Special

MmuEX0041276 @ mm10

Exon Skipping

Gene
ENSMUSG00000023033 | Scn8a
Description
sodium channel, voltage-gated, type VIII, alpha [Source:MGI Symbol;Acc:MGI:103169]
Coordinates
chr15:100957461-100959694:+
Coord C1 exon
chr15:100957461-100957589
Coord A exon
chr15:100959340-100959431
Coord C2 exon
chr15:100959603-100959694
Length
92 bp
Sequences
Splice sites
3' ss Seq
ACTTTGGTTTGATTCTGCAGGTA
3' ss Score
9.14
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
Exon sequences
Seq C1 exon
GTACACATTCACAGGGATTTACACATTTGAATCACTGGTGAAAATCATCGCCAGAGGTTTCTGCATAGACGGCTTCACCTTCTTACGAGACCCGTGGAACTGGTTAGACTTCAGTGTCATCATGATGGC
Seq A exon
GTATATAACAGAGTTTGTAAACCTAGGCAATGTTTCAGCTCTACGCACTTTCAGGGTACTGAGGGCTTTGAAAACTATTTCGGTAATCCCAG
Seq C2 exon
ATATGTGACAGAGTTTGTGGACCTGGGCAATGTCTCAGCGCTGAGAACATTCAGGGTTCTCCGAGCTTTGAAAACTATCTCTGTAATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023033-'22-25,'22-24,23-25
Average complexity
C2
Mappability confidence:
100%=100=100%
Protein Impact





	

	
In the CDS, with uncertain impact





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0052026=Ion_trans=FE(17.1=100)

							
A:
PF0052026=Ion_trans=FE(12.4=100)

							
C2:
PF0052026=Ion_trans=FE(12.4=100)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000080842





     
                   









    
Main Skipping Isoform:
ENSMUSP00000104537





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000143876, ENSMUSP00000143879, ENSMUSP00000144013, ENSMUSP00000144232, ENSMUSP00000144371
          









    
Other Skipping Isoforms:
ENSMUSP00000104536, ENSMUSP00000104538
  



Associated events







Other assemblies


mm9




Conservation


Human
(hg38)
chr12:51688758-51688849 
ALTERNATIVE
HsaEX0056574
(SCN8A)
Human
(hg19)
chr12:52082542-52082633 
ALTERNATIVE
HsaEX0056574
(SCN8A)
Rat
(rn6)
chr7:142598064-142598155 
ALTERNATIVE
RnoEX0078601
(Scn8a)
Cow
(bosTau6)
chr5:28297742-28297833 
ALTERNATIVE
BtaEX0031586
(SCN8A)
Chicken
(galGal4)
chrLGE22C19W28_E50C23:104801-104892 
ALTERNATIVE
GgaEX1051194
(SCN8A)
Chicken
(galGal3)
chrE22C19W28_E50C23:79439-79530 
ALTERNATIVE
GgaEX0008581
(SCN8A)
Zebrafish
(danRer10)
chr23:27384255-27384346 
ALTERNATIVE
DreEX0064542
(scn8aa)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGTGAAAATCATCGCCAGAGGT

				
R: 
TTTTCAAAGCTCGGAGAACCCT

				
Band lengths: 
167-259

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 1 annotated functions for this event 


PMID: 15664175
This event
Mutually exclusive exons 5A and 5N alter voltage-dependent gating and/or interactions with a blocking subunit. From Vuong et al, Nat Rev Neurosci 2016.


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Pre-implantation embryo development
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types





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