Special

MmuINT0109819 @ mm9

Intron Retention

Gene
ENSMUSG00000038146 | Notch3
Description
Notch gene homolog 3 (Drosophila) [Source:MGI Symbol;Acc:MGI:99460]
Coordinates
chr17:32257838-32261324:-
Coord C1 exon
chr17:32261227-32261324
Coord A exon
chr17:32259806-32261226
Coord C2 exon
chr17:32257838-32259805
Length
1421 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
CTGCCCCTCCCCCGCCTCAGGAA
3' ss Score
8.66
Exon sequences
Seq C1 exon
GGAAATCTGCCTTACACTGGGCTGCAGCTGTGAACAACGTGGAGGCTACCTTGGCTCTGCTGAAAAATGGAGCCAACAAGGACATGCAGGACAGCAAG
Seq A exon
GTGAGCCACTGGGGGCCTACAGTGCTACAGCCCCTGAATGTGACAAAGCAGAGTCAGGGAGGAATAAGCCTGTTAGGGGCATCCATCTTGCTTGCAGTCAGCTCTCAGGAGTGGGATTCTGGCCTGAAGGCTGTGAGAGCAAACTGTTGAAGTCGCTGTGTGACATCGAACGCAGTTGTCCCCATTGTGACAGGGGAAGCAGCAGCATGAGCTGCTGAGCTTGAACAAGCCTACTTTTCTTCCTTCCTTCTTTCTTTCTTTTTGAGACTAACTTCCTACCTCAGGTTGGCCTTGAACTCACAATTCTCATATTTCTACTAACTAAATGCTGGTATATGCTCTCATGCCTGGCTTTTTCTTTTTTCAATGATATATTTTATTTTTAAATAGTGTGTGCGTGTAAGTATGTGGACATGAGTTGCAGATATCCTTGAAGCAAGAAGAGGGTGTTGAATCCCCCTAGAGCTGAATCTATAGGCAGTTGTGAACTGCCCGTGTGGATACCAGGGATGGCACTGAAGTCACCAGGCTGAGTGACAAGTGTGGTTACCCACTGTGCCGTCTTGCCGTCTTGCCAGTCTTTACATTGTTTCCTTCTCTTTTGGAGATCATGTCTTACTGGTTAATTTAGCAAAAGCTGACCTCAAACTCTTGGTGAGTCTTCTGCCTTAGCCTCTCAAGTGCTGGGGTCATAGGCTCAGGTTCTCTCTCTGTCTGTCTCCATCTCTGTCTTTCCCTCCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTAAGACAAGGACTCACTTTGTAGACCAGGCTAGCCTAGAACTCAGAGACCCTTTTGCCTTTGTGTCCTGGATGGTAGGACTGAAGGTGTACAGGACCACCAGAACCCCAACAACTCACTTTTTAATCTTTTGTTTTTTTGGTTTTTCAAGATAGGGTTTCTCTGTATAGTCCTGGCTGTCCTGGACCTCACTTTGTAGACCAGGACAAAGAAACTGGTAGAACTCAGAAATCTGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGCTTTTTAATCTTTTATAACTCTTTTTAAAACTTTTATAACATCACCATGCAGTTTATTTTGATGACTGGAAGTTTTGATGCCCCTTTAAATTTTGTGCCTAAGGTAAGTCCTGGCCAGATGTGCCTGCTACAGAGAGAGCTTGTTTCTTCAACAGAGCTGGAATCCAAACTCAGGTCCATCTATTTCCAGGGTATCAACTCTTAGTTCTCAGGCTGCCCTAGAGATTAGAAAGCTAGGTGTTGGCCAGAGTGACTGACCTCCGTGGGTTCTGCCCCTCCCCCGCCTCAG
Seq C2 exon
GAAGAGACGCCGCTGTTCTTGGCCGCTCGGGAGGGCAGCTATGAGGCTGCCAAGCTGCTGCTGGATCATCTCGCCAACCGGGAGATCACAGATCACTTGGACAGGCTGCCCCGGGACGTGGCCCAGGAGCGGCTGCACCAGGACATTGTGCGGTTGCTGGACCAGCCCAGTGGACCTCGAAGTCCCTCTGGTCCCCATGGCTTAGGGCCATTGCTCTGCCCACCAGGGGCCTTCCTTCCTGGCCTCAAAGCGGTGCAGTCTGGGACCAAGAAGAGCAGGAGGCCACCTGGCAAGACCGGGCTGGGGCCACAGGGAACTCGTGGTCGGGGCAAGAAGCTGACACTAGCCTGTCCAGGACCTCTGGCAGACAGCTCTGTCACACTGTCACCGGTGGACTCTCTGGACTCACCACGGCCTTTCAGTGGGCCCCCTGCTTCCCCTGGAGGCTTCCCCTTGGAGGGCCCCTATGCCACCACGGCCACCGCGGTGTCCTTGGCACAGCTAGGCGCAAGTAGGGCGGGTCCTCTGGGGCGCCAGCCTCCTGGGGGCTGTGTGCTCAGCTTTGGTCTGCTCAATCCTGTAGCTGTTCCCCTCGACTGGGCCAGGCTGCCTCCACCTGCCCCTCCAGGGCCCTCATTCCTGCTGCCCCTGGCTCCGGGACCCCAGTTGCTCAACCCAGGAGCCCCAGTTTCTCCCCAAGAGCGGCCCCCACCCTACCTGGCTGCTCCAGGACATGGAGAGGAATATCCTGCAGCAGGAACCCGCAGTAGCCCCACCAAGGCCCGCTTCCTGCGGGTTCCCAGCGAGCATCCTTATTTGACCCCGTCTCCTGAGTCCCCAGAGCACTGGGCCAGCCCATCCCCCCCATCCCTCTCAGACTGGTCTGACTCAACACCTAGCCCAGCAACTGCTACCAATGCCACAGCCTCTGGAGCCCTGCCTGCTCAGCCACACCCCATATCTGTTCCCTCCCTCCCTCAGTCCCAGACTCAGCTGGGACCCCAACCAGAAGTTACCCCCAAGAGGCAGGTGATGGCCTAAGTTCTTGGATTTGAGGGGTGCTGAAGTGACACTCCTCTATGACTTCTTTCTTCCTCCTTTTTAATCTTACTCTCATCCCTTTCTCTCTGTCCCAGCCTTCCTGCACCTCTCTGTCTTGTAGTGTGACCAAGTTGGTCACCAGCCCAGACCCCCAGTCTTCCTTTATTTATAATGGGTAGGGGCTGACCTTCCACCACCTTGGCCCCCTAAGGGATCTGGGACCTCCTTTTGATCCCTCTCCCTGCCTCAACTTCCTCCCCCCCCTCTTTCTGCTTCTCATTGTCTCACACTCTGACAAGAGTGAGTTATTATTTTTTTCTTTTTTACATTTTGTATAGAGACAAATTCATTTAAACAAACTTATTATTATTATTATTTTTTACAAAATATATATATGGAGTTGCTCCCTTCCCCCCGCTGCAAATTCCTCCAGCGCCCCCGTGGGGCTGAGTCTGTGGGCCCGTTTGGCCAATCCGGACTCTGTGTACTGAGTACACAGATATGACTAGGGCTCCACGTACTGAGTATGTGGCCCTCGTATGTACCAAGTAGCCAGCCTTGGGCACACCCTCCCCTGGGGTCAGGGGACATTTGGGAGCCTCCTTCCCCTCCCCATTCCCCTTCCTCACTTCACTGCATTCCAGATAAGACGTGTAGACTCACTGGGAAAGGGGTCTTGTCTGCTCAAAGCCTCAACTCCAGGCTCACCTCCCAGAGCCTGGCTCACCTTTTAGGGCCTGGGGTGGGGGGGCACGTCAGGGGAGATGTATTTTGTATGCATTCCACTTCTAATTGTAAATACAGGGCAGAAGGTGGGAGTGGCTCTCCCTCTTCCTGTTGTTCTCTTGGCTCAGCCTGCCTAATAGAAATGTTTTTAGGCTGTTTTTGTAATATGGCACCTGGTCACAGTCCTTTGTAGCTGAATTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038146-Notch3:NM_008716:32
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.333 A=NA C2=0.821
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF127962=Ank_2=FE(34.0=100)

							
A:
NA

							
C2:
PF127962=Ank_2=PD(33.0=8.9),PF119363=DUF3454=WD(100=19.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000085016





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr19:15161715-15162464 
LOW PSI
HsaINT0114902
(NOTCH3)
Human
(hg19)
chr19:15272526-15273275 
LOW PSI
HsaINT0114902
(NOTCH3)
Rat
(rn6)
chr7:14139802-14142452 
LOW PSI
RnoINT0102293
(Notch3)
Cow
(bosTau6)
chr7:8968434-8969251 
LOW PSI
BtaINT0102925
(NOTCH3)
Chicken
(galGal4)
chr17:7840512-7840747 
ALTERNATIVE
GgaINT0124461
(NOTCH1)
Chicken
(galGal3)
chr17:8528940-8529175 
LOW PSI
GgaINT0124461
(Q9W737_CHICK)
Zebrafish
(danRer10)
chr3:53276814-53276901 
LOW PSI
DreINT0105528
(notch3)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GTGAACAACGTGGAGGCTACC

				
R: 
TCTTCTTGGTCCCAGACTGCA

				
Band lengths: 
343-1764

			

		

	





	
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






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