MmuINT0120804 @ mm10
Intron Retention
Gene
ENSMUSG00000057672 | Pkn1
Description
protein kinase N1 [Source:MGI Symbol;Acc:MGI:108022]
Coordinates
chr8:83691049-83692936:-
Coord C1 exon
chr8:83692636-83692936
Coord A exon
chr8:83691201-83692635
Coord C2 exon
chr8:83691049-83691200
Length
1435 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGC
5' ss Score
8.02
3' ss Seq
TTCTTTTCTTGTTTCCTCAGATG
3' ss Score
11.41
Exon sequences
Seq C1 exon
AGTGAGCCTCGAAGCTGGTCGCTGCTGGAACAGCTGGGTCTGGCTGGGGCTGACCTGGCAGCCCCCGGGGTGCAGCAACAGCTGGAGTTAGAGCGAGAGCGACTGAAGCGGGAGATACGGAAGGAGCTGAAGCTGAAGGAGGGCGCTGAGAACCTGAGGCGAGCCACCACTGACCTGGGCCGTAGCCTGGCCCCTGTGGAGCTGCTGCTGCGGGGCTCCGCTCGACGCCTAGACTTACTGCACCAGCAGCTGCAGGAGCTGCATGCACATGTGGTGCTGCCTGACCCTGCAGCTGGAAGCG
Seq A exon
GTGAGCAGAAAGCCTGGGAGCTGTGTTCTGTCAGGATACTGTCCTGGGTTCACAGAAGCCACAGGAGAGGCCAGGCTTACAGGGCCACTAGCACCTGGATGAATACAGTCACACCTGTTTCCCAGACCCCACTCAAAGCTGTCTTTGGCATTAGGAGTACCTAGATATAGACTCACCAGCATCCAGGTAACACCAGAGACCCACACTGTCACCAGATACCTAAGGACACCATTACAACTATTTTCAGACAACGACTGAGAAACATGCTATCACATGAGAATCCAGAAGCCCACAGTCACACTAACAGACACCCAAATACTGCACATCTGTCACCCTCATGGCTCCCTAAATCATTCCAATATGTAAAGAAGGAAGGAAAGAAGGAAGGAAGGAAAGTGGAGAACAAGTGAGTAACTTACCTGATGTCCCTCTGGCTTCTGTGTATACACATGTGCATGCACACATGTGTACTTGTACATAAAGAAAACCCACAACACAATTTATCATTGCCAGAGTTCAGTCACTTTATGTGTGTACATGCAGTAACAAAGCAATGGTTCCTTCATCTTGTACCTAAGATGGTCATGGTCACAGGGACACCAGAAGACACCCAGAGTTTATACTGTCACACACATGTTCAGAGAAGTACAGTCAATTATGCCACCTGGGCAACACAGCAAACCCGATTACGTGATTCCAGAGACAGGAGCACAATCTCGTCCAAACAGCGTCCAAGGTTTGCGTCCTGTCACTTATACCTAGAGAGACACACTAACTAACCCACAATGACACTAGAGCTCTCCCACTAGGTCACACCAACCTTGAGAGGTATCCCACCACTGTCCCATCCACAGCAGACTCTACCTACAGCCTACAGGCTCAGCCCCTCTACATATGGCTGTGTCAGCTTTTGGGGTCCAATACTGCTGGAGTTCAGCCAAGAGTCTCATAAGCCCTTTCTGCAGTTCCCCACCACTGCATCTCTCTTGTGTTACAGACCTCACCTCTGACAACGACAACAGCCAAGTCTCAAAACAATCCTAGAAACCCCTAGAGATCAGAACTGAGCTGTACCAACAAGAAGCAGTGTCATTGTAAGCTCACACATATACACTGTTACACCCACATCTAGGGTTCTACCACCAGTGGCCTACAGACATAATCACACACACACCAGTGGGCTTATACACCCTAAGGCAGATGGGGGCATTTTTTCCAGCTAACCCTGAAGACCTGCATACCTGGTCACTAACTCACTCTCCCTCATGCTGAAGCCCAGTCTGTCACTGAGAGCCAGATGTCTCCTGCCCGTGTACTGGCCCCTAGGCTCCTTTTCTGGATGAAGGTTTCCTATTGGCTGGGACAAAATCTCCCAGGTCTCCTGGGTACACTGAAGTGACCACTGTGTGATTCTCTTCTTTTCTTGTTTCCTCAG
Seq C2 exon
ATGCTACCCAATCCCTTGCAGAGGGCAGCCCTATCTGCTCATCCACCAACCTGAGCAGAGTGGCTGGGCTGGAGAAGCAGCTGGCCATTGAGCTCAAGGTCAAACAGGGGGCAGAGAACATGATCCAGACCTATAGCAATGGCAGCAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057672:ENSMUST00000005616:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.196 A=NA C2=0.314
Domain overlap (PFAM):
C1:
PF0218511=HR1=WD(100=68.3)
A:
NA
C2:
PF154561=Uds1=PU(48.6=70.6),PF0218511=HR1=PU(44.4=62.7)
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:
ACTGAAGCGGGAGATACGGAA
R:
GCTGCTGCCATTGCTATAGGT
Band lengths:
349-1784
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