MmuINT0120852 @ mm10
Intron Retention
Gene
ENSMUSG00000026785 | Pkn3
Description
protein kinase N3 [Source:MGI Symbol;Acc:MGI:2388285]
Coordinates
chr2:30081053-30082962:+
Coord C1 exon
chr2:30081053-30081236
Coord A exon
chr2:30081237-30082815
Coord C2 exon
chr2:30082816-30082962
Length
1579 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
CTCTCTTGACTCCCAACCAGGGA
3' ss Score
5.97
Exon sequences
Seq C1 exon
GCCCAGGCCCAGCTCCAGGAATCCTCCCAGAAGCTGGACCTCCTACGGCTGGCCCTGGAATTGCTGCTGGAGAGGTTGCCTCCCACCCACTCTCTACGTAGCAGGGTGACCCAAGAACTTTGGATGGCAATGCTTGGGAACCCCCAACCTTTGGGGACACTTGTGAAACCTATTGCCTTGACAG
Seq A exon
GTAGGTAGCAAGGATTCCCTTTCACGTCAGAGGGTCCCTTACCTTTTAGAGAGGACGCTGAAGCATTTGGGAGAGAGTTCAGTCCTGCTGTGTGACCTTGGATCCCTCATGTTCCCACTCTGATTCTTGGTTTATCCATCTGTAACATAGATTCAATAGTAGTGACCCAGCATGATGGCGCACGCCTTTAATCCCAGCACTCGGGAGGCAGAGGCAGGGGGATGTCTGTGAGTTCCAACCTGGTCTTTAGAGTGAGTTCGAGGCCAGCCAGAGAGACATGGGAGAGACCCTAAGTAAACAAAGGGTGGAAGTGCTCTCCTGATCCACAAGATAGTTTTGTAAACCCAAAAGTTTCTGATGTTCAGAACACACTTGGAGCCTGGCCAGCGTGGATGGGATTTAAATGCCCGGCCTTCGGTAGGGAGTAGATTGACAATCAGTCCACTCCCTGGCAGCCTTGGGGCCTGGGCAGCTTGGACTACCTGTAAGTTCTTTCATGAGGTCTGTTCTTGTAGCAGCAGCTGACTGGCAGTCAACAGATCATGGGAGCTGCAAGCTAGAGCCCGGCTGGTGCCTGCTTCAGAACACAATAGATAGGGCTAGACAGAGCTCTGTTACTATTATCTTGGATAATCAAGGAGGGCTCCTTAGAACAGGGGGGAGTCTGAGCTTGGCCTTGGAGGGCTCTCGGGAGTGCTGATGGCCAAGCCAGCAAGTCCGGCAAGACAAAAGGAGCCTCTTGTTTAAAGGCAAAGAATTGGGGACACGTTGATAAAGTTCTTTCTTACTGCGTATGAGGTCCTGGGTTCAGTCCCAGCACCAAATTAACTGGGTATGGTAGCACACACCTACAACCCAACCCCCTGGGAAGTGAGGCAGGAGGATCAGGAGTTCAAGGGCATCTTTAGCTACATAGTGAGTTTGAGGCCAACTTGGGCTAACAAGATCCTGCTTTTAAACAAAAACATTTGCTAGTTTGTAGCCGAACTTCCATTTCCTAAGACAAGTGTATTGCCTGGGCCGCCCTTGGTATTTCTGTAAGGTCTCCAAGTATTACCTCCAGACCCAGCCTAGTAAAATGGTGTCCTCAGAGCCGGTTTATGCCCTCAGGAGCTCCTGGGTATCTGCTGCTTCCTCCTCTTGTCCTCTACCCTTGGAGACAAAACTCTCAGTGATCTTAGACAAAACATGTTTTGTCCCCATTGGGGGCTCTCCCTCGCTGATCAGGTGGGAAGGAATAGGGCAGGCAGCTAGAGTGATGCTCGGGTGCCTGCCCCTGTGCACTTGAGACCATGGTGCCCACCAGACCCTGAGCTCAAGGTAGCAGTTTCCCTCATCCTGTGGCTTTACAAAGCTTGGGAGAAGTCCTGTTCTTACATTCCTGCTGTGTTCTGCCACTGCATAGGCACTCAGGAAGGAGAGCTAGCCGGGCTGCTAAGGATGCTGGGTGGTAACTAAGTGTGGTAGGTAGGGTTTAGATCGGCTGCTCCTAGCTCTGACCCTCCTAGAGCAGGTGGTGTCCCTCTGGGGTTCCATTGGTGGTGGCTGCTGACAGAGGGCTCTCTTGACTCCCAACCAG
Seq C2 exon
GGACACTGCAGGTTCGCCTCCTGGGCTGCAAAGATCTGCTGGTAGCTGTGCCTGGACGGTCTCCCATGGCTGTCCTGGCAGGTAGCCCTTCTGAAAGCTGGCTCCGAACAAGGTCCCGGCAGCAGCGTGGTGGAGGCGAACTGGCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026785:ENSMUST00000045246:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.038 A=NA C2=0.040
Domain overlap (PFAM):
C1:
PF0218511=HR1=PD(43.1=50.0)
A:
NA
C2:
NO
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:
CAGGCCCAGCTCCAGGAATC
R:
GCCAGTTCGCCTCCACCA
Band lengths:
326-1905
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