Special

MmuINT0139656 @ mm10

Intron Retention

Gene
ENSMUSG00000075318 | Scn2a
Description
sodium channel, voltage-gated, type II, alpha [Source:MGI Symbol;Acc:MGI:98248]
Coordinates
chr2:65748772-65752134:+
Coord C1 exon
chr2:65748772-65748876
Coord A exon
chr2:65748877-65751863
Coord C2 exon
chr2:65751864-65752134
Length
2987 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGA
5' ss Score
4.19
3' ss Seq
GCCTGTGTTATTTATTCCAGAAC
3' ss Score
8.89
Exon sequences
Seq C1 exon
TTTGGAGGTCAAGACATTTTTATGACAGAAGAACAGAAGAAATACTACAATGCAATGAAGAAGCTAGGCTCAAAGAAACCACAAAAACCGATACCTCGCCCTGCT
Seq A exon
GTAAGAACAGAATTCTTTCTTATCAGTGAGCATGATGGTATATGACCCTTTGTCAGCCAAAGTTCCAGAAAGCAGCATTTTTACGAATTTCCATGTTTATATTCTGACTTGATAGCCCACATTTCTGCCATGAAGATGCATATGCTAAAATTATTTAAAATATAATGTATTATATATAAAACAAATGTAAATGCTTTTGGAGTCTCAGACAGTAAATCAGAAAGAATTACTGACACTGAGGCTATTCTTATAATGTAGTGACAATATTAAAAATATTCACATATGTCACGTGGACACAATGGATACTCTCTACTGCCTTGTTTGTGGTTTGATTGGCACAGGCAGTCCCACTGCCTGTTCAGATCAACAGGTTGAATGGAATCGTTATTGAAGCACAATCACTGTTTTTTCCTCTGCTTTTAAACGCAGCTTATCTTTGTATTTTATCCAATGCTCCTGCCCTGAAGGGGGACTATGCTATCTATCCCTCTCATGAGTTTCATAGCTCTTCCATTGTCCAGTTTTTCAGTTACTGCTAGTTCTTGTCTGAGAGTCAGGAGAGCCCCTCAGCTCTTTGATTATTTCTGAAGAAATACATCAGATATTTCTCGGTGTTCTTGGTGCTCTTCCAAATCAGTACTGAGTTTAAGACCAGTTAGTATTCTCCAAGATTTTATGGATCTATTGACAGCAATAAATAACTAGGTTCGACAAATTGTTCAGTACGAAATCTGCCAGTAGCTCAGAGACTGTGAGATACTACATTAGATAAAAGATAAGAAAAGGAAAACTAAGCCCAATGTTTGAGAAATAATATAATCTGAGTAGTTGCAAACAGGGGTATAAGATAGTCCCTCTGTGAGAAAATGTATACTCTAAATCCTTAGAACTAAGCATTTAGGAAGAAGAGGGGTATGTTTGAATTACTAAGTAGTACACTCAAGGTTTAAAACTTATTCACCATAATTAAACAATATAAATAGGATCTTGTTATGAGAACGGCAGAGTTGCATCAAAAAAAATGATTGTTAGAGCAGAATATTGGAACTGGGAGGAGGTGCTAAAGCAAAGATAACAAAGGCCTAATCAATATATTGTCAAATTATCACATCAACAAAATGAGCACACCTCAAGAGTAGAATCATTCATCTATGAATGGGGGGGGGGAGAGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCTGACTAATTAGGGAAGCTGACTAACTAGGGAAAGTTTTTTTTTCCCTTGAAGTGATTCATTACTGAGGAGTCAAGAAGAACGAAGGTCAACAGGCAGTGTGGGTTGAGATTTGAGCCGTATGTAGCCAAAAACCTTGACAGGAATGTCACATCGGGGTGCAGACAGTGGGTCCATCTGGGTCCTGCTGACTTAAAAGGAATTAAATGGGTCAGCCTTTATAGGAGTTATCTCTATCCTAAGACCACCAGAAAGCCATCAAGGTGACCCAGTCCATTTTGGTTTTATGATGATGACTCAACAACTTTGACCGAGATAGAGGATTATGCCCCGCAGATGAAGTTTGGAGCTAATTTGGTAGTCATAGGTATCCAACATCAGAGGGAAAGTGGATTTGGGGACTGTTGCCAAAGTGAAATTAAATCAAAGATGGAAGCTGAAAGTCAAGGTCAGGAAGGATGGAATGTTGGTTTGTCAATGGGAAGTTCAGAGTTGCAATGTAGGATACCTGGAGTGAGAATCATCGACATCCATTTGTAGCATTGAGTAGCCAAACATGGGAGAAGAAGACTTAGCAGTAGAGCAAAGGGTTCCAAAAATTGAGAGATTAAGTTTGAAGCACAGCAAAAGACATTCTGGAAGGGAGAGAGTGCCTAAGCACAAAAGAAGTTACACAGGATGTGAGCCAAGAATGGACAGTTCAGATCAGAGAAGAAAAGGAACTGAGTCCTTCAGGAGATGTTGAGTAACACAAGAAAAGAGTACGGGAGCCCAGAATTGTGAAATGAATAAGGTTATTAAAGAATTTCTTTACACTAATTGACTTTGATATCTACCTCCCAGCAACAACAAAAAAGGAAGAAGAATATTAGATAAAAGATTTGTCAGTTTCTCTGAGTCTAGAATTGTCCTCAGAACACAAAGACAGAGAGTTGTTAATTAATGCTTAGGACTCAGATTAATTTACAAAACATGTGCTGTGGCAGGCCAAGCCTTCGGGGCTATACAATTTCTCTCATCTCATCCAGCGACCTAAGATTTAAATGGGCTAGGACTCAGGATTAGTATTGGACATTGAAGCATTGCATTAAAATGTTATATGAGCAAGATTAAGGAGCTGTGTCTAGTTCTGCTGACAAGAACATTAAGACCAATTGTTGCTTCAAAGAGGAAGCCAGATTAAGTAACCCTTGGAGGCTGTGTCTGTGAGAAATGTGGCACCGCTTTTTCCCAGGGACCCTCCAAAGCAGATGAAGAAAGAGTAAACTAAAACAAAGCAAATCAGGGGACATCATCTGCAATGCAATGCCCTGAATCTTGTGATGGGTAGAAGAACAAGGTCTTCTGAGGGCACAGGACTGCTGCATCTTAAAACAGTGTTATCCACCAGAAAATGGGTGGTGCTGATTTCATGGAAGGAACAGGAATAGAGGAACAAACTAAATGATAGGATAGAATTTGTGTGTTATTCTGAGCTATAAAGAAAATACAGAAATCTTGCAAAGACAAACTAGAGTGCATAGAGACTAAGGCAAGAAGCTGGGATTGCAAGTAGTCAGTAGAGAAGCCTGGGAGGAAAAAACCTTATGAAGAAGCAAGAAGTAGGAATCCAGCCGAGTCAGCCCAAGAAATTCAGTAGTTGCTCATAGATGACAACAGATAACACAAGAATGGTATATTTTCACAGAATATAAAATTTCATGTTACTAAGCAGAAACCAGATACGTTGACGAGAACTTTTAAAAGAGTTTCTGAGTGTACTTGCCTGTGTTATTTATTCCAG
Seq C2 exon
AACAAGTTTCAAGGGATGGTCTTTGATTTTGTAACCAAACAAGTGTTTGACATCAGCATCATGATCCTCATCTGCCTCAACATGGTGACCATGATGGTGGAAACGGACGACCAGAGCCAAGAGATGACCAACATCCTGTATTGGATCAACCTGGTGTTCATCGTCCTGTTCACCGGCGAGTGTGTGCTCAAGCTTATCTCACTCCGTCATTATTATTTCACCATTGGATGGAACATTTTTGATTTTGTGGTGGTCATCCTCTCCATTGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075318:ENSMUST00000028377:25
Average complexity
IR
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:
NO

							
A:
NA

							
C2:
PF0052026=Ion_trans=PU(20.4=47.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000028377





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000097645, ENSMUSP00000143882
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr2:165381198-165386745 
LOW PSI
HsaINT0145814
(SCN2A)
Human
(hg19)
chr2:166237708-166243255 
LOW PSI
HsaINT0145814
(SCN2A)
Rat
(rn6)
chr3:51813497-51817507 
LOW PSI
RnoINT0131567
(Scn2a)
Cow
(bosTau6)
chr2:30986668-30991646 
ALTERNATIVE
BtaINT0129397
(SCN2A)
Chicken
(galGal4)
chr7:19319984-19321009 
LOW PSI
GgaINT0046962
(SCN2A)
Chicken
(galGal3)
chr7:21298089-21299114 
LOW PSI
GgaINT0046962
(F1NN72_CHICK)
Zebrafish
(danRer10)
chr6:10015787-10015906 
LOW PSI
DreINT0131460
(scn1lab)
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
  • 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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