Special

MmuINT0037429 @ mm9

Intron Retention

Gene
ENSMUSG00000032316 | Clk3
Description
CDC-like kinase 3 [Source:MGI Symbol;Acc:MGI:1098670]
Coordinates
chr9:57603059-57606157:-
Coord C1 exon
chr9:57606091-57606157
Coord A exon
chr9:57603176-57606090
Coord C2 exon
chr9:57603059-57603175
Length
2915 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
GTTTCTCTCCTCCTCTATAGAGG
3' ss Score
8.45
Exon sequences
Seq C1 exon
ATGAGATCGTGGGGAACCTGGGTGAAGGCACCTTTGGCAAGGTGGTGGAGTGCTTGGACCATGCCAG
Seq A exon
GTGAGCGTGCTGGTACAAACATCCTTGAAAGAGCTAGTGCAGCTCTTTTTGGAGGGCCGCACCATTGCTGGATGTGTTGGGTTTGCTGATCTCATGAAATAAGGGAGGCATCCTTGGGGTTTGACAAGCCTGTGACATCACTACAAGAACTTTTAGCTAGTGTGTGCCTCCTCCCTGGTTACCCACTTCTCAGCTGTGGCATTGGATATGTGGCCCAGTGCTGCATCCCATGAGCTTTTGGATATTTTTGGCCAGGCTTCATCTATCTGGTTTCTTGGGCAGAGGAAAAGGTACATATAAGGTCCTGGGAACCTTTAAAGAATACAAAGGGAGTCAGTGCAGGGCCAGAGGAGGTGGACTTCATCTCTGCCAGCAGGGCCAGGGGCTTCCTTTGAAATGAGTTACATCTATGTTAAAGATAAGACGGCTGTGGGGAGGGACCTTGTTTCAGAAGGCTAAAGTAGTGGCCTCTCCCCTTGGCCAGAAGGTTGAGGATGCTGCTGGCTTGGCCTGATAGTACTTTTGCCCCTCCCATGTCTTCCTGAGAGATCCCAGCCGAAGGAAATGAGACTTTGGCCTTTCTCACCAAACAGCTACCAACTACCCCAGTGCGGCTAGGGTCATGAGTAGTCCATGCTGGCTGGGAAGGCAGTACCTGTATGTGCCATAATGCTGGGGCCAGATCATTCTCTCCAATCCTAGCAGTATAACACTTACTGCTTATCATCTGTCAGCCTAGAGTCTGCTTCCTTCCCTGTAGCTGTATGTTAGAGAGGCAACCCTCTGGAGAGCCAGTTCCTGCCTTAATAATCTCTAATTGCTTTAGTTACAGAGAACTGGTATCCTCATTTGAGCTATGCAGGGCACCGCTTCAGAAATGAAATATGAAGATGCTCGGGAGTTGCCCAAGTTACACCTCAGCCATTGATGACAGAGCTGGGCTTGCTGTTCTTGGTCTCCCACATTAAGTGAGCTGCTCAAAAAAGACCATTGCACCCAAAATCAGCCATCCCCTCAGCTATGAGATGAAGTGCTAATGAGAAACTTCCTCCTGCACCCATTTTCTATTCAACCATTTCTAGGTTCTTCATCATGAACCTAGAATGAGTATAAAGGGACACATACACACAGTCCTGTGACCAGATGTAGACAGGACAGGTCCAGGAACTCTAACCTAGGAAGACAGCTATACTATGGGCTGTCCCTCTTTGAGTAGTTGGGGGTAGGAAATGAGTCCCTGAAGTCACTAAAGGACAGACAAGGTCCTGGGTCCTTTAAGGTAAATGAATGCAAAGGGAGTCAGTGCAGGATCAGTGGAGGTGGACTTCAGCTCTGCCAGCAGCCTGGCAGGGGCTTCCTTTGAAATAAGTTATACATATGTTTAAAGATAAGACGGGGGCCTGGAAGCCGGGCAGTAGTGGCGCACACCTTTAATCCCAGCACTTGGGAGACAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAGCCCTGTCTTTTTTTTTTTTTTTTTTTAAGATTTATTTATTTATTATATGTAAGTACATTGTAGCTGTCTTCAGACACTCCAGAAGAGGGAGTCAGATCTCGTTACGGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCTGGACCTTCGGAAGAGCAGTCGAGTGCTCTTACCCACTGAGCCATCTCACCAGCCCCCAAGAAGCCCTGTCTCGAAAAACCAAAAAAAAAAAAAAGACTGGGCTCTGGAGAGATAGATGACTCAGTGGTTATGAGCACTGACTGCTCTTCTAGAAGGTCCTGAGTTCAAATCCCAGTAACCACATGGTGGCTCACAACCATCTGTAGTGGGATCTGGTGGATCTGGTGCACTCTCTGGTGTGTCCAAAGACATCTACAGTGTACTTATGTACATACAATAAATGAATAAATCTTTTTTTTTTTTTTTTTTTTTAAAGGTAAGACTGTTGTGGGGAGGGACCTTGTTAGAGAAGTTGGTAGTGTGGCCTCTTTCCTTTAGGCCTGCACTGTCCAAGAAACCAGAAAAGAAAATTTAAAAAAAAAAAAAAAAAAAAAAAAAGAGGGTTATCAAAGCAGGGCATTCTGAAGAGGGTGTCTTTGCCCAAAGGCTGATGAACTTGTTCCTAGCATCCAGGCCAACCCTTGAGGTATCAGGATACACCGTAGTGGGCCAGGACCACCTCATTTCAGGTCTCCACTGGTATCTTAGTACTAGCTCTCTTTGGCAACGTAGGCTGACATGTTTCCTTGTCTGCTCACATCCTGCAAATGGCCTTCTAGAGTAGGAGTGGAGTATGAAGGGTAGAGCAACAACTGCAGGAGCGAGATCTTGGGGGACACGGACAGAAGGTTCTTGGCCCTCTGTAGCTGGTGGTAAATTAGAGGCAGATAGTTGGGGGAAAGGACCTAGAATAGGGTGCAGTATAAGGAGTGACCAAGCTTCCAGCTAAAATTCCACTACTGGTACCCTAACTGCTTGTTCGGTCTCACTACTACCCAAGCCAAGAAAGCTTGGCCTATAGAGTAGGTTGCCAGGTAAGCTTCCAGGGATCTGGGGTAGTCAGGATTACCTCAGCTCCTCTGCCTGGCTTCTCCCTGGGGAGCTGGGAGTTTCTGAGATCCTGAATGGACATGACAACTTGAAAGCTGAGACAGCCCTAACAGATAGATGCCAGGGAAGCTTGAATGGTGAGCAGGTCTGGTGTTGCTTTTAACAGGCTAGATCTCAAGTATGAATACAGTCTTAGGACCTGTGGTTTACGTAGTAGAGTTTGTTAGGAGTTGCTGAGTTTCAGGGAAGGGGAGAGAGCTGGACATTTGGCTTATGGGAACCTTTGTTTCTCTCCTCCTCTATAG
Seq C2 exon
AGGGAAGTCACAGGTTGCCCTGAAGATCATCCGTAATGTGGGCAAGTATCGGGAAGCTGCTCGTCTAGAAATTAATGTTCTCAAGAAAATCAAGGAGAAAGACAAGGAAAATAAGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032316-Clk3:NM_007713:5
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=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0006920=Pkinase=PU(6.9=95.7)

							
A:
NA

							
C2:
PF0006920=Pkinase=FE(12.3=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000067341





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr15:74622561-74624901 
ALTERNATIVE
HsaINT0036452
(CLK3)
Human
(hg19)
chr15:74914902-74917242 
ALTERNATIVE
HsaINT0036452
(CLK3)
Rat
(rn6)
chr8:62532908-62535265 
LOW PSI
RnoINT0037396
(Clk3)
Cow
(bosTau6)
chr21:34442891-34445154 
ALTERNATIVE
BtaINT0039401
(CLK3)
Chicken
(galGal4)
chr10:1977344-1978061 
ALTERNATIVE
GgaINT0030405
(CLK3)
Chicken
(galGal3)
chr10:1857480-1858197 
LOW PSI
GgaINT0030405
(Q5F445_CHICK)
Zebrafish
(danRer10)
chr19:9239748-9242069 
ALTERNATIVE
DreINT0047608
(clk2a)
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"