGCTTAGGAGCATGCTGAGGATGTCACCGTATATATTGATAAATAAAGCACACCTAAACATACAACTAGGAGGGAAGGCAGGGGACAGGGCAGCATTCTGGAGGAGCTCTCTTGTGTTTAGAGGGAAAATGGGAGAGGAATAAAAGTGAGAATCATTTGAGGCAGTAAGTTCTCTATCTAACAAACTCAGTAGAGGACAATAGATGACTAATGTAGATACAGGAATAAGCAGGATGGGTGATACATTCTTAAATATGCAAAATAGCACTTAGTGTTTGTTTTTATCAAAACCAATAGATAATTTCATTGATACTAAAGAAAGCCAATTAAAATACAAACAGTTCAATATTGATTATAAAAACATCCTTTTCAAAGTGTCTTCAGTTTCTTCATGCTATAAATTAGTGATAATTGTCTTTTAACAGTTTAAAGTTTTTAACCCAACTTAAAATTGTAATTACAG
Seq C2 exon
ATGATGTTTGTGCTGTTTTGAAGCTAGATAATACTGTGGTTGGTCAAACTAGCTGGAAACCCATTTCAAATCAGTCGTGGGACCAGAAGTTTACACTGGAACTAGACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004591-Pkn2:NM_178654:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.270 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF051368=Phage_portal_2=FE(32.5=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:
ACTTTGGAAGTTCGTCTTATGGGG
R:
CCTGTCTAGTTCCAGTGTAAACT
Band lengths:
294-1166
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: