Special

MmuINT0139621 @ mm9

Intron Retention

Gene
ENSMUSG00000064329 | Scn1a
Description
sodium channel, voltage-gated, type I, alpha [Source:MGI Symbol;Acc:MGI:98246]
Coordinates
chr2:66134810-66137854:-
Coord C1 exon
chr2:66137681-66137854
Coord A exon
chr2:66134933-66137680
Coord C2 exon
chr2:66134810-66134932
Length
2748 bp
Sequences
Splice sites
5' ss Seq
GATGTAGGT
5' ss Score
4.9
3' ss Seq
TTGTTATTTGTATTGTACAGGTT
3' ss Score
8.5
Exon sequences
Seq C1 exon
GCCTTTGAGGATATATATATTGATCAGCGAAAGACGATCAAAACCATGCTGGAGTATGCTGACAAAGTCTTCACTTACATTTTCATCCTGGAGATGCTCCTCAAATGGGTGGCCTATGGCTATCAAACATACTTCACCAATGCCTGGTGTTGGCTAGACTTCTTAATTGTTGAT
Seq A exon
GTAGGTATTTTCCATGTCGTGCCTTTTGTTTGAGGGAGTTTGTCTTGTTTGTATCCCAATTCTAAACCAATGAATGAGTCTCGGGCCACTGTGTTGTGATGACAAGATAGGCTCCCCAGCCCTAAACTCTCTCACCTAATAATAGCATAGAACTTACAAGTTCTGGACTAATTTACTAACTAATTTAAAAAGAGGAGATAAGATCTAGTAGGAAAACCAAATTTAAACAATGATATTGGTAATATATAATGCAAATGATAGAAAAAGACATTTAAAAGGTATGGTGTCTATTCTGCCATGTTATAAACTTGACCGACTCCAGATTGGGTCTTCATGCACTTATTCATTGATGTTCTTCCCCAGTGGTAAATAATAGCAAGATACAGAAGGGATGGTGAGCACTATTGTAATCTTATAAATCTTTCTTATCTACTGGAAGATTTTACGGAGAGATTTTTAAGTCTATTACAAGTAAGGTTACAGAGGGTAGGGGAAAACAAACCTACTTAATGATGAGGAAGAAATTTTCTTTTATGTAAATGAGATTTACAGAGTCCTTGATGTACCAAATATCCTTATGGAGAATTTTAGTTATGAATAGTGAGAATTTGAGAATAGTGAGTTATGGAGAATTTTAGTTATGAATAGTGAGAATTTGAGAATAGTGAGTTATGGAGAATTTTAGTTATGAATACTTAAAAACAAGTAACAGGGCCACTCAGTGAGGCCAAAATGGAGTGAGCAAATTGATGGAAATCTCAAAGGAGTCATCAGTTTTACAGAAAAGAGAGAGGAAATTAATCAATAGGCATTAGCTTATGCTTTCATAACTCCAAGTGGGGTTAGGACTTGGTATTTTGCAAATTCTTTACTCTTGATATTCATTTATGTCCTTTTAATATTTTATTACTTTTAAACTTTTCATACAGTGTAAATTTTTCTACGGTGTATTTTGCATTATATTGCTTACCTTCCCCCAAGTCCTCCCAGATCCTCCTGTCTTGATATCCTGACAACTCCATTCTCTTTATAAAAAGAAAAGGAAGAAAGAGAAAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGGGAGGGAGAGAGAGAGAGAGAAAGAAAGAGAGAAAGAAAAGAAAGAAGGAAGGAAGACAGACAGAAAGACAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAAAAAGAGAAATAAAGAAAAAGAAAGACAGACAGACAGAAAGGAAGAACGAAGGAAGGAAGGAAGGAAGAGAGAGAGGAAGGAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGGAAGAAAAAAGAAAATAAAAAAATAAGCAATAAAACACAAGCAAAAACAAACAAAAAACTACAACAACAAAAAAAAAAAAAACGAAAACAACCAACCACTAAACCATAATAACAACAAAATAAGAGCACACAAACAAAAATCAAATTCGAGAACATTTGGGTAGACCAGCTACTTCTGCTCTTGCAGACTGCCCTGAGTGTGGTTCATATACCCAGTGTCACTCCCTTGAGGAAAACTGATTTTTCTCTCCCAGCATTATCAAATAGCATCTTGGTTAGGGGTAAAAACTTCCTGCTCACCTCCCCTCCCCCACGCTACAATTTAGTCCAGTTTAAATTTTCCACAAGTCTTGTCCGTCAAGTCTGTCACCATTGTGAGCTCATATGTCCCTCACCCTGTTGTATCTGGAAGACACTAATTTTCTTGGAGTCACTCCCCACCTCTAGCTCTTAAACTTTTTTAAAAAAAAATTTTATTAGTTATTTTATTTACATTTCAAATGTTATCCCCTTTTTTTTTGTTTCCCCTCTGAAAACCCCTTATCCCTTCCCAACTCCCCATGCTTACCAACCCACCCACTCCAGCTTCCTAGCCCTGGCATTCCCCTACACTGGGGTATAGAAGCTTCATAGGAACAGCGTCCCACAAGGCCATCCTCTGCTACATATGCAGCTGGAGCCATGAGTCCCCACCATGTGTTCTCTTTGGTTAGTGGTTTAGTCCCTGGGAGCTCTGGGGGTCCTGGTTGGCTCATATTGTTGTTCCTCCTAGGGTGCTGCAAACCCCTTCAACAGCTTGGGTCCTTTCTCTAACTCCTTCACTAGGGACCCTGTGTTCAGCCCAATGGTTGGCTGAGAGCATCCACCTCTGTATTTGTCAGGCACTGGCAGAGCCTCTCAGGAGACAGCTATATCAGGCTCCTGTCAGCAAGCACTTGTTGACATCCCAGAGACTGCTCCACCTGGGGATCCATCCCATATACAGCTACCAAACCCAGACATTATTGTGGATGCCAACAAGTGCTCTTAAACTCTTTAGCCTCCTCTTCCACATAGCTCTCTAAGGAGTGAGAGGAGGGGTTTCATGAAGATATCCTATTTAGTACTGAGCTTTCCAAGGACTCTCACTCAGCACTGTCCAGTTGTGGGTCCCTGTTAACCATCACCTACTGCAAGAGAGAGCTTCTCTGGCGAGGGTTAGGTGGGGCAGTGATCTATGGATAAAGCCGTTCATCATTAGGAGTCACTATTGCTGTGTTTATTCAGTAGAATAACAGAACAGCTATGAATAAAACTTTATCTGTTGTATTAGTTGATAACTGCAAATTGGACGAAAGCGGTGTTATTGATTCATTGTTATTTGTATTGTACAG
Seq C2 exon
GTTTCATTGGTCAGTTTAACAGCAAATGCCTTGGGTTACTCTGAACTCGGGGCCATCAAATCCCTAAGGACACTAAGAGCTCTGAGACCCCTAAGAGCCTTATCACGATTTGAAGGGATGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000064329-Scn1a:NM_018733:20
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:
PF0052026=Ion_trans=PU(17.0=67.2)

							
A:
NA

							
C2:
PF0052026=Ion_trans=FE(17.5=100)

						

					

				








    
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)
chr2:166009842-166012108 
LOW PSI
HsaINT0145779
(SCN1A)
Human
(hg19)
chr2:166866352-166868618 
LOW PSI
HsaINT0145779
(SCN1A)
Rat
(rn6)
chr3:52416562-52418041 
LOW PSI
RnoINT0131532
(Scn1a)
Cow
(bosTau6)
chr2:30392466-30396512 
LOW PSI
BtaINT0129360
(SCN1A)
Chicken
(galGal4)
chr7:19126684-19128510 
LOW PSI
GgaINT0047676
(SCN1A)
Chicken
(galGal3)
chr7:21103081-21104907 
LOW PSI
GgaINT0047676
(E1C4S3_CHICK)
Zebrafish
(danRer10)
chr9:50224438-50225208 
DreINT0131423
(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"