MmuINT0120809 @ mm9
Intron Retention
Gene
ENSMUSG00000057672 | Pkn1
Description
protein kinase N1 [Source:MGI Symbol;Acc:MGI:108022]
Coordinates
chr8:86207902-86208680:-
Coord C1 exon
chr8:86208535-86208680
Coord A exon
chr8:86208116-86208534
Coord C2 exon
chr8:86207902-86208115
Length
419 bp
Sequences
Splice sites
5' ss Seq
GAGGTGACA
5' ss Score
3.85
3' ss Seq
TCTCTGCCTTCCTGCCTCAGGCT
3' ss Score
9.67
Exon sequences
Seq C1 exon
GAGATCCAGAACTGGGAGCCGTAGAGCTACGCATTGAGGAGCTACGACACCATTTTCGAGTGGAGCATGCAGTGGCAGAAGGTGCCAAGAATGTCCTGCGCCTGCTCAGTGGGGCAAAGGCCCCAGACCGCAAGGCAGTCAGCGAG
Seq A exon
GTGACATTGAGGGTTCTGCTAGGGGCGTGGTATTTAAGGGACATAGGAGAGATAGGGGGTTCACAGCAACAGGTCCTGGTGAGGGTGGAGCTGTAACTCAGATGGACTGCCGCTAGGTGTGAGCCTTAGTAGGACAGGGGAGAGACAGTCCGTGTCTAAGCTAGGAGCAGTGGAGAGTCCCAGGGAGACCTGAGGCCTAGCCCAGAGCCTGGCAGAGGTGGGGCCCATCAAGAAACTTTAATGAGGGTGGGGCCTCAGAGGGCCCTGGCTCCAGCAGGGGGCAAAGCCTAGTTTCCAGGCTCTACCTTATGGGTCTAAGTAGGTTTGAGGTTTAGGCCTGAGGAAGAAGTTGCTGGAGGTGGGTGGGTTCTTGGGGAAGGGTCTATGCCTGTCCTCAGCTCTCTGCCTTCCTGCCTCAG
Seq C2 exon
GCTCAGGAGAAATTGACTGAGTCCAACCAGAAGCTGGGCTTGCTGCGGGAATCACTGGAGAGGCGCCTTGGGGAGTTGCCTGCCGATCACCCCAAGGGGCGGCTGCTTCGGGAGGAGCTCACTGCAGCCTCGTCCTCAGCCTTCAGCGCCATACTGCCTGGGCCCTTCCCTGCCACTCACTACAGCACCTTGAGCAAGCCTGCACCGCTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057672-Pkn1:NM_177262:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.306 A=NA C2=0.542
Domain overlap (PFAM):
C1:
PF0218511=HR1=PU(53.4=79.6)
A:
NA
C2:
PF0218511=HR1=PD(43.8=44.4)
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:
CCAGAACTGGGAGCCGTAGAG
R:
AGGCTTGCTCAAGGTGCTGTA
Band lengths:
342-761
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: