Special

MmuINT0139786 @ mm9

Intron Retention

Gene
ENSMUSG00000023033 | Scn8a
Description
sodium channel, voltage-gated, type VIII, alpha [Source:MGI Symbol;Acc:MGI:103169]
Coordinates
chr15:100843670-100846525:+
Coord C1 exon
chr15:100843670-100844026
Coord A exon
chr15:100844027-100846054
Coord C2 exon
chr15:100846055-100846525
Length
2028 bp
Sequences
Splice sites
5' ss Seq
GTGGTTAGT
5' ss Score
4.94
3' ss Seq
GGCGGCTGCTGCTTCTATAGGTG
3' ss Score
6.59
Exon sequences
Seq C1 exon
CTCCGAGTCTTCAAATTGGCCAAGTCCTGGCCCACCCTGAACATGCTGATCAAGATCATTGGGAACTCCGTTGGCGCCCTGGGCAACCTGACCCTGGTGCTGGCCATCATTGTCTTCATCTTTGCCGTGGTGGGGATGCAGCTCTTTGGAAAGAGCTACAAGGAGTGCGTCTGTAAGATCAGCCAGGAGTGCAAGCTCCCGCGCTGGCACATGAACGACTTCTTCCACTCCTTCCTCATCGTCTTCCGAGTGCTGTGTGGGGAGTGGATCGAGACCATGTGGGATTGCATGGAAGTGGCCGGCCAGGCCATGTGCCTTATCGTGTTCATGATGGTCATGGTCATCGGCAACCTGGTG
Seq A exon
GTTAGTACCAACGTCTTCTTCTCCACCACCTTCTCTGGTGAACTCTTTCCTGGCCCAGATCTGTGTTAAGGCCCATCAGCTACCATCTCCCAAATCTCAATGACCAGAAATGTCCGCAGACTTTGCCACGTGTTCAGTGGGTAACTTGTGCTCCTGAGAGCAGGGAAAGCAGCTCACATGGTCGCTATAAAGTGGCTCACACAGTCCCTATAGAGCAACTCACGCAATCCCTATAAACCCACATCAGTTCTCCCAGTTCTTCTGTAAAAAGCTTCCTTGCACTGGACACATTCCTTGAAGCCAACCATGGCTCTCCCATAATAAAGACAGTCACCACGAAGCATCTGCAATCCCTGACATTCTCCACACGCCTCCCCCAAGTCCAGCTCCTTCCCCCACCCCTTTTCTGCAGGCAGCTCCTTCCTTTATATTTCTCTCTTCACATATTCTTGTACCCACAGCCTTCCTCACAGCATGTCTTGGCTGCATCTTTGCATTTCTATAGTAGGATCAGAGAACTACCTGCATCATACTCACACAAGGTGCATTTAGTAAAAGAAAGATCGAGCCAGGCCCTGTACCAGATCAGAGTCTCTTCAGGGTAGGCCAAGGAGATATATGTGCTACCAGATGGTAACAGTGTTACCAGACATCCAGCTGCCTCCAGCTGGCTACACTGTATCAGCCCTTCTCTGTCTCTGCCCCAACCTTCTGATGTAGCTAACAGGAATGACTCCTTGAGATCTTGGTCATCATTTATACCCCTTCATTTAAGAGCAGTTAGCAAGCTGGGTGGTTCACTCCTGTAATGCCAGCCATCAGGAGGCTGCGACATCGGGATTGTGAGGTTACGGCCAGTTTGGGCTACATAATGAGACCAAAACAGGAGTGTGTGTTATCCAACACAGTAAAATGAGGAATTTTACTTGCATTTCACTCCTTGGCATCTGGCTCTGCAGTAGACACTGAAGTCAGCGTACTGTCCTGCTCAGGCTTTGAACTCGTGACTCTGGTGGTCCTGCCTTAGCTTTCCATGTAGCCAGTTTACAGGCCCTGCCCCTGCTCCTAGCAAAGGGGTTTTTGTAAACACTAAGAAAGCAGAGATAACTCACTCTTTTTTTGCTTAGTTTTTAATACGTTACAGGACCTTGCACACATATTGTGCACATGTTCTGCCATTAAAGTGTACCCAAACTCCAGAGCACATTCTTGAGGGAAGGTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTACGTGTGTATATATATACATACTAGTTTTGCCTTTTTGGTTTGTTTACGAAAGTATGGCTCTAGGAACTTAATTTTATTTTTCTAACACGGGCCCTTGGAGACATCTGCTATTAGAAATGCATGACTCTGCGCACTCCTCTGCCCTCCCCAGTCATCCATACAGGCATTTTTGGTTTGGGTTTTGAGTAATTTTCTTTCAAAGTGAATACAGCCTTTGCTTCTGTCATAAGAAAATTAATATATTTTGGGCCTTGTCATACAAACGTAAAAGTAGAGAAGAGCCAGGAAAAGTGCAAAACTACTTACAGTAAAACCAAAAGAAATCTGCATCTGGTAGTGTGAACATTTAAAATAACACACGGAGAGGCTGAACACTTAGCACGCTAGCGTGCACAAGGTCAGGCGTTCCATCTTTTGCACACACACACAAAATGGATAAAATGAACAGCTGGGTGTGGTGGCACACGCCTTTAATCCCAGCACTCGGGAGGCAGAGGCAGGCGGGTTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTTGAAAACCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAACTATGACAGGAGCCAACACAGCACAGAAACCTCTATGTGACTCTGTTGGCTTCCAATTTGTAACTCTGAGGAAAGAGGATAACTTCCTAAGACAATTCCACATTTGCTCCTTTTTCTGCGGCGGCTGCTGCTTCTATAG
Seq C2 exon
GTGCTGAACTTATTTCTGGCCTTGCTTCTGAGCTCCTTCAGCGCAGACAATCTGGCGGCCACGGACGACGACGGGGAAATGAACAACCTGCAGATATCGGTGATCCGGATCAAGAAGGGCGTGGCCTGGGCCAAAGTGAAGGTGCATGCCTTCATGCAGGCACACTTCAAGCAACGGGAGGCTGATGAAGTGAAACCTTTAGACGAGCTGTATGAGAAGAAGGCCAACTGCATCGCCAACCACACCGGCGTGGACATTCACAGGAACGGCGACTTCCAGAAAAATGGAAATGGCACCACTAGCGGCATCGGCAGCAGCGTGGAGAAGTACATCATCGACGAGGACCACATGTCCTTCATTAACAACCCAAACCTGACCGTGCGGGTGCCCATTGCTGTGGGCGAGTCTGATTTCGAGAACCTCAACACAGAGGATGTTAGCAGCGAGTCAGACCCCGAAGGCAGCAAAGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023033-Scn8a:NM_011323:15
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=0.223
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0052026=Ion_trans=FE(62.1=100)

							
A:
NA

							
C2:
PF0052026=Ion_trans=PD(4.2=5.1),PF065128=Na_trans_assoc=PU(61.0=84.7)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000080842





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000104535, ENSMUSP00000104536, ENSMUSP00000104537, ENSMUSP00000104538
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:51766028-51768864 
ALTERNATIVE
HsaINT0145950
(SCN8A)
Human
(hg19)
chr12:52159812-52162648 
LOW PSI
HsaINT0145950
(SCN8A)
Rat
(rn6)
chr7:142655580-142657738 
LOW PSI
RnoINT0131694
(Scn8a)
Cow
(bosTau6)
chr5:28237615-28240454 
ALTERNATIVE
BtaINT0129524
(SCN8A)
Chicken
(galGal4)
chrLGE22C19W28_E50C23:90707-91418 
LOW PSI
GgaINT1024554
(SCN8A)
Chicken
(galGal3)
chrE22C19W28_E50C23:65345-66056 
LOW PSI
GgaINT0000892
(SCN8A)
Zebrafish
(danRer10)
chr23:27353163-27356816 
LOW PSI
DreINT0131538
(scn8aa)
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"