Special

MmuEX6100084 @ mm10

Exon Skipping

Gene
ENSMUSG00000039844 | Rapgef1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:MGI Symbol;Acc:MGI:104580]
Coordinates
chr2:29699686-29700851:+
Coord C1 exon
chr2:29699686-29699838
Coord A exon
chr2:29700186-29700302
Coord C2 exon
chr2:29700668-29700851
Length
117 bp
Sequences
Splice sites
3' ss Seq
GGATTTTCTGTCTCTTCTAGTCC
3' ss Score
9.3
5' ss Seq
TAGGCAGGT
5' ss Score
0.17
Exon sequences
Seq C1 exon
CCAGCCTGAGCTCCCTCTGACAGACCGAGAAATGGAGATTCTGAACAAGACGACAAGTGTGTCACCATCTGCTGAACTGCTCCCAGACTCCACCAGTGAAGAGGTCGCACCCCCCAAGCCCCCTTTACCTGGCATCCGGGTGGTTGATAACAG
Seq A exon
TCCACCAGCATTACCACCCAAGAAAAGGCAGTCTGCTCCATCCCCCACTCGGGTGGCTGTGGTAGCCCCAATGAGTCGGGCTACCAGTGGCTCCAGTTTGCCTGTTGGAATCAATAG
Seq C2 exon
GACTTTGATGTTGAATGTTACACCCAGAGGCGCCTGTCAGGAGGCAGCCGCTCCTGCGGTGGTGAGTCTCCTCGCCTGTCCCCCTGCAGCAGCACAGGCAAGCTCAGCCGCTCAGACGAGCAGCTGTCCTCCCTGGACAGGGATAGTGGGCAGTGCTCACGGAACACAAGCTGTGAAACACTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039844-'23-24,'23-23,24-24
Average complexity
S*
Mappability confidence:
100%=100=100%
Protein Impact





	

	
Alternative protein isoforms (Ref)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=0.973 C2=0.819
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NO

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000088680





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000092703, ENSMUSP00000099936, ENSMUSP00000121615
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr9:131628549-131628672 
HIGH PSI
HsaEX0052247
(RAPGEF1)
Human
(hg19)
chr9:134503936-134504059 
HIGH PSI
HsaEX0052247
(RAPGEF1)
Rat
(rn6)
chr3:8255198-8255318 
HIGH PSI
RnoEX0073984
(Rapgef1)
Cow
(bosTau6)
chr11:101768056-101768179 
HIGH PSI
BtaEX6046934
(RAPGEF1)
Chicken
(galGal4)
chr17:6276522-6276638 
Chicken
(galGal3)
chr17:6904947-6905070 
HIGH PSI
GgaEX0004871
(RAPGEF1)
Zebrafish
(danRer10)
chr8:11785376-11785496 
HIGH PSI
DreEX0060806
(rapgef1a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CATCTGCTGAACTGCTCCCAG

				
R: 
ACTGCCCACTATCCCTGTCC

				
Band lengths: 
242-359

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 1 annotated functions for this event 


PMID: 7735837
HsaEX0052247
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: x-ray crystallography. ELM ID: ELMI001098; ELM sequence: PALPPK; Overlap: FULL


		










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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