Special

MmuINT0139735 @ mm9

Intron Retention

Gene
ENSMUSG00000032511 | Scn5a
Description
sodium channel, voltage-gated, type V, alpha [Source:MGI Symbol;Acc:MGI:98251]
Coordinates
chr9:119422099-119425182:-
Coord C1 exon
chr9:119425021-119425182
Coord A exon
chr9:119422220-119425020
Coord C2 exon
chr9:119422099-119422219
Length
2801 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACA
5' ss Score
8.1
3' ss Seq
TCCCCTCCCCTCCCCCACAGACT
3' ss Score
12.56
Exon sequences
Seq C1 exon
CAGGAATCCCAAGTTGTGTCTGGTGGCCACGAGCCCCCCCAGGAGCCCAGGGCCTGGAGCCAGGTGTCAGAGACCACATCCTCTGAAGCCGAGGCCAGTACGTCTCAGGCAGACTGGCAGCAAGAGCGGGAAGCGGAGCCCCGGGCCCCGGGGTGCGGTGAG
Seq A exon
GTAACAGTGGGGTCTGCTGCTGGGGCCAGGGTCAGGCTGTGAGGGGCCGCAGCACTGGCTACGTTTACCAAGGGAAACCAGAGCAAGTGTGTCACGGGCAGCATGGAGATGGTTGCAGAGAAGAGGGTGGGAAGCCAATGTCCTGACAGGGAGAGATGGTGTCCATCCCAGCTCAGGACTCTGAGGCCCGACTAAGCCAGTCCATCCACGTGTTCACCCTTCTCACGCTTTGCCCTTGTGTTCTTGTGCTGATCGGCAAGCGTTTGTCCTGTGACTTTCCGTGTCCAAAGAGGGCTTGGATGATCTTCAGAACAGACCTCCCCACATCTGTCAACTGATGCCTCCTCCCTGTGTTCCCTGCAAAGATTACAAAGAGGGGATGGGGCATCTCAGCCTGTTATCAGGAATTACCGTGGCCACAAAAAGACTTTACTTTGAATTAACTGCCACACACTTGGGAGCTTTTGTGTTTAAAAAAAAAAAATCCACACTTTTTGTTTCTCTTGAAAACTTGAGAGTGGTACTACCCTACTGTAGACAGGAGGTAGCCATTCCCCAGCCTGCCCGATTGCATGTGTGACCTGCCTGGCTTCCTCCGCAGAGCCTCCAAGCCAAGGGCTAACCAACTGCGCTGTTCAGCCTCACTTGCTTCAAGCATGTGGAAAGGAAGTCATGTGCTCAGAGAGTGCCGGGTGACCTCCGTCCTCAGCCCAGTGCTTGGGACTTTGGTCCTAGTGTAAGACAGGCCCCAGGATGCTCCACCGTCGTGACTGATCTTGGAGCATGAGGCCCTGGTGACTGTCCTCACCATGGGGGTTGGCCTTCTCCCTAGATGGCCTAACACTTGACTTGGGTTAGGAGGACCCGGGATCCTAAGCCTCAGGAGAGAGTGTGAGCTTTGTGGCTTCTTCCCTTCAGGTGTTTGTGGTCTGGGGAGAGGAGGCGAGAAAAATGCCGTGGTGTTCCCGAGGAAAGGACTTCTTCCAGGCTGGGCCTGTAGCTGGGTTGGTAGAGGGCTTGCATAGTGCACCCCTAGCACTGCATAAACTGGGAGTATCGGCCTACAGTTGTAATCCCAGTGCTTGGGAAGTAGAGGCCGGAAGATCAGAAGTTCAAGGTCAACAGCAGCTGCAGTGAATTCCTGTTTCTGACAGAAAGGAACAGGGAGGGAGAGGAAAGGAGCTTCCTCCCTCCTGCAGTAGGATCCTGAGAACTCCATGACCACCCTCTGGGCCATGCTCAGCTCTGAGCCTGCAAAACCCCAGCTGGATAGCCAGCGCATGGGCCAGGAGACGGAGCCCTACCCCTCTGGCCACTCCAAGCAGGCTGTCCCCTCCCCTGAGACTTAGTCGCTGAGACCACAAACCTCAGAAGTGACAAGTAACAGGAGGTACAGATGTGGGCATGGGGATTCATCCCAGGAAGGGGAAAGAAGGCAGCAGGGACCAGAGCCAGGCTCCAGCATTCAATCAAGAGCCTAGGCTGGCCGCGGGCAGCCAGCTGAGAGGAGAGTGAGACAGGGTAGAAGCAAGTCGGTGGGGGATGAGGGGTCCTTTCTTTATGGAGGCTCTCCTGACTCTTCTGTCATTAAGTTCTGTTCCCCAGAAACAGAGGTAGGGACGGGGACTTCTGTGTAAATGACTTGTAGAGGCAGTGCACCCTAGAGAGGCCAGGAAGGACACAAGAGAAGCATATTTGGAGAAGAAAGGAGCTAGACCAAGGCCAAGAGCAGGTTTGACTTCAGCGTGTGCTAGTGGGGAGCTACAGAGCATCAAACTGGACCCCCTGCGCTGTCCCACATTAAGGCTGAGGTGACTACCCAAGGGCCAGTCCACTGGCTAAGCTGGAGGAGGGGCCGGCTAAGCCTCAGGTTTCACGGTGGCGGGACAGGGTGTTCTACCTACTCACAGGCATGTGACATTGCCCTCAGCCACAAGGCACAGACACTCACAGGCCGTCATATGTCCTTCCTACAGCAGAGGTCCTCACCCTTCCTGAGGCTTCGACCCTTTGATACAGTTTCTCATGTGGTGGTGACCCCCACACACACACCAGAAAATCATTTCGTTGTTACTCTGTAACTATAATTTTGCCACCCTTTGATTCAGTTTCTCATGTAGTGGTGACCCCCCCACACACCAGAAAAATCATTTCGTTGTTACTCTGTAACTATAATTTTGCTACTGTTATCGATCCTAATGTGAATTTTGTGGGCAATAGAGATTTGCCGAGGGGGTTGCAACCCAAAAGGTTGGAAACCACTGACCTGGGACCTCCCTGGGAACCAAGCAAGTTCTCAAGGTCTAGGGCCAGGGAGGGAAGGTTCCAGCACTTTCTCTGCCCCAGTTGTAGCGTGTGTGAGGTGAGCGGGATGCATGTTCTGCTGCTGGCATGTTCTCTGTATGTCTGACCTGCTGCTGTGTGCCCGCGTCTTGGTTTTGATTCTGTTCTGGATAATGTGTCTGGGTACTAATGGGTGATTCCCTAGTCCCCGCCATTTTGTCTGTCTTGTCCAAGCTAGATGTGTTCCTTCCTCTGAGTTCTCAAAAATCCCTCACTCCGGCACACCCCAGCCCTAAACCCCACACGCCAGAACCACAGACCCAGGAGTCCTGAATCCCAGACTCCACTCCACCCTCCCTGAGTGGCTCTGTGGCAGACATTGAGACACCTCCACCTCAGAGTCACGGGTGTGCAAAGAGGGAGCCATCTGCACTCAACCTAGGCTTACCCCAGATGCTAGGCTGGAGCTGGAGGCTGGTCCTCAGCCCACACCATCCCTCCCCTCCCCTCCCCCACAG
Seq C2 exon
ACTCCCGAGGACAGTTACTCCGAGGGTAGCACCGCTGACATGACCAACACCGCAGACCTCCTGGAGCAAATCCCAGACCTCGGGGAGGACGTCAAGGACCCAGAGGACTGCTTCACTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032511-Scn5a:NM_021544:18
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=0.683
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF065128=Na_trans_assoc=FE(19.8=100)

							
A:
NA

							
C2:
PF065128=Na_trans_assoc=FE(15.2=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000112838





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000066228, ENSMUSP00000113272
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr3:38576782-38579333 
LOW PSI
HsaINT1041032
(SCN5A)
Human
(hg19)
chr3:38618273-38620824 
HsaINT0145893
(SCN5A)
Rat
(rn6)
chr8:128198614-128201360 
LOW PSI
RnoINT0131647
(Scn5a)
Cow
(bosTau6)
chr22:12046531-12049373 
LOW PSI
BtaINT0129474
(SCN5A)
Chicken
(galGal4)
chr2:5559149-5565161 
ALTERNATIVE
GgaINT1024546
(SCN5A)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr6:10029231-10034423 
ALTERNATIVE
DreINT0131451
(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
  • 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"