Special

MmuINT0139675 @ mm9

Intron Retention

Gene
ENSMUSG00000057182 | Scn3a
Description
sodium channel, voltage-gated, type III, alpha [Source:MGI Symbol;Acc:MGI:98249]
Coordinates
chr2:65332980-65335783:-
Coord C1 exon
chr2:65335427-65335783
Coord A exon
chr2:65333454-65335426
Coord C2 exon
chr2:65332980-65333453
Length
1973 bp
Sequences
Splice sites
5' ss Seq
GTGGTACGT
5' ss Score
8.61
3' ss Seq
TTTCACTCTTTTGTTTTTAGGTT
3' ss Score
12.22
Exon sequences
Seq C1 exon
CTGCGAGTCTTCAAGTTGGCAAAATCCTGGCCCACACTGAATATGCTCATTAAGATCATCGGCAACTCGGTGGGCGCACTGGGCAACCTGACCCTGGTGCTGGCCATCATCGTCTTCATTTTTGCCGTGGTCGGCATGCAGCTGTTTGGAAAGAGCTACAAGGAGTGTGTTTGCAAGATCAATGAGGACTGCAAGCTCCCGCGCTGGCACATGAACGACTTCTTCCACTCCTTCCTGATAGTGTTCCGCGTGCTGTGTGGGGAGTGGATAGAGACCATGTGGGACTGCATGGAGGTCGCGGGCCAGACCATGTGCCTTATTGTGTTTATGTTGGTCATGGTGATTGGGAACCTTGTG
Seq A exon
GTACGTATGTACTGCAGATCTTTGTGAATAAGAATGAGTTTGGGGCGTAGGAAATATAATGGCTTAGGCAGTAAATATCCCGCCAATTTTACTGCCAGCCACTGAGTGTCAAATCCCCTTACAAGCAATCACTGAAGAACCATCTTATTTAACCTCTCTGAGGTCGAAGCTCCCTGTCTGTGACCATCGGATAAAATGCTCATTCTATGGAGGCTATTAGGCAGAGGGGTGCATTTAAAGCATGTTTGGGGTGGAAAACACTCTTTACTTTTTTATGTCGAAAAAAATGTATCTTCTCATCTAGGCTCACTGTATCCTGATATTATTTTCATATGACAATCTCTTTAAACCCTAAAAATTCAACTACTTTTTACATGTCATAATTCACATTGTCTTATTTAAAGGTGTGGATTAGACAGAAACTCTAAGGACAAGCTTTAAAGAAATAAAGTATTCTACTTTAGCTGTGGTTTCTAATTACTGTAGGGTACAAAATATGTTCTTATCTGCATTTGCTTTACTAAAAAGAATTACATTGTAGGATAGGCAATTACATGCACACAAACATATATATATGTATATGTACATATATATATATATATATGCAAGCATACACAGAAAGAAAGAGGCAAGCACATAACACAGAGAGACAGAGACAGAGATGAAGACAGAGAGACACAGAAGGAGCAGATTTAAAATATCTTATTCCTTAGACTCTAGAAGTGGATGGGCAAACTGCCTTTAGTTGCGTCCCCACCGCTGAGCCTCCTTAGCTTCAGTTAATCACATTGGATAAAAGGAATAGATTTGAATGCAAAAGAGAACCTAGTGGGGAGAAGTGGGATGGGTAGGTGTAGTAGGGGTGGGGGTGGGGTAGGCGTGGTCAGTGTGTATTGTACACATGAATGAAATTGTCCAAGGACAAATGTAAATTATTTTAAAAGCCCTAACATAAAGGTATGTGTCCTAATACTTAAATTCCTGAATCATATATAGTAAGAACCTATATAATAAGGTCTTCCTTTTGAGGAGTACACTTCAAATAATACTCAGAAGAATAATAGTGGGATATATACACATTCTTTTCTTTTCTTTTTTTTGGGGGGGGGCAGTTCGAGACAGGGTTTCTCTGGAGAAAATTAGATAGCCCTACATTCAGAACAAAATATGATTTTTAAATAGAAAGTAACCCAGAGATCCAAGTTTGCACTTGTTCTCCTACTACATGAGGAAACTCAGTAATTACATTTTAGGCTAAAAATGTCCCTGTGCACAAATATCCTTTTACATCAGACATGATGAGTTATCCCTGTAGTAGCTACAGACCACCAGGCACCCACCGCTGGGAGTCACAACGACACTCCACAAACCTGAGGAGAGGAGGGGTTTGCATTAGATGAGTCTGGCTGAACCATAGAACGTTTTAGAATTTTCTCCACTTTCTACACTATTTGAACAACTAAATTTTAAAGTCTGCTTGATGGGAAATGTGTTAACCCCTTGTGTAATTTGCTATCTCTGCTGTTACAGATTGTAGCCACTGGACCAAAGACATCTATGTTTCTACCATATACTGGTTTTGTACATATTAGCAGGTTATTCAATGGACAAGCTAGATAACAAAAATGAAAAATACCAATTTTTTTTTTTGGTGGTATGGCAAAAACCATTGAAAGTGGGATTTTTGTCTTCTCATTGGCGAGTCCCAGTAGATTTGATTTAGTTGTTTCTTTTTTTACCCTGTTATTATCAGTGGAGAGGGGCTTCTAAGTTACCATTCCCCTTTACCACATGTAGACATAATCATGCCCTCCCAATATTGTGTGACTTTAGTGTGGCGCCTGGTGTACACTAATCATTTGAAAGCATTTCATAAAACCACGGTAGCAAAGATCTGTGCTCCGTGTCCACCCACGGACTAGCCTTACCCGAGTGTCAGTTTTAACACGGTCCTTTCACTCTTTTGTTTTTAG
Seq C2 exon
GTTCTGAACCTCTTCCTGGCCTTATTGTTGAGTTCCTTTAGTTCAGACAACCTTGCTGCTACGGACGATGATAACGAAATGAACAACCTCCAGATCGCGGTGGGAAGGATGCAAAAGGGGATTGATTATGTGAAAAATAAGATACGGGAGTGCTTCCGAAAAGCGTTTTTTAGAAAGCCGAAAGTGATAGAAATCCACGAAGGGAACAAAATAGACAGCTGCATGTCCAATAACACGGGCGTAGTTGAAATAAGCAAAGAGCTTAACTACCTTAAAGACGGTAACGGAACCACCAGTGGCGTGGGTACTGGAAGCAGTGTGGAGAAATACGTAATTGATGAAAATGACTACATGTCATTCATCAACAACCCCAGCCTCACCGTGACGGTGCCAATTGCCGTGGGAGAGTCTGACTTTGAAAATTTAAACACGGAAGAGTTTAGCAGTGAGTCAGAACTGGAAGAAAGCAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057182-Scn3a:NM_018732:16
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=0.122
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0052026=Ion_trans=PU(91.2=99.0)

							
A:
NA

							
C2:
PF0052026=Ion_trans=PD(4.2=5.1),PF065128=Na_trans_assoc=PU(60.9=84.8)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000065023





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000041322, ENSMUSP00000097647, ENSMUSP00000128936
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:165128102-165129939 
LOW PSI
HsaINT0145838
(SCN3A)
Human
(hg19)
chr2:165984612-165986449 
LOW PSI
HsaINT0145838
(SCN3A)
Rat
(rn6)
chr3:51568680-51570797 
LOW PSI
RnoINT0131588
(Scn3a)
Cow
(bosTau6)
chr2:31244236-31246356 
LOW PSI
BtaINT0129415
(SCN3A)
Chicken
(galGal4)
chr7:19434203-19436485 
ALTERNATIVE
GgaINT0048560
(SCN3A)
Chicken
(galGal3)
chr7:21413691-21415973 
LOW PSI
GgaINT0048560
([1])
Zebrafish
(danRer10)
chr6:10034916-10039693 
LOW PSI
DreINT0131450
(scn1lab)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCTGGCCATCATCGTCTTCAT

				
R: 
CGCGATCTGGAGGTTGTTCAT

				
Band lengths: 
358-2331

			

		

	





	
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"