Special

MmuINT0120813 @ mm9

Intron Retention

Gene
ENSMUSG00000057672 | Pkn1
Description
protein kinase N1 [Source:MGI Symbol;Acc:MGI:108022]
Coordinates
chr8:86201830-86204996:-
Coord C1 exon
chr8:86204853-86204996
Coord A exon
chr8:86201906-86204852
Coord C2 exon
chr8:86201830-86201905
Length
2947 bp
Sequences
Splice sites
5' ss Seq
GAGGTACAG
5' ss Score
6.62
3' ss Seq
AGCGGAGTGTGTCCCCACAGGTC
3' ss Score
7.52
Exon sequences
Seq C1 exon
GCTCGGGAGCTGGAGCTGGCTGTGTTCTGGCGAGACCAGAGGGGTCTGTGTGCTCTCAAATTTCTGAAGTTGGAGGACTTCTTGGACAACGAGAGGCATGAGGTGCAGCTGGACATGGAACCCCAGGGCTGCCTGGTGGCTGAG
Seq A exon
GTACAGCCTGGTTTCTGACTTCTGACCCCAAGATGTTTCCTGCCTCCTTGCCTCCAATTGCTTAGCATGGGGAGGTTAATTTCAGAGGTTTCTGAATCTTCATGGGAAGTAAGCCTCACGAAGGCTGGGATTGGTGCCAGGCGAATCAGCAGCAACAGACCACATACGTGATCGTGTTCCCAGAAGGCTGGGCCTCGTCAATTGCATGTTGGTCTGGCAATAGGCAGGACTCAATGGGTAGAATGCTTGCCTAGCATGCACAAAGCCATGGGCCCCATTTCTAGTTCAGATAAAACTAGGTGTAGGTACTGGAGAGATGGCTCAGCAGTTAAGAGCTCTGGCTGCTCTCCAGAGGACCCAGATTTGATTCCCAACACCTACATGGCCACTTACAGCTGTCTGTAACTCCAGTTCCAGGGGAACTGACACCCTCTTTTGGCCTCAGTCACTAGGTTCTCATGTGTTGCACAGACATACATGCAGGCAAGACACTCATATACATTAAGCAAACAAACAAGCAAACATTAACACTAGATATAATACAACATCGAGCTACATGATGAGCAAGAGGACAGGAATATAAAGACTTTAACAAAAACACAGCCAAAGCCGAGTGAGTGGTGGTGCTCGCCTTTAACCCCAGCCCTCTGGAAGCAGAGGCAAGCAGACCTCTGAGTTTGTGGTTAGCCTGATCTACGTAGTGTGTCCCAGGCCAGTCAGGTCTATAGAGAGACCCTGTCTGAAAAACAGAAAACATTTCTTCCACTGCAGCTTAGTGGAAGCACTGGGTGCGCCTCGTGTGTGCTGGGCTTGCACTGGAAGCTCTCGCTTCACCCCAAGCATCGCAGCAACAGACGCAGGTGGAGGCGGGTGTGGCTGCAGCTGACAGAATCTTCCTGAGAGCGGTTGTCACTGAGCCTACCGTGTTGAGTTCTGCCATGGGGAGAATGTTCTGTCTGAACTGTGGCTGGTCTAACTGGAAACCACTTTTTCCCACCGACGCTTTGAGTAATTTAAATGTGATTTCTACACATGGCATCTGCACAGGGACACTCCGGGTCTAGAGATCAGTGCCTGTATGTGCTGGAGTTGCAATCCTAGGCTGTCATCGTGGTTCACACAGGGATGGCCCACATCACTGCGGCTTCTGAAGCAAGGGGCCAGGCTCCATCCCTCCTGGCTCTGATTCAGTCTAAGAGAGGGGTCTGAGAATATATATTTCTGCCCACGGCCCCTTAGCCCTGTGAATCTGGGCTTGTTGCTCAGCATCTCACTATGCCAGCAGCATAAGTGGAGGAGGCGTGTGCACCCAATGGAATACAGAAGCAAAGAGACACAGGAGGGGGCTAGGCTCCCAATATCCTGTGTGTGGGCATACACCAGTGACCCCACTTCCTCACTCGAGGACCTCCTAAATAGAGCTACAGGCTTGTGACAAAATCTTCAGTACACAGGGCCATTTTGGGATTGCTGAGCGATGATGCTCGTGTGGCTAACCTGCAACTATACTTGGGAATCAAGTCATAGGTGGTGGGAGACTTGTTTCCCAGACTTCCATGTCAGGCTGTTTTTTTGTTTTTGTTTTTGTTTTTTAAGATTTATGTATTTATTATGTATACAGTGTTCTGCCTGCATATATGCCTACAGGCCAGAAGAGGGCATCAGATCCCATTACAGATGGTTGTGAGCTACