Special

MmuINT0109836 @ mm9

Intron Retention

Gene
ENSMUSG00000015468 | Notch4
Description
Notch gene homolog 4 (Drosophila) [Source:MGI Symbol;Acc:MGI:107471]
Coordinates
chr17:34717865-34718436:+
Coord C1 exon
chr17:34717865-34718117
Coord A exon
chr17:34718118-34718323
Coord C2 exon
chr17:34718324-34718436
Length
206 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CTATCTCACCCCCACCACAGGCC
3' ss Score
8.18
Exon sequences
Seq C1 exon
TGTGCCCCAGGCTATGAGGGACAGAACTGCTCAAAAGTACTTGACGCTTGTCAGTCCCAGCCCTGCCACAACCACGGAACCTGTACCTCCAGGCCTGGAGGCTTCCACTGTGCCTGCCCTCCAGGCTTCGTGGGACTGCGCTGTGAGGGAGATGTGGATGAGTGTCTGGACCGGCCCTGTCACCCCTCGGGCACTGCAGCTTGCCACTCTTTAGCCAACGCCTTCTACTGCCAGTGTCTGCCTGGGCACACAG
Seq A exon
GTAAGGCCTGGCATCTCTGGGGCATATCTAAGACCAGGACAATCTTGACGGTCCCTTCCCAAAAGACAGCCTCTCTCCTCACCCTCTGCCTTCACACCTCTCCCCTTAGAAGTCCCCTACATCTTCTTGCCCACATATCATGTGCTGAACCGTCAGGAGGCAGCCACTGAAGCCAGGTGTGACCTCCTATCTCACCCCCACCACAG
Seq C2 exon
GCCAGCGGTGTGAGGTGGAGATGGACCTCTGTCAGAGCCAACCCTGCTCCAATGGAGGATCCTGTGAGATCACAACAGGGCCACCCCCTGGCTTCACCTGTCACTGCCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015468-Notch4:NM_010929:19
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=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0000822=EGF=PD(25.8=9.4),PF0000822=EGF=WD(100=36.5)

							
A:
NA

							
C2:
PF0000822=EGF=PU(79.4=71.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000015612





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:32203883-32204136 
LOW PSI
HsaINT1025125
(NOTCH4)
Human
(hg19)
chr6:32171660-32171913 
Rat
(rn6)
chr20:4346703-4346889 
ALTERNATIVE
RnoINT0102310
(Notch4)
Cow
(bosTau6)
chr23:26991452-26991696 
LOW PSI
BtaINT0102942
(NOTCH4)
Chicken
(galGal4)
chr17:7833915-7834005 
LOW PSI
GgaINT0124451
(NOTCH1)
Chicken
(galGal3)
chr17:8522343-8522433 
LOW PSI
GgaINT0124451
(Q9W737_CHICK)
Zebrafish
(danRer10)
chr3:53280392-53280481 
LOW PSI
DreINT0105517
(notch3)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CCCAGGCTATGAGGGACAGAA

				
R: 
AGGGTTGGCTCTGACAGAGG

				
Band lengths: 
293-499

			

		

	





	
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






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