Special

MmuEX6099902 @ mm10

Exon Skipping

Gene
ENSMUSG00000015846 | Rxra
Description
retinoid X receptor alpha [Source:MGI Symbol;Acc:MGI:98214]
Coordinates
chr2:27741053-27748781:+
Coord C1 exon
chr2:27741053-27741203
Coord A exon
chr2:27741764-27741943
Coord C2 exon
chr2:27748612-27748781
Length
180 bp
Sequences
Splice sites
3' ss Seq
CCTCTACCCCCACCCTGCAGGCA
3' ss Score
9.03
5' ss Seq
AAGGTAGGC
5' ss Score
10.08
Exon sequences
Seq C1 exon
CTCAATTCACCCATGAACCCTGTGAGCAGCACTGAGGATATCAAGCCGCCACTAGGCCTCAATGGCGTCCTCAAGGTTCCTGCCCATCCCTCAGGAAATATGGCCTCCTTCACCAAGCACATCTGTGCTATCTGTGGGGACCGCTCCTCAG
Seq A exon
GCAAACACTATGGGGTATACAGTTGTGAGGGCTGCAAGGGCTTCTTCAAGAGGACAGTACGCAAAGACCTGACCTACACCTGCCGAGACAACAAGGACTGCCTGATCGACAAGAGACAGCGGAACCGGTGTCAGTACTGCCGCTACCAGAAGTGCCTGGCCATGGGCATGAAGCGGGAAG
Seq C2 exon
CTGTGCAGGAGGAGCGGCAGCGGGGCAAGGACCGGAATGAGAACGAGGTGGAGTCCACCAGCAGTGCCAACGAGGACATGCCTGTAGAGAAGATTCTGGAAGCCGAGCTTGCTGTCGAGCCCAAGACTGAGACATACGTGGAGGCAAACATGGGGCTGAACCCCAGCTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015846-'21-12,'21-10,29-12=AN
Average complexity
A_S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms (Ref)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.482 A=0.000 C2=0.579
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF118253=Nuc_recep-AF1=PD(28.4=64.7),PF0010513=zf-C4=PU(15.7=21.6)

							
A:
PF0010513=zf-C4=PD(82.9=95.1)

							
C2:
PF0010425=Hormone_recep=PU(4.7=15.8)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000076491





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000097822, ENSMUSP00000109567, ENSMUSP00000115165, ENSMUSP00000133044
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr9:134408940-134409119 
HIGH PSI
HsaEX6063838
(RXRA)
Human
(hg19)
chr9:137300786-137300965 
HIGH PSI
HsaEX6063838
(RXRA)
Rat
(rn6)
chr3:6277183-6277362 
HIGH PSI
RnoEX6016111
(Rxra)
Cow
(bosTau6)
chr11:105997303-105997482 
HIGH PSI
BtaEX6047573
(RXRA)
Chicken
(galGal4)
chr17:7334731-7334910 
HIGH PSI
GgaEX1050639
(RXRA)
Chicken
(galGal3)
chr17:8015708-8015887 
HIGH PSI
GgaEX1050639
(F1NH64_CHICK)
Zebrafish
(danRer10)
chr19:7346448-7346627 
HIGH PSI
DreEX6071901
(rxrba)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CTGAGGATATCAAGCCGCCAC

				
R: 
ATGTCTCAGTCTTGGGCTCGA

				
Band lengths: 
255-435

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Ribosome-engaged transcriptomes of neuronal types
  • 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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