MmuINT0120816 @ mm10
Intron Retention
Gene
ENSMUSG00000004591 | Pkn2
Description
protein kinase N2 [Source:MGI Symbol;Acc:MGI:109211]
Coordinates
chr3:142810361-142810865:-
Coord C1 exon
chr3:142810691-142810865
Coord A exon
chr3:142810488-142810690
Coord C2 exon
chr3:142810361-142810487
Length
203 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTT
5' ss Score
8.17
3' ss Seq
ATTGCTTTGTCTTCTATAAGTGA
3' ss Score
4.13
Exon sequences
Seq C1 exon
GCAAAACATTTCTCAGAGCTCCTCAGATGAATATTAATATTGCCACTTGGGGAAGACTAGTGAGACGAGCTATTCCCACAGTAAATCATTCTGGCACATTCAGCCCTCAGACTCCTGTGCCTGCAACAGTGCCAGTCGTTGACGCACGCATTCCTGATCTAGCACCTCCGGCCAG
Seq A exon
GTACTTGTCTTAGAAGGCTTGAGTGTATCTTCCATAGCCATTGCTAGGATGTCTAACGTGCTGTGTTCAGTCTCAGTCTTTCCAAGTGGAATTGCAGAACTGTTGCTCCTTATTTAAAAGAAGTTAGTTTGCTTTTATTTTGCAGCTACATAAAAATAAAGACTTTGATTGCAGCTTTGGTAAATTGCTTTGTCTTCTATAAG
Seq C2 exon
TGACTCTACAGTAACCAAATTGGACTTTGATCTTGAACCTGAACCTCCTCCAGCCCCACCTCGTGCTTCTTCCCTTGGAGAGACAGATGAATCTTCTGAATTGAGAGTTTTGGATATACCTGGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004591:ENSMUST00000043812:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.503 A=NA C2=0.837
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TTCTCAGAGCTCCTCAGATGA
R:
TGTCCAGGTATATCCAAAACTCTCA
Band lengths:
292-495
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