Special

MmuINT0109775 @ mm9

Intron Retention

Gene
ENSMUSG00000027878 | Notch2
Description
Notch gene homolog 2 (Drosophila) [Source:MGI Symbol;Acc:MGI:97364]
Coordinates
chr3:97930035-97935357:+
Coord C1 exon
chr3:97930035-97930167
Coord A exon
chr3:97930168-97935120
Coord C2 exon
chr3:97935121-97935357
Length
4953 bp
Sequences
Splice sites
5' ss Seq
GGGGTATGC
5' ss Score
6.16
3' ss Seq
CTGTCTTTCTTCTCTCATAGGCC
3' ss Score
12.51
Exon sequences
Seq C1 exon
TGTGTTCCAGGATATCAGGGTGTCAACTGTGAGTATGAAGTGGACGAGTGCCAGAACCAACCCTGCCAGAATGGAGGCACCTGCATCGACCTTGTGAACCATTTCAAGTGTTCGTGTCCCCCAGGCACCCGGG
Seq A exon
GTATGCAGTCTTCAGTCTTCGTTACTCTTTCCACCAGGGACATTCCCTCTAGGCATACATTCTTAGTGCTGAAGCAACTTTTAAAATCTGAGACAATTTAAAGAAGACTAGCTTCATTGGAGCCACTTACTCAGTTATCTGCTCTCACTCTGATCTCCTGCCAGCTTCCATTCAGGTTTGGTTGTTTCTTAGCTTATGTTCAGGAAAACAGAATGCAGAATGAACATAACCCTAGATAACCAGGTTTTTTTGGTGCTTCAAGTGAAATCAACTGTCAACCTTTTAAAGGAAGCGAATCCACATAGGCCTGCTTTTTAATTGTTTAAGCTAGCCAAGTCTGTCCATAGAACGAGGGAATCTATGAGATGTGTTTGGCTGCTGTCCTGGGAGGCAGCAGACAGGAGGCTGTGCTCCTGCACCTGCACCTACTACACCCCTGGACTGTGGACCACAGAGCATCAGTGTGCTCTGGGAATTGCCACTTGCTCCAGACTGCCTCCTGGAGAGAGCATTGCTTGCTAACATTGCTTGTTAGGGACATCTGGTGCTGAAGGAAATGCGTAGCCTGTGAGCAACATGGCAAAGATAGCAGTCGTGCGTTTAGGCAGCAATCAAACAGAGGAGACCCTCATAGCTGGCTTTGTGTTTACGTAGACTTTTGTGCCAGTGCATTTGAATACCTTCTTTTTCCTAGAGATCAAATTTGGCTAAATTGAGGCAGAAGAATACTCCATTAATAGGTATGTAATACAGAATGAGTCTTAGGGAAGGGAAAGCTGAAGACTAGCCTACAACTAACTGTTTTAAAATTCATTACATGGTTTCTAGTCTAGAAATAGGAAATTCCATGGTGCAAAGTTCCAGGTGCTTACTAGTGTATTCCTTTGTATTTACCCATCCATCTACCTGTCCGTCCATCCGTCTATCCATCCATCTATCCATCTACCTGTCCGTCCGTCCATCCTTCCATCCATTCATCTATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCTTTTGTGACAGGGCATTTTTGAGTAGTAAAGCTAAATGCATAAGGTAAGAAGCAAATTGATTCTCTGTCTTCTCCTTTGGGAGGTTCATAGCCATCCCCACCCCCATCTGATCTCCCCTTCTCTCCCCCACCCCATCTCTCTTTGTCTCCCTCTGTCTTCTACTCTCTCCCTCTTCCCCTCTCCCTTTCTACATCCCCCACTCCATCTCTCTCCTTCTCTCTTTCTCCAGTCCCTAGTCCCATCTCCCTCTTTTCCTCTCTATCTTTTCCCATCCCTCCTCCTTTCTCCCCTCAGTCCCTCTCCCTATCTCTTCCTCCCCTTTCCCTCCCCCCTCTTGTTCCCGCTCTCTTCCCTTCTCCCCTATGTCTTCTCCTCTCTTTCATCCCTCTTCTCTCTTCTTACCTCTTCCCCTCCTCTCTTTCTGTTCCCAGAATTCCAAGTAGCCTCAGCCTCAAATTCACTATAGGCATGTACTACCATGCCCGAGTGGTTAATGCCTTTAAATAATGGTATTGGTTAGAACAAGCTACAATTCTAGTGGTAGCTAATTATATATATCAAGTCTCAGATAGCACAATAGTGGTTTTGTTGGGGTTTTTTGTTTGCTGTTTTGGCACTCAGACTTGCACAGGTGTTGGGTTGCTGCCTTTCTTTCTCTGTGCTTTGGGGCTGCAGGCTCCAAGGCAGCCACAGCAAAGGTGGAGAAACTGCATAGGGCTGTGCAGGGGCTTTTACTCAGTGTGGAGGTGACACACATCACGCTCCCAGAGGTGTGTCAGAACCACTCATTACTGTTCTTCCAAGGCCTGTGGAGGCTGAGAACCCAGGAAAGGGCATGCGTTTGTACTGTACCACAGACTACCACATAGACATAGATGCATCCAGTCCCAGAGTGGAACATCTCCTAAGCCAATGAGATTTTTGTCTTTTCTCAATCAATCAATCAATCAATCAATCAATCAACTGATCAATCAATCTCTTTTTCTCTCCCCCTCCTTCTCGTCTATTTCCTCCTCTTCCTCCTCCTTCTTTTTCTTTGTTTTTGTTGTTGTTGTATTGAGACAGAGTTTCTCTGTATATCCCTGGCTTTTCTGGATCTTGTTCTATAGACCAGGCTGGCCTTGAACTCAGGGATCTGCCTGCCTCTTCCTCCTGAGTGCTGGGATTAAAGCCTTGTGCCACTGCTTGGCTCCTAAATACTTCTTTGTGGTAGCTTAGAATAATAATCTAGTATATCTATTGATCTGTTGACTGTTTCTGAGCCAGCTCCTCAGATGTGTCTTCTCGCTGATGTTCCTGCCGTGGTCTTCACCGAGAACTTAGCAGTTAGTCTTACTGATGGTCTCTCACGATACCTGGCTCTCCTTTGCAGTGTTTCCAAGATTGCCTTTTAATGGTCTGTTATAGTGTGGTTCTCTTCCAGTGTGGTCTGTTTGAATGTTTGTTGGATTATATCCTGTGTGCTGATCTTTCCAGGTGCCTGACATAGTGTATATTTGTTCTGACTTTTCCTCTCTGGCCATCCACCCTGTCCACCTGTGACTGCTCCCAGCGACTCTGGAGTTCTCTTACAGTACAGTGAGTTATTCCAGTGCTTGTTCTCAGCACTGTACTCCCAGGCCTTGGATGTTGCCTGCGCATACCTCCTGCTCCCAGTGCATAGGCTAACCTAGAACACTTCTGTCATCCTGTGTTTGCTTCAGGCTAAGAATGAGGTCACGCTCACATGATAAGCTGTGCATCACTGATAGTTCCGTCTACATGGAAGCTTTATGCTTATTTTACTCCTCATGCCAAACACCAAGTATCCTGTGAGACTGGGAGCACGTCCTGGCTTTGTTTGCTTCCACTTTCTGGTTCCCATTTTAATCTAATCTGTGAGTAGATAAGGTGATATGTGCATGTGGACAGGGTAAACATGTCCACATATGCATGGAAAGACATGCAGTAAAGACACACTCCCCACTGTACTCACCCCCAGCACCGCGCCCTCCCTCTCCCCTCACACTGCAGACAGCCTCTTGTGTGTTTCTAGAGGAGTTAAAAGGCTATCTTTCAGAATTGCATTATGTATGTAGGAGCCAAATTCAAAGATAGTTTTACCCCCTCCATTTTTAACTCTAAAGATGTATCAAAGATGCTGTTTTTCTCTTGACCTTTTTACTTAATTGGAATATTTTCATATCAAAATAGGGAACTTCTTCAGTATTTTCTCATAGCTTCAGAATTCCCCTTTATGACAACATTATGTATTGTGCTTAACTGGTCCTCTAGTGATAGACATTGGTGTTTTTTTTTTTAAAGGACACATATAAGTGCACGTTACAGAATGTGTTTTCAGAAATAGAGTCTGCTGGGCCACTATACCGAGGTTAAGTGTCATTTAAGTGGCAATGCTGGCTGCATCCTCTCTATGTAATTCATCATCTAGCATATTTACAAGTTCCTGTTTTCCCACTGGGATTTATCCCTTCCTCCTTTCTGTAGATGCTGTCTGTCCTTACTATGTGCAGAAGTTGTTTGTCTTTGCTGTGTGATGTGGATATTTTCCTGATGTACTGGGGTTGCAATCTTTCAGACGTCTTATTCTGAGGTCGGAATCTTTCAGATGTCTCTGGGGATTTTTTACATGCAGATTATTTCTAATCATATTGAATTTATCCATCTTTTTTATGGCTGCTTGCATCTGAGTGGTAGTTGATTTTATCCTCCATGCTTCAAGATTTATAAAGACATTCTTCTGTGTTTTTATCCTGGACTAGAATCCTGAAGTGGCTTTCCCATGTGACTGGATGGTTGATGTTTTCTACAATGACTTGAGATGGAACTTTGATCAAATTCTAAGCTCCGGTGTGCATTTGGGCTGTTGTTCTGTCCGTCGATTCACAACAAACTTTTAACCATGAAGGACTCTTTTTCATGCTCTCCTGGCTGTGATTTGGTTTTTCTATATCATTTTTTAGTCAGTTTGCCATTAAAAAGTATTGCTGATATCTTTTTGAGATCATATTACCTTCATATATAATACAGTGAGCATGCCTTTTCATGGAGTCGCATAATCAGATAATGTATGTCTTCCATCTGTCCACGTCTCCTCTGTCTGTCCTTCAGAGCACTTGCCTGCAAGGCCACACAGCTTGCTCTGATGCTCTCAGCCATTTGCCTTTTGACACTGCTGCTGACAGTGAGGTACATCTGTGTCTCCTTCCCTTTTTATGTCTTGCTTCTCTTAAAGTATACCAAAGTGCTATAGAAGTATCTTCATTTTTAACCTTTTCAAATTACCTTGTGGAGTAGTCATTGATTTTGTTGTTTCTAAACGTGTTCACAGATATTTTAACTAGATGGCTCCTAGATCTTCAGTGTGTTACTTAGCCAGAATAATCTTCAAATTCTTAGCAAGATATTTCCACTCTGTTGTTGTCTTAAATAAAAGATATTAGTGTACCTATCCTCTTTTAAAGAAAAAAAAAGTCAGTGTTTATAAAACATAAAATACTATTGCCCAAAATCTAACCCCAGCATAGCCTATGTAGTGATTAGATGTGCTCCCTGTTGAACTGTTTCACAGTTTGATGGGAGTTGATAAGGGGTGGAAAACTCCCACAGTCTCCTGAGCTTTGACTCCCGTGTGCTTGCGATGGCGCAGTTGTCCCTGCTGCTCTGGATTGGGTGAAACACAAGTGGAGCCTCAGGGTGCAACTTCCTCTCCTGTTGCTCCCCGGGAAGCAGCTGCACGAGCTGCATGCAGCTGGCATGGGCTAAGAATATTTTTTGCCTTGCCCAATTTAAAAGCTCCCACTGTAGATTAAGGATTATACTCAAATTAATCTCTAAAGCCCACAAGGGCATTTATCCCTTGCTAATGGCGGGTTCAGTGGATTTTTGTAATTCTGTCTTTCTTCTCTCATAG
Seq C2 exon
GCCTGCTGTGTGAAGAGAACATCGATGAATGTGCTGGGGGCCCCCACTGCCTTAACGGTGGCCAGTGCGTGGACCGGATTGGAGGCTACACTTGTCGCTGTTTGCCTGGCTTTGCTGGGGAGCGGTGTGAGGGGGACATCAACGAATGCCTGTCCAACCCTTGCAGCTCAGAGGGCAGCCTGGACTGCGTTCAGCTCAAAAATAACTACAACTGTATCTGCCGCAGCGCCTTCACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027878-Notch2:NM_010928:22
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=17.8),PF0000822=EGF=PU(90.3=62.2)

							
A:
NA

							
C2:
PF0000822=EGF=PD(6.5=2.5),PF0764510=EGF_CA=WD(100=47.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000078741





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000102643
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:119929213-119935471 
ALTERNATIVE
HsaINT0114854
(NOTCH2)
Human
(hg19)
chr1:120471836-120478094 
LOW PSI
HsaINT0114854
(NOTCH2)
Rat
(rn6)
chr2:200297314-200302761 
LOW PSI
RnoINT0102249
(Notch2)
Cow
(bosTau6)
chr3:23461938-23463857 
LOW PSI
BtaINT0102881
(NOTCH2)
Chicken
(galGal4)
chr8:4207723-4209846 
LOW PSI
GgaINT0038702
(NOTCH2)
Chicken
(galGal3)
chr8:4248605-4250728 
LOW PSI
GgaINT0038702
(NOTCH2)
Zebrafish
(danRer10)
chr3:53280737-53282217 
LOW PSI
DreINT0105516
(notch3)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"