Special

MmuINT0142254 @ mm9

Intron Retention

Gene
ENSMUSG00000043535 | Setx
Description
senataxin [Source:MGI Symbol;Acc:MGI:2443480]
Coordinates
chr2:29029077-29032495:+
Coord C1 exon
chr2:29029077-29029241
Coord A exon
chr2:29029242-29032396
Coord C2 exon
chr2:29032397-29032495
Length
3155 bp
Sequences
Splice sites
5' ss Seq
AGGGTGACG
5' ss Score
2.31
3' ss Seq
TTTGTGCCTTTTATAAACAGACC
3' ss Score
8.65
Exon sequences
Seq C1 exon
CTCATATATAAATGTTCAAGAAATAAAGTTGGTGATGGAAATAATTAAACTTATTAAAGAGAAAAGAAAAGATATTTCCTTCCGAAATATTGGCATAATAACCCATTACAAGGCTCAGAAGACGATGATCCAGAAGGATTTGGAGAAAGAATTTGATAAGAAAGG
Seq A exon
GTGACGTATTTTTACATGTATTTCTGGTATTTAGGTTGAATTAGGTTGTTTCTTAACAGGACTGGGGGACTGGGGTTGAATCAGGGTCTTTGTATTCTAGGCAAGTGCTCTAACGTCTCTGTTATATTGCCCAGTCTTTTTATTATTTTTGTGATCATGTCTGTAAGTTTCCCATTTGCTGTCCTCCTGCCTCAGCCACCAGGCCCTACTAAGATTGTGGTTTTGTCTCCTTATCTCTACACTAAAATTAAAGATTAAAATCTGGAAAGTCTAGCCAGGCGTGGTGGCGCACGCCTTTAATCCCAGCACTCGGGAGGCAGAGGCAGGCGGATTTCTTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTGGGAAAACTAAGGAAAAAAAAAATCTGGAAAGTCAGTGTCAGGTGTGTGGTGAGAAACATTTAACTCCAGCACTTGGAAGGTGGAGGCAGGACGATCAGTCAAGGTCATCCTTGGTACCGTAGTTTCTTTTCCCGTTACTATGACAAAATATTCTGACAAAAGCATTAAAGGGTTTATTTCACCTCACAGTTTATTACAGCCCATCATGATGGGGGAATCAAGGCAGCAAGACTCTGAAGCATCCAAGCAGCAGCAGAAGAGCAGTGAATTTATGCATGCTAGTGATGAGCTCGGTTCCTCCACTGTTACACAGTCCGGGATCTCCAGCCTAGAGAATGGTGCCACCCACACTGGGTGGGTCTTCCCAACTCAACTAACACCATCAATAAATAACCCCCAGAGACATGCCCCCAACCCATTTCTTAGGCTAGTACAGGTTTTACCAAGTTGACTATTAATACTAATCATTATATTCTGCTGCATAGTGAGTTCAAGGCTGACCTGGGCTATGTGATCCCCATCTCAACAAAACAGTCTGGAGAGAGATGGCTCAGTGGTTAAAAGCACTTGCATTGCAATCATAAAGATCAGAGTTCAGATCTCAGTACTTAGACAACAAGCTGAGGGTTGTTTCTTTGTAACCACAGCTCTGACTTGGGCAGAGATGGGGATGTTTTGGGGTTTGCTGGCTTCCAGGCTGTCTGAGAAAGCATGTGCTTTCAAGCTGCTTCTTGTGGCCTTTCCTCACATGCACACATGCACTGTTACTCCTAAGATAAAATACCAAAACTAGCAACTTTTAAAGTTTCTTATCTAGAAACACACAAAACTGACTTTAGAGAAAATTTTAAAAATCCGGAGATTCTATCTCTCTCTCTCTCTCTGTCTCTCTCTCTCTCTCTCTATCTATCTAGCACACCTCTCAGTGTAGTGACCAAAACCTGAAAAACAGGTTAGACTTGACTGCTGAGTTTCGCCAAATGTCAATCCACAGTCAGCACTAACACAGCTGTGTGTCTGCAGTCCTTGCACTCTGGAGTCTGAGGCAGGAGGATCTAGAGTTTTAGACCAACCTGGGCTACGTAGGTAATACCCTATGTGAAAACAGCAGAAAAAGCCAGTAATACTTAGGACTTGACAAAAGCCTAATAAAACTTCCTGGTTTTCTTTTTTTAATTTATGTAAAGCAGGCACACCGTGGTGTGCATATGGTCAGAGAACAACTTTCAGTAATTGGTTCTGGATAGAACTCCAGTCATCGGCTTGGTGGCAAGCTGCCTTACACGTTTTGAACCATGTTGCTGGCTCCAAGGACACTGTAATTTTTTTATGACACCAAAGCAGAGAAGGTGTTACAAGAGCCACAGGACCGATAACACTAATGATTGTAGATTTAAGAATGCTAAATGGACAGCTGCAGACTGAATCCAGAGCATATTAAGGGACTGTATATCATGACCACATGAAATTTATCCCAGAGTGCAGTGTTGGCTAACTATCTTGCTGGAATAAGAGAAGGAAGCAAGAGTTGGCAGCTCACTCTTGGAGCCTCCATACTTGGGAATACAGGGCAGGATAAACATAATGAGCTTGAAGCCACCCTAGGTTTCTGAATGGAGACTGTATCTTAAAGAACAGACAATTAGTATGGCATGTGGGTCACCTTCTCAATCTAACAGATGACAGAAAAGACTTAACAAAGCCTATCATCTTTCACAACAGAAAAAACTATTAGGAGTACAGAGAAAATTTCTTAACTTGATTGTCTATGGAAAACACATAGGTAACATTGATCTGTCATGGTTCAGCAGTCTTTCCTGTAGACCACGGAGGACATTTTTCTTACTACTTCTGTTGTCCATTGCAATAGACACTCTAGCCAAAGCAAGACTTTGTTGTGTGTAAGTCTGTAAATAATTCAGCATGGTTATATATAGATCCAGTTAATGAAGCTACATAAAGAAGCTCTTAGGGTTAACACTTGAGTTTAAGAGACTTGTAGAATACAGGATCAATATGTAAAAAGTGGTTGTCGGTTAATAGTCTGCTCAAGAAGTTAGAAACATTCTATTTATAATAAATAGCACCAAAAGTAATAAAATACTTAGAAGTAAATAAGACCAGTAGTAGTATAAGATGTATCCACTGAAAACTACAAAGCATGTTACAAGAAAAAATTAAATACTCAGGACACAGGAAGAAGGTCGTGGATAAGAAGACACAGCCCCAGTGGCTGTACTCAAAGAAGACTGGTACTTTGTCTGCCAGAATTCCACCCGCCTCTGACAGAAGTCAAGCTGATGAAGCTATAGAAGACTCTGAAAGGCCTAAGGAAACATACATACAAATATATATAGCCTCAGACTAGGAGATGGTTTCTTATGGACTTCATAAACACTAAGAATTGTGTTTCAGAAGATGCCATCAAAAGAATGAAGGATGTTATGCTGACCTCAAGCATATCTGAATGTACTGTCCTGTCTGGAACATACAACAAACCTTACAACTCGGGACATTCGGATTTTGGTTTTCACAACAGTGTTTTTCTCTCTGTAGCCCTGGCTATCCTGGAATATACTCTGTAGACCAGGCTGACCTCAGAGTCTCTCTGCCTCTGCCTCCAAGTGCTAGGATCAAAGGTGTGCGCCATCACTGCCCGGAATCCAATGAAGAGTTTTAAATACTGCCTATGTGCATGTATTTCATAATTTAAATGTTTTAGTAAACTTTGTGCCTTTTATAAACAG
Seq C2 exon
ACCTGCAGAAGTGGACACAGTAGATGCCTTCCAGGGCCGGCAGAAAGACTGTATCATCGTTACCTGTGTCAGGGCAAGTGCTGTGCAAGGCTCAATAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043535-Setx:NM_198033:23
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=0.075
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF130871=AAA_12=FE(27.2=100)

							
A:
NA

							
C2:
PF130871=AAA_12=FE(16.3=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000051492





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000119176
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:132271809-132275255 
ALTERNATIVE
HsaINT0148413
(SETX)
Human
(hg19)
chr9:135147196-135150642 
LOW PSI
HsaINT0148413
(SETX)
Rat
(rn6)
chr3:7722607-7725708 
ALTERNATIVE
RnoINT0133896
(Setx)
Cow
(bosTau6)
chr11:102381724-102384672 
LOW PSI
BtaINT0131696
(SETX)
Chicken
(galGal4)
chr17:6494943-6495432 
LOW PSI
GgaINT0124341
(SETX)
Chicken
(galGal3)
chr17:7126534-7127023 
LOW PSI
GgaINT0124341
(SETX)
Zebrafish
(danRer10)
chr21:3801380-3804602 
LOW PSI
DreINT0133566
(setx)
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"