Special

MmuINT0139619 @ mm9

Intron Retention

Gene
ENSMUSG00000064329 | Scn1a
Description
sodium channel, voltage-gated, type I, alpha [Source:MGI Symbol;Acc:MGI:98246]
Coordinates
chr2:66137681-66140577:-
Coord C1 exon
chr2:66140423-66140577
Coord A exon
chr2:66137855-66140422
Coord C2 exon
chr2:66137681-66137854
Length
2568 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
GTGTAACCTTTTCTTTCTAGGCC
3' ss Score
9.7
Exon sequences
Seq C1 exon
GCTGTGTCCAGAGATTCAAGTGCTGTCAAATCAGCGTGGAAGAAGGAAGAGGGAAACAGTGGTGGAACCTACGGAGGACGTGCTTCCGAATAGTTGAACACAACTGGTTTGAGACCTTCATTGTGTTCATGATTCTCCTGAGTAGTGGTGCCCTG
Seq A exon
GTGAGTGAACCTTAACCCAAAGTGCTTCAGTAGCAACTGGGAAAATCTCACACTCTTTAAGCCTTTGTTTCCCATTGCCTTAGTTATCAATGAGTCTTCAATAACAACACCCTTTTATCTTCCTGCCAGATAGTTAATGACTAGCTGCATTTCTGGGTTTGCATCTATGTGTGCACACACATTTCTAATCATTCATCGATGTTTGCTTATCATGAAACAGATCAAAAAAAACGGGTCCCTTTTGCTTAGTCATTATAAACAAAGTGAATATTCCTCTTTGCTTAACTAAACATGACTATGAGGAGCACATCAGAGTTCATGTTAGTGCTATTATAGTGGTTATATATCCTCTGAGTTCTGATGAACTCTTTGTGGAAGCTTGGTAGGTCGTTGGGGACCTCTTCTCTGTCCCTTTTCATGTGTGTTCACTATTCTTGGGCTACTCAGGAAACAAATGATATTGGTAATGCTAAGTAGTGGGCACCATACCTAAGTGATTACTTAAAGACTGGATTATGTTTATAGAAACATGTTAATTTCATCAGAATCTATTTAAATTTAGATGAAAATTGTTTACATATATACAACTATATTGACAGAATTTTAGATATAAAAATATATTGAAGTCATAAAATAAAATGTTTGGAGAGATTGATAATAGAGAAACTATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATGATATATAGATTTAGATAAATGATAGAATATATACATAAATAAATAAGCACAAGTGTTTGCCTGATTAAAACACAATGACTTACAAGTTTTAAAATCAAGTATATATTTTTCTATAAAATTGTTGATGGAATAACTGTCTTCTACATATCATTATCTACATATCTGCATATCATAGACAAAAATGACTTTTCATCATTGAAAGAAATATATATTAGAAGTAAATTACCAGCTGAGGTTTATGTTAGGAAAAGGCATAGGTGGATCTAATTGAAAAGTAATATGACATTCCTATTAAGTAATGTCATACTATACGTACCAAAAAGTAAAATTATCAGCTAGATGTGGTGGTGCACACCCTTAATTCCATCAGGAAGAGGTAGACAGATGTTTGTGAGTTAGAGCCCCAGCCTACTCTACAAAGTGAGGATAGCCAGGGCTATTATACAGAGTAACCCTGTCTTGTAAAACAAACAACAAACAAACAAACAAACAAAACAAACAAACAAAAGAAAAGAAAGAAAAAGTAAAGAAGTAGAATTATCAACAAAACCCCAAAAAAGCAGTTAACTGCTTAGTAAAATAAAATTGGACAGTATATTGATAAATCACTTATTGATTTAATCTCTCTCCTATAAAAAAAACATAATAATGAGAGAAATTTGGTTTTTGCTGGAAGTCAAGCTACTGGTCTCACGTAGACAACTGTTCTAGCCACTGAGTCACACCCACAGCATAGAAACAAAGAAACAGGGTACAGAGCTAAAGAAAGAATTGTCAACTGAGGAATATAGAATGGCTGAGAAGCACCTATAAAAGTGTTCAACATCCTTAATCATAAGAGAAATGCAAATCAAAACAGCCCTGAGATTCTACCTCATACCAGTCAGAATGGCTAAGGTCAAAAAGTGGAATGGATACAGAAAACGTGGTACATTTACACAATGGAGTCAGCTATTAAGACAATGAAATTATGAAATTCTTAGGCAAATGGATGAAACTAGAAAATATCATCCTGAGTGAGTTAACCCAATCACAAAAGAACACACATGGTATGCACTCACTGAGAAGTGGATATTAGCCCAAAAGCTCCAAATACCCAAGATACAATTCACAGACCACATGAAACTAAAGAAGGAAGACCAAAGTGTGGGTGCTTTGGTCCTTCTTAGAAAGGGGAACAAAATACTCATAGGAACAAATATGGAGACAAAGTATAGAGCAGAGACTGAAGGAAAGGCCATCCAGAGTCTGTCCTACCTGGGAATTCATCCCATATACAGTCACCAAACCCAGACACTATTGTGAATGCCAAGAAATGCTTGCTGAAAGAAGCCTGATATAGCTCTCTCCTATGAGGCCTGTCAAAGCCTTACAAATGCAGGGGGATGGGGGATGGGATAGGGGCTTTCCAAGAGTGGGGAACTGGGAAAGGGGATAACATTTGAGATGTAAATAAAGAAAATATCCAATAACAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGACACGCCATGGCTGCATGGAATGTGACATTAAGAAATACATCCTGGCTTAGCCAATTGACTCAGGAAATTACCATTTCACTTCAGGAAGAGTGAAGTCATGAAGACACCTCCCCCCTCTCTGGTTTTAGTAGCTATCTAAAGTATATCTTTCTCTCTGGTTTATAAGGATAAAACTCAGAGAGTAACAAAGCAATAGCAATACTGTATCCCCGTTCTTCCATCCCAAGGAAATACCATGTGCATATATAATCAGAAAAAGCTAGCTGTAAGATTCTAGTAGTGTTTGAAAGCTAAAATGTGTAACCTTTTCTTTCTAG
Seq C2 exon
GCCTTTGAGGATATATATATTGATCAGCGAAAGACGATCAAAACCATGCTGGAGTATGCTGACAAAGTCTTCACTTACATTTTCATCCTGGAGATGCTCCTCAAATGGGTGGCCTATGGCTATCAAACATACTTCACCAATGCCTGGTGTTGGCTAGACTTCTTAATTGTTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000064329-Scn1a:NM_018733:19
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:
PF065128=Na_trans_assoc=PD(19.7=84.6)

							
A:
NA

							
C2:
PF0052026=Ion_trans=PU(17.0=67.2)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000107985





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000076697, ENSMUSP00000092558, ENSMUSP00000107985f5314A, ENSMUSP00000107990
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:166012283-166013743 
LOW PSI
HsaINT0145778
(SCN1A)
Human
(hg19)
chr2:166868793-166870253 
LOW PSI
HsaINT0145778
(SCN1A)
Rat
(rn6)
chr3:52418216-52420096 
LOW PSI
RnoINT0131531
(Scn1a)
Cow
(bosTau6)
chr2:30390598-30392291 
LOW PSI
BtaINT0129359
(SCN1A)
Chicken
(galGal4)
chr7:19124474-19126509 
LOW PSI
GgaINT0047675
(SCN1A)
Chicken
(galGal3)
chr7:21100871-21102906 
LOW PSI
GgaINT0047675
(E1C4S3_CHICK)
Zebrafish
(danRer10)
chr9:50225383-50227056 
LOW PSI
DreINT0131422
(scn1a)
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"