Special

MmuINT0120911 @ mm9

Intron Retention

Gene
ENSMUSG00000054065 | Pkp3
Description
plakophilin 3 [Source:MGI Symbol;Acc:MGI:1891830]
Coordinates
chr7:148269954-148273709:+
Coord C1 exon
chr7:148269954-148270158
Coord A exon
chr7:148270159-148273534
Coord C2 exon
chr7:148273535-148273709
Length
3376 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCC
5' ss Score
8.63
3' ss Seq
CTTCACCCCATCTTGTGCAGGGA
3' ss Score
7.24
Exon sequences
Seq C1 exon
GCTCGCAGCCTTCAGGCAGTGCCTAGACTGGTGAAGCTCTTCAACCACGCCAACCAGGAGGTGCAGCGCCACGCCACAGGTGCCATGCGCAACCTCATCTACGACAATGTAGACAACAAGCTGGCGTTGGTAGAGGAGAATGGCATTTTTGAGCTGTTGCGGACACTTCGAGAGCAGGATGATGAGCTACGCAAAAATGTTACAG
Seq A exon
GTACCCTTGTGCCTCTTCCTCTCATTCTGTCCCCCTCCTCTGCCCTTGCTCTGTCCTGTCTTCACCGCCCTCTCATCATACTCCCCTCTCTTCCTCCCTTGTCCTCAGCAATCTTTATCTTGTGCCTTTTCAGTCCCATTTTGCATTTTTGGGGGGCCTTGTTCAAGTTTCTTGCTGTTGTTGCTTATCTTGCTATCACTTGGTGGACATGCATGTATTCAACAGCGTCCATGTGGAGGTCAGAGGACAACTTTGGTCAGTTTTCTCCTTCCACCCTGGGTTCTGGGGATCAAACTCAGGTAGTTGGGCTTGTGCAGAAAGCACCTTTACCTGCTGAGCCATTTTGCCAGCCCATTGAATGACTGATCTATTGACTGATTGATTGACAGGAACTTACTATATAGCCTTGGCTGTCTTGAAACTCACTACATATATCAGACTAGTCTTAAACCCATAGAGATCCACCTGCCTCTGCTTCCTGAGTGCTGGGACTAAAGGTGTGTGCAACTATGCCTGGTTTATTTTGTTGTTGGTGGTGGGTTTTTTTTTTTGTTTTTTGTTTTTGTTTTTTTTCGAGACAGCGTTTTTCTGTATAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGACTGGCCTCAAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGCGATTAAAGGTGTGCGCCACCACCTACCAGCTATTGTTTTTTTAAAGGTTTGTTTATTTTTATTTTTTAAAGATTTATTTATTTACTTACTTATGTATTTATTTTTTAATGGTTTTTCGAGACAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGTGTGTGCCACCACCGCCCAGCTGTATTTATTTTTTTAAAGATTTATTTATTATTATTATATATAAATACACTGTAGCTGTCTTCAGATGCACCAGAAGAGGGAGTCATATCTTATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCAGGATCTTCAGAAGAGCAGACAGGGGGGCTAGTGAGATGGCTCAGTGGGTAAGAGCACTGACTGCTCTTCCCTAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAGCCATCCGTAATGAGATCTGACGTCCTCTTCTGGTGTGTCTAAAGACAGCTACAGTGTACTTATTTAATATTAAATAAATCTTTAAAAAAAAGAAAAAAGAAGAAGAGCAGACAGGGCTCTTAACCACTGAGCCATCTCACTAGCCCCTATTTTTATTTTTTATGTATATGAAGTTTTTCATATGTGAATGTTTGTATGAACATATGAATATTTGCATGTTTACCATATACATGCCTGGTACCCAGAGAGGTCAGAAGAGGGCATTGGATTCCCTGAAAGTAGACTCACAGATGGTTATTAAAAGCCATGTTGCACCGGGTGTGGTGGCGCATGCCTTTAATCCCAGTACTTGGGAGGAGGCAAGGGGATTTCTGGGTTTGAGGCCAGCCTAGTCTACAGAGTGAGCTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCGAAGAAAAAGGAAAAAAAAGCCATGTTGGAAATAGGAACTAATTCTGTGTCCCCTATAAGACCAGCAAGTGCTCCACTCAGCTGTTTCTCCAGCCCCTGATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTTGCTTGCATGATACCTGTATACCACATGCATGCCCAGTGCCCATGGAGTTCAGAAGAGGGCATCACATCCCCTGGAAATGGAGTTAGAGATGATTGTGAACTATCCTGTAGGTGCTGGGCATTGAACCCAGGTCCTCTGGAAGAGCAACCTGTGCTCTTAATCACTGAGCCATGTCTCTGGCCCTCCCCAACCCATTCTCATTGTCCCACTCTGTACACTGGCCTTCATCTCACTATGTGTCACACTGTGGCCATAAACTCATGGTAATCCTACACAGGCCTTGTTGGGATTACAGGCATGAGCCATCACAGCAAGCTAAACTTTTTTTTTTTTTTTTTTTTGGTTGGTTTTTTTTTCGAGACAAGGTTTCTCTATATAGCCCTGGCTGTCCTGGAACTCAATCTGTAGACCAGGCTGGCCTCAAACTCAGAAATCTGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGTGCCACCACTGCCCGGCAAGCTAAACTTTTTATTATCAGTGTTTGTCACTGTTGTGTGTATTGTTTGTTTTTGAGACAAGGTCTCACTATATAGCTCTGGCTGACCTAGAACTCATGTAGACCAGGCTGGCCCCATATTCTCAGAAATTACTTGCCTGTGTTTCACAAATGCTGGGGTTAAAGGCGTGTAACTTATGCCTGTCAATTGTTTATGAGAGAGGGTTTCTCTGTGTAGCCCAGGATAGCCTCAAACTCATGGCAATTCTGTTTTCTAGCTTCCTAAATTCCTAGATTATGTGTCTCACCTACAAAAACTATTTTTACTGGGCTGGAGAGATGACTCAGTGGCTAAGAGCACTGACTACTCTTCAGGAGGTCTTGAGTTCAAAATCCCAGCAACTACACAGTTGGCTCACAACCATCTGTTAATGAGATCTGGCGCCCTCTTCTAGCGTGTCTGAAGACAGCCACAGTAGACTTCCATATAATAAATAAATAAATCTTTGGGCTGGAGCTAGCGGGACCAGAGCGAGAAGGAAAAAACAAACAAACAAATTTTGCATCTTTTTATTCTTATTTTCTGTGGTGCTAGCTATGGTACTCGAGTGTACAAGCAGGGGAAGTGCTCCTCCACTGAGCAGCATCTCTGAGCCCAGGCTCTCTCTTTCCATTTGCTTCCACTCCTAAGCCTTCAAATCCCCACACCTTGTTTGACTCTTTTGCTCTGCTCCTGCCCCATGCCTGCAAAGGTCACCCTGAGGACCTCTCCAGAGAAACTCTGGAGTAAGACAAGGCTCCAAGGAAGTGTGGGGTCAGGAGCTGAGGCTATGGCCCGGTAAATAAGACTGTTCGCTGCTCTTCCAAGGGACCCAAGTTCTGTTCCCAGGACTTACGGCAGGCAGCCCATAACTGCATGTTAACTCCCGCTCCAGGCAAGCTGATGCTTTCCTCTCGACCCCACGGGTACCTGTACTCATGTGCTTATGATATACCCATGCATGGACACACACATAATTAAAAACAGAACAAAACAAAAAAAATCTTTGTAAAAAGATGTAAAGAGCCTGCTCTGCACCATCCCCAAAAGAAGCCAACCCTGACCCCATCCTTCACCCCATCTTGTGCAG
Seq C2 exon
GGATCCTATGGAACCTGTCCTCCAGTGACCACCTAAAGGACCGCCTCGCCCGGGATACACTGGAGCAGCTCACAGATCTGGTGCTGAGCCCCCTGTCAGGGGCAGGTGGGCCTCCCCTCATCCAGCAGAATGCCTCAGAGGCAGAGATCTTCTACAATGCTACTGGCTTCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054065-Pkp3:NM_019762:5
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=0.034
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0051418=Arm=PD(80.5=47.8),PF0051418=Arm=PU(80.5=47.8)

							
A:
NA

							
C2:
PF0051418=Arm=PD(17.1=11.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000101654





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000069961
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr11:399197-399966 
LOW PSI
HsaINT0126237
(PKP3)
Human
(hg19)
chr11:399197-399966 
LOW PSI
HsaINT0126237
(PKP3)
Rat
(rn6)
chr1:213892840-213894853 
ALTERNATIVE
RnoINT0112322
(Pkp3)
Cow
(bosTau6)
chr29:51275318-51275659 
LOW PSI
BtaINT0112670
(PKP3)
Chicken
(galGal4)
chr5:1564480-1564723 
ALTERNATIVE
GgaINT0055153
(PKP3)
Chicken
(galGal3)
chr5:1583135-1583378 
LOW PSI
GgaINT0055153
(PKP3)
Zebrafish
(danRer10)
chr7:32678954-32681520 
LOW PSI
DreINT0016709
(PKP3 (2 of 2))
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"