Special

MmuALTA0016217-2/2 @ mm9

Alternative 3'ss

Gene
ENSMUSG00000043535 | Setx
Description
senataxin [Source:MGI Symbol;Acc:MGI:2443480]
Coordinates
chr2:29026683-29027928:+
Coord C1 exon
chr2:29026683-29026870
Coord A exon
chr2:29027762-29027835
Coord C2 exon
chr2:29027836-29027928
Length
74 bp
Sequences
Splice sites
5' ss Seq
TAGGTGGGT
5' ss Score
5.56
3' ss Seq
CCTGGTTCTGTCTCACACAGAAA
3' ss Score
8.44
Exon sequences
Seq C1 exon
AAAGCACAGGAGTATGGCTATGACCAGTCGATGATGGCCCGATTCTGCAAGCTGCTGGAAGAGAATGTGGAGCAGAACATGATTGGCAGGCTGCCGGTGTTACAGCTTACCATTCAGTACAGGATGCATCCAGACATATGTCTTTTCCCTTCTAATTACGTTTATAACAAAAACCTGAAGACAAATAG
Seq A exon
AAAATAAAAGAAGAAGATATTGATAAAATGTGTGCTTTAGAGCATATTTTCTGAATATGATTGCTTTTCTATAG
Seq C2 exon
ATTGACTGAATCCATTCGATGTTCATCAGAGTGGCCATTTCAGCCCTACCTCGTGTTTGATGTTGGAGATGGTTCAGAACGACGGGATAATGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043535-37-34,37-33-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption when splice site is used (sequence inclusion)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.016
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF130861=AAA_11=PD(0.1=0.0),PF130871=AAA_12=PU(21.4=87.3)

							
A:
NA

							
C2:
PF130871=AAA_12=FE(15.3=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000051492





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000119176
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr9:135152619-135152620 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr11:102385955-102385956 
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCCGGTGTTACAGCTTACCAT

				
R: 
TCCCGTCGTTCTGAACCATCT

				
Band lengths: 
183-257

			

		

	





	
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
  • 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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