Special

MmuINT0120827 @ mm9

Intron Retention

Gene
ENSMUSG00000004591 | Pkn2
Description
protein kinase N2 [Source:MGI Symbol;Acc:MGI:109211]
Coordinates
chr3:142453866-142457147:-
Coord C1 exon
chr3:142457067-142457147
Coord A exon
chr3:142456979-142457066
Coord C2 exon
chr3:142453866-142456978
Length
88 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGT
5' ss Score
10.75
3' ss Seq
ATTTATATTTTGTGATCTAGCTA
3' ss Score
6.13
Exon sequences
Seq C1 exon
CTGCTAAGGAGAAATCCTGAGCGGCGCCTGGGAGCTGGTGAGAAGGATGCAGAGGATGTCAAGAAGCACCCGTTTTTCCGG
Seq A exon
GTAAGTGTAAAAGCTCAGAGTTCTTTTATGAAACTTGAGTGACTGGGAACACAAAACTAAACCGGCTGATTTATATTTTGTGATCTAG
Seq C2 exon
CTAACCGACTGGAGTGCTCTAATGGACAAAAAAGTAAAGCCACCATTTGTACCTACCATTAGAGGACGGGAAGATGTTAGTAACTTTGATGATGAATTTACCTCAGAAGCACCTATTCTGACTCCACCTCGAGAACCAAGGATACTCTTGGAAGAGGAGCAGGAGATGTTCCACGATTTTGACTACGTTGCTGATTGGTGTTAAGTTTCTAGACCCTGAGACCAAGCAGACTGACCAACAAGAAGACCTCTTGAAAACAGCAGCCCTGCATTTCCTTTCCGTGCCACCAGGAGCTTCTGAGATTATATAAAGCACATGAAGATGTGGTTACAGTACTGTTTTATACCTTAATGTTTTCAACGTAAATCTGAACACTGGAAGCAGTTTCATGGAGTTTAGGCTGAGTGAACATTGGCCATGGAAATCCATTACAAATAAATACTTTTACATCAATACTCTTATTTTTAAAAAGAAGAAGAACCACTTTTTTATAGTCCCCATGTTTGCCCTAGGCCTGCCTTAAGTGGAAGGAAGATTAATCACTTAACTATATTTTACAAAAGAAAAAATAGGGCTTTGGATGCTATTACTCGTAATATAAAAAGTGTGATTCTATTTCACTAAGGCAATTATTTTTTTAAGAAATCACTATAATATGAAAAAATGTGGCAGTTTGTACACCTTTGGTGGCTTGATTTAAAGAAAAGAATGAGAATGTATTGATGTCTATTTGATGAATTTTCTATATTTATCAGGAGAACACTTTATTGCCTTAAGTTTACCAACCATGTAGCAGAGCCTCCTAGCTTTCCAGCAGAGCTACCTGCCAAATGAGTTTGTGTATTAAACAATGCTGCAAAAAGATAGGGACATCAGCATTCACTTAACAGTAACAATGAGGACTTCTAAGCAGCTGGAACCAAGATACCATGCTAACTCTATGCATTCCCAAAGTCAAGGCACCGTGGAGGATGTTCAGTCAGGTCTTCCAAAGTCAGTGAACCTGATTAACCCTTTATTGATATGCATTCTACACGTATTTCAACCTAGACATCTTGTTCTTGTGTCTGCTGTAGAAGGAAACTCTATCTTTGTTAAACCATAGAGATTATCATGGTATACATGCTGTGAACATGTATATGTACAAGTTGTAATGTATTCTGTGTTGTAGGCATATTATTTAATTTCACCACGTCATCACTTTTGTACAGTGGCCAAGCAGACACCTCCAACTCCAGCATTTCCATTAAGTGCATTTGTACATTTTAGGCCGCTGGATCCAGATTTTATATTGGCAGTTACTGAGGGCTAAAGCAATATATTGTAACAGAATGTATAAATATTTTTGATAAAACAGTCTATATTTTATAAAAAGTTATTATAACACTAAAGCTGTACCTCAAAAGTCTCACAAATAATTTGATCAAATGCTCTACGCATCCTCAGAGGATCCGTTCCTGGCTTTGTATCGCTCTTACCATATGCCTGTTTGCAAATCATGATCTTCACTGGGCTGGAATTTTATTAGATTTTTGTTTTGTTTTTCCCTTTTTTCTCCTAGGCTGTCACTCTGTTGTTCTCCCTCAGTTCAGTAATATCAATAACTCTTTGCTTAGCATGTTAGGGCCATGATACCTCAGGAACAGCAGAATGGTAACAACCACACTCGAATTAACCATGTAATCACAGTGAGCTCATCTCTTACAATTTTCCAAATCTGCGTTATTGAGAAGCAGGAAAGTACACAAATAATGAAGAGTTGAGCTTGAAACAGCTTTGCTGACATACATTGGCCTGTTGTTATTGTACTCTGAGAATGATTACAATTGTCCAGAGATTCTTTATATTACCTTCCAAATTCATTATTATTTTTCACTTAAGATCCTTTGGAAGAAAATTTTCTAAAAAGAGAAGCAATATGTTGCTGTAAATTGCTTTAAAATGCCAGTTAGTTGCCTTGGAAGAGAACAATAGAAAAAAAAAAAATAGCGTAATTGTCTAGCTTTAATTGACCAGTGTTAACTCAGTCTGAAAATAAAACACTAACTACTTTTGAGGTACAGTCTGCATACCTTTGTTGGTTCTGAAATATGCATAGAAAGCAACTTTTCAAATGGGCTTTTAGCATTAAAAACTGACATAGAGTTATATACACAGTGTACAAAAATTTTTTTAATTGAAGTCAATCATTAAAAAATTTAGAGGTCAGGGCATAGTCACACAATTATGCTGAAAAAAAAAGCACTCATTTTTCTGTAGTTTAAATATATATATATATTTTAGCCAGATTTTAAATTTTCAGAGTGTAAATAGATTTTGCTATTACTGTATGTGTATTGACTGCTCAAGCACTTTGTAAGGAAAGTGGATACTTTAGAATGGTACCCTATGCATCCAAATGAAATGTGCCTTTACATCATTCTAAGAAAAAGGGGGTTTTGCAGTCATAAATTACCACAAATGCACAAATTAAAGTTTAAAATAGATTGAAATTTGTAATTTTGGTTTTAAGTTTTCATTCCTTTTAGAATTGTCCTTGTGTTAAAATAGTTGGCTAAAAACGTTAGCTCTACTTGGAGGTCTCAAGAAAATTATTTTTAGTTAGCTTTCTTTTCATCCTGGAGAAGGCACATTGTCCACTTTACTTGGAATAATGGGGAGATTTCATCTAGGTCTGTATTCTACAGCTTCTTTCATCCATGCACAGAATGGCCACTGTCACTAGACACCAAGACCAGGAAAGTTGCCAGGAGGAGAGAAGCAATGATGTTTCCAAGACTAAAAAGCAAATATGCTAATGTAAAGTGTAACATGGGAGCTTCCTCGTGTTAGAGCAGTGGCTCTCATCCTAGGGGGTATGAGAGGGGTTAGAATGGCCACTTCATAGGAGCTGCATATCAGATGCTTATATTGCAATTTATAATAGTAGCAAAATTACAGATATGAAGTAGCAACAAGATACCGTTAAGGTTAAGGGTCACCACAACATGAGGAACTGTATTAAAGGGCCGAAACATTAGGAACTTTGAGAACCACTGTGTTAGAGGGTAACATTTTAGTATTGGATCTAACATTTGAGAAAATTGTCTAATTAATAAAGCAGAATGCTAGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004591-Pkn2:NM_178654:21
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.185 A=NA C2=0.164
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0006920=Pkinase=PD(9.6=92.6)

							
A:
NA

							
C2:
PF0043319=Pkinase_C=WD(100=70.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000039566





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000087567, ENSMUSP00000133691, ENSMUSP00000134559
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:88833158-88833244 
LOW PSI
HsaINT0126150
(PKN2)
Human
(hg19)
chr1:89298841-89298927 
LOW PSI
HsaINT0126150
(PKN2)
Rat
(rn6)
chr2:248738187-248738273 
LOW PSI
RnoINT0112271
(Pkn2)
Cow
(bosTau6)
chr3:55232107-55232192 
LOW PSI
BtaINT0112593
(PKN2)
Chicken
(galGal4)
chr8:14118290-14118369 
ALTERNATIVE
GgaINT1021751
(PKN2)
Chicken
(galGal3)
chr8:15877012-15877091 
Zebrafish
(danRer10)
chr6:25325067-25325160 
LOW PSI
DreINT0016694
(PKN2 (1 of 2))
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GAGGATGTCAAGAAGCACCCG

				
R: 
GGTTCTCGAGGTGGAGTCAGA

				
Band lengths: 
167-255

			

		

	





	
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"