Special

MmuEX0037335 @ mm10

Exon Skipping

Gene
ENSMUSG00000061136 | Prpf40a
Description
pre-mRNA processing factor 40A [Source:MGI Symbol;Acc:MGI:1860512]
Coordinates
chr2:53177353-53190100:-
Coord C1 exon
chr2:53189969-53190100
Coord A exon
chr2:53188448-53188527
Coord C2 exon
chr2:53177353-53177433
Length
80 bp
Sequences
Splice sites
3' ss Seq
AAATTAGTTTCTTTCCACAGAAA
3' ss Score
7.37
5' ss Seq
AAGGTAAGT
5' ss Score
11
Exon sequences
Seq C1 exon
ATGGGGCATCCTGGCATGCATTATGCACCAATGGGCATGCACCCTATGGGTCAGAGAGCAAACATGCCTCCTGTACCTCATGGAATGATGCCACAGATGATGCCCCCTATGGGAGGGCCTCCAATGGGACAA
Seq A exon
AAAGATAAAATAAAACAATTTGCTACTGCCAGACGCTTCTCTCTTTTCTGGGGCCTTCTGTGTCCATTGGGCCAGGCAAG
Seq C2 exon
ATGCCTGGAATGATGTCTTCAGTAATGTCAGGAATGATGATGTCTCATATGTCTCAGGCTTCCATGCAACCTGCCTTACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061136_MULTIEX2-2/6=1-3
Average complexity
S*
Mappability confidence:
100%=100=100%
Protein Impact





	

	
In the CDS, with uncertain impact





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.891 A=0.250 C2=0.635
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NO

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000147910





     
                   









    
Main Skipping Isoform:
ENSMUSP00000075655





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000117406, ENSMUSP00000147939
          









    
Other Skipping Isoforms:
ENSMUSP00000147599, ENSMUSP00000147671, ENSMUSP00000148161
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr2:152714550-152714629 
ALTERNATIVE
HsaEX0050372
(PRPF40A)
Human
(hg19)
chr2:153571064-153571143 
ALTERNATIVE
HsaEX0050372
(PRPF40A)
Rat
(rn6)
chr3:38738379-38738458 
ALTERNATIVE
RnoEX0070102
(Prpf40a)
Cow
(bosTau6)
chr2:43588173-43588252 
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: 
TTATGCACCAATGGGCATGCA

				
R: 
GTTGCATGGAAGCCTGAGACA

				
Band lengths: 
182-262

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 1 annotated functions for this event 


PMID: 31911676
HsaEX0050372
[CRISPR screen]. Conserved poison exon with mixed impact when depleted: HeLa Enriched at 14 days (FC=1.375, FDR=0.000), PC9 No Change at 14 days (FC=1.346, FDR=0.041), Late Xenograft Depleted (FC=0.722, FDR=0.001).


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Pre-implantation embryo development
  • 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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