Special

MmuEX6099762 @ mm10

Exon Skipping

Gene
ENSMUSG00000026923 | Notch1
Description
notch 1 [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26465063-26466615:-
Coord C1 exon
chr2:26466467-26466615
Coord A exon
chr2:26465350-26465566
Coord C2 exon
chr2:26465063-26465150
Length
217 bp
Sequences
Splice sites
3' ss Seq
CCTGCCGCCCCTGCCCGCAGGTG
3' ss Score
12.99
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
Exon sequences
Seq C1 exon
CTCCATTGTCTACCTGGAGATCGACAACCGGCAATGTGTGCAGTCATCCTCGCAGTGCTTCCAGAGTGCCACCGATGTGGCTGCCTTCCTAGGTGCTCTTGCGTCACTTGGCAGCCTCAATATTCCTTACAAGATTGAGGCCGTGAAGA
Seq A exon
GTGAGCCGGTGGAGCCTCCGCTGCCCTCGCAGCTGCACCTCATGTACGTGGCAGCGGCCGCCTTCGTGCTCCTGTTCTTTGTGGGCTGTGGGGTGCTGCTGTCCCGCAAGCGCCGGCGGCAGCATGGCCAGCTCTGGTTCCCTGAGGGTTTCAAAGTGTCAGAGGCCAGCAAGAAGAAGCGGAGAGAGCCCCTCGGCGAGGACTCAGTCGGCCTCAA
Seq C2 exon
GCCCCTGAAGAATGCCTCAGATGGTGCTCTGATGGACGACAATCAGAACGAGTGGGGAGACGAAGACCTGGAGACCAAGAAGTTCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923-'49-49,'49-46,53-49
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact





	

	
ORF disruption upon sequence exclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=0.233 C2=0.733
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF076847=NODP=FE(79.4=100)

							
A:
PF076847=NODP=PD(14.3=12.3)

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000028288





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr9:136502272-136502488 
HIGH PSI
HsaEX6064059
(NOTCH1)
Human
(hg19)
chr9:139396724-139396940 
HIGH PSI
HsaEX6064059
(NOTCH1)
Rat
(rn6)
chr3:3912954-3913170 
HIGH PSI
RnoEX0060457
(Notch1)
Cow
(bosTau6)
chr11:103992326-103992542 
HIGH PSI
BtaEX6047249
(NOTCH1)
Chicken
(galGal4)
chr17:7837831-7838047 
HIGH PSI
GgaEX6015413
(NOTCH1)
Chicken
(galGal3)
chr17:8526259-8526475 
HIGH PSI
GgaEX6015413
(Q9W737_CHICK)
Zebrafish
(danRer10)
chr5:65015994-65016207 
HIGH PSI
DreEX6014340
(notch1b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TCCATTGTCTACCTGGAGATCGA

				
R: 
CCGGAACTTCTTGGTCTCCAG

				
Band lengths: 
236-453

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 2 annotated functions for this event 


PMID: 16530045
HsaEX6064059
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: inferred by author. ELM ID: ELMI002957; ELM sequence: LWFP; Overlap: FULL


PMID: 20028974
HsaEX6064059
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: coimmunoprecipitation, inferred by author, isothermal titration calorimetry, x-ray crystallography. ELM ID: ELMI002957; ELM sequence: LWFP; 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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