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTTCCCACCGCTGAGCCCCCTCCACGTCAGTCTTGTGGGTGCAGACCCCTTCCTCCCTCAGAGAAGGGTCTGACTGCCTGCACCCTCCCTTTTCAAGATGGAAGCCTGGTGTGATTTGAATATGAATGTTCCTGTCTTAGGTATTTTTCCTGTGACTGTAGTAAAGAACCCTAGCAAAAGCATTTTAAGGGGAAGAGGGTTTCTTTTGCTCAGAGTCCACCATGGTGGGGGAGTCAAGCAGGAGCTAGTCACTCTCATAGGAAGTAAGGCTGGGAAGCAGAGTGGTGAGTGCCGTGCTCCGCTTGCTTCTCCTCTCCATGCTGTCCAGGACCCCCACCTAGGCAATGATGCCTCTCACAGCTTTGTCAGGTCTTCCCTAGTAGACACAGGGAATCCCTCACAAGTGCCTGGAGCCTGGGTAGTCAGCTTGACAGCTAACTTTAACTCTTTCAGTCCCCATGAGGGCTCACACTTGCTCCCCAGCTGGCGGCTCTTTGGAGAGGTAATAGAACCCTCAGTCCTGCTGCTTTCTGTTCCCTGGTCCTCGGAGATGTACCTGGGCTTCAGGCTTCTACCACAGTGGGCCCCACTGCCTGAGGCGCCATGTTATCCTCCCATGGTGGGCTGTACTCCCTCAGCTATGGCAGAGTAGAGCTCCCCGAGAGTGTCCTGTCAGGTACTCTGCCACAGTGAGGAGAACGCAGCATGCACTTATGAGGGCAGACAGTGAGTGCACTGACCACTGCTTCCATGCTCATCAGCTTTCTCTTGCTTGACAGAACACTCGGGAGAAATAAACTTACAGGAAGCAGGATGGTTTCAGGGTTGCAGCACTCACCTCATTGCTTCTGGGCTTGCAATGAAGCAGGCCGTGGAGTAGAGCTGTTCACATGCAGGCAAGGAGACAGAAGGAGGAGAAGGGAGTAGGTCTGGTAGCTAGAGACCTGCTCTTGCAGTCACACCCTTCCCTGTGAAGCCCCCTGCTTCCTTCCCAGCAGTCTGATGCTCTGAAGCCATCGCTCGATGAACCCATGAGTGGATTCATTGACCCTCCTGTACGTAGTCACTGCCAACAGCTCAGCTTTGCACTCGGCTGCTAGAGCCAAGCCACATGTCCTCAGGGACACTTGGTGTCATGGTGCCCCATACATAGGTTGTGTGTGTATCTATTCCTGCGACCACTGCAGCGGAGTGTGTCCCCACAG
Seq C2 exon
GTCACTTTCCGAAACCCCATCATCGAGCGGATCCCTAGGCTCCAAAGGCAGAAAAAAATCTTCTCCAAGCAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057672-Pkn1:NM_177262:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000116235





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000005616, ENSMUSP00000105443, ENSMUSP00000115054
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr19:14458376-14463666 
LOW PSI
HsaINT0126135
(PKN1)
Human
(hg19)
chr19:14569188-14574478 
LOW PSI
HsaINT0126135
(PKN1)
Rat
(rn6)
chr19:24811177-24814081 
ALTERNATIVE
RnoINT0112257
(Pkn1)
Cow
(bosTau6)
chr7:12408557-12412413 
LOW PSI
BtaINT0112578
(PKN1)
Chicken
(galGal4)
chr17:5226612-5227544 
ALTERNATIVE
GgaINT0124755
(PKN3)
Chicken
(galGal3)
chr17:5854143-5855075 
LOW PSI
GgaINT0124755
(PKN3)
Zebrafish
(danRer10)
chr1:45131177-45131313 
LOW PSI
DreINT0114953
(pkn1a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
Functional annotations
(Submit an annotation)

	


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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"