Special

MmuINT0037418 @ mm9

Intron Retention

Gene
ENSMUSG00000068917 | Clk2
Description
CDC-like kinase 2 [Source:MGI Symbol;Acc:MGI:1098669]
Coordinates
chr3:88974215-88977465:+
Coord C1 exon
chr3:88974215-88974331
Coord A exon
chr3:88974332-88977298
Coord C2 exon
chr3:88977299-88977465
Length
2967 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGC
5' ss Score
6.95
3' ss Seq
CTTCCCCTGTCTCTCCCCAGCCT
3' ss Score
11.42
Exon sequences
Seq C1 exon
GGGCGGAACACAAGTTGCCCTGAAGATCATTAAGAATGTGGAGAAGTACAAGGAAGCAGCCCGACTAGAAATCAACGTGCTGGAGAAAATCAATGAGAAAGATCCTGACAACAAGAA
Seq A exon
GTAAGCAACCAAAGGAACATGTGAGGAGGCCGAGGGGCTCTGTCCAGAAGGAAGGCTCCAGGCTGAGGCTAGGCGGGCAGGGGATACATCCAGTCTTGTCTTTTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTTTTTTTGGCATGCTTTTCTCTGTGTAGCTCTTGCTGGCCAGAACCTGGTTGTAGAACAGGCATTCCTCAAGCTCACAGAGACCCTTCTGCCTCTGCCTCCTGAGAGCTGAGAGTATAGGCATGTGCCGCACCCATTAAACTTGATCCTGTGCTTGTGGCAGAGCATCAGGATAGCCTGTGAGAGTCTCTTATCCATCAGCTTGTGTTACAACACCTGCAGTCAGGGAATGAATAGGCCTGGCATTGGTGGGCATCACTGTAGGTGGTGCAGGCCTGTGATCCCAGCCACTTGGGAGAGGAGGAAAGACAGATAGAAGCTTAAGACAGCCTGGGCAATTTTAATAAGAAAGATCTTTTTTCATAAATGGAAATGGAGCTAGAGATTGTAACCCAGGGATGGAATACCAGCCAACTATCTCACAGGGTCCTAAATTCAAACCCCAGTAAAATACACAGAAACACAGTCTGTTCTGGAACTTGAAGAAGAAATTTGAGATGAGGGGAGAGATGGCTCATCCTAAGAGTGATAGGATAAGCAGGGCAGTCATGGCCCACACCTTCAATCCCTGCACTTGGGAGGCAGAGGCAGAGGCAGGCGGATTTCTGAGTTTGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTATACAGAGAAACCCTGTCTCGGATACCACCCCCACCCCCACCCCCCCACCAAAAAAAAAAAAAGACTTGAGTTCAGTTCCCAGCACCCACACAGAAATTTAAAATAGCTCTATGGGTGCCAGGCACTAGTTGTGCATGCCTTTAATCTCAACACTCAGAGCCATGTGTAGGCAGATCTCTGAGTTTGAGGCCAGCTTGGTCTGCAGAGTAAGTTCCAGGACTGCCAGGGCTATGCAGAGAACCCCTGTCTTGAAATGAAACAAAATAGCGGGGCTGGAGAGATGGCTCAGTGGGTAAGAGCACCCGACTGCTCTTCCAAAGGTCCGGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCGTAACAAGATCTGATGCCCTCTTCTGGTGTGTCTGAAGACAGCTACAGTGTACTTACATATAATAAATAAATCTTTAAAAAAAAAAAAAAAAAAGAAACAAAATAGCTCTGGGGATCCAGCACCTCTAGCCTCTTCAGAAATCTGCAGTCATGTGCAATAACTAACTCACATCATTAAAAATAAAATCTTTGAAAGAAAACATTGGGGCTGTTAGTAATAGAACACTGTCCTGAAATGCAACAGGACTTGATTCTAATTGACGAAGAGTAGCAGGTTCTAGAATTGTGTTGAATCTGTGGGTATTTATACAGTAACAATTTTGTTCACATGCTATTCATTGGTTAAAGTTAAATAAGATGGTTACAGTGACGGTTGATTGGTTTGTTTGTTTTGAGGCAGTACCTCATTTAGCCCAGGCTAGCTTCTGCTCATTCTTATAGCCAACGGCAAGGATAAACTTGAAAACTCTTGATCCTTTTGTCTCTGCCTACCATTATAGAAGTGTACCTAGGGTTGGTTGGTTGGTTTGTTTTAAAGATTTATTTATTTATTATATATAAGTACACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGACTCAAATCTCGTTACGGATGGTTGTGAGCCACCATGTGGTTGCTGGGGTTTGAACTCAGGACCTTTGGAAGAGCAGTCATTACTCTTAACCACTTAACCATCTCTCCATCCCAAAGTGTACCTAGTTTTGTGTGGTATCAGGTATTAAACTTCTGTACATGCTAGGCAAATACTTTACCAACTAAGCCATATCCCCAGCCAAACAATATTTAACATACACTATAAACTTCGCCAACGCAGTGGCTGATACTAACATTCAGGGGATGGGGATGGGATATAGTTGCTCATGAATTTGAGACCAGGATGTGACTAGGACATAGAAAGTTCCAGGTCAGACTGCTTGAATGAGACCCAGACAACAAAAAAGGTGACTTTGGTAACTGAGAACCCATATTTGGAATTTCATGCTAATAGGTCTTGAGCAAATAGTTGTTTTGTTCTGTTTCATTTAAAAAATTTTTTAATTTGAGATAGGATCATACTACATAACCTAAGTTGGCCTAAATTCATTGTGGTCCCCCTGGCTCTAGACTCCTGTGTGCTCTGACTGCAGAAGTACTCCTCCTACCCTGCTTGACAGATAGATTTTGTTTTCCTTATTTTGAGGGCTGAGATTTGAAATGGCCTCTCACATGACAGGAAAGTGCTGTATTCCTGAATTACAGCCCCTGTTACAGTAAGTTTTGAACTATTCAGAATAGTACAAGAAGAATAGTACAAGAATGTGTTTGGGAGAATTTGTCAGGTAGCGCTTTTTGGTCCTTCTCTAGATGACCTGAATTTTGTTGATGATTTTAATTGTTTTTGTTTGTTTGTTTGTTTGGTTGTTTGTTTGTTTTTTTTTAAGTGACAGGGTATCATGTAGCCCAGGCAAACATCTTCAAACTTACTATGTAGTCGAGGATAATCTTGAATTTATGATTCTCCTGCCTCCAACTCCCAAATGCTGAGATTACAGATTCATGCCATCATAATTGTTATATGGAATGCTGCAGATTGAACTTGGGCCTTCTGCATGCTAAGTAGGCACTCTGCCAACTTACCTACATTCCTAGTCCTTATCAGAGACATTAGCTAGCATGTTTTTGTACGACTGTAGAATCAACAACCATACAGACTTTCATTTTGGTGGGGTGCTGGGTTTTGGGAACTTATTAGACATCCAACTTCCCCTGTCTCTCCCCAG
Seq C2 exon
CCTCTGTGTCCAGATGTTTGACTGGTTTGACTACCATGGCCACATGTGTATCTCCTTTGAGCTTCTGGGCCTTAGCACCTTCGATTTCCTCAAAGACAACAACTACCTGCCCTACCCCATCCACCAAGTGCGCCACATGGCCTTCCAGCTCTGCCAGGCCGTCAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000068917-Clk2:NM_007712:6
Average complexity
IR-C
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=FE(12.3=100)

							
A:
NA

							
C2:
PF0006920=Pkinase=PD(29.5=92.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000113861





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000088445, ENSMUSP00000113390, ENSMUSP00000122634
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:155266896-155268009 
ALTERNATIVE
HsaINT0036440
(CLK2)
Human
(hg19)
chr1:155236687-155237800 
ALTERNATIVE
HsaINT0036440
(CLK2)
Rat
(rn6)
chr2:188482761-188485332 
LOW PSI
RnoINT0037385
(Clk2)
Cow
(bosTau6)
chr3:15427136-15427934 
LOW PSI
BtaINT0039390
(CLK2)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr25:1648818-1649038 
GgaINT0140047
(Q5ZJ82_CHICK)
Zebrafish
(danRer10)
chr19:9242187-9242311 
LOW PSI
DreINT0047609
(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"