Special

MmuINT0109754 @ mm9

Intron Retention

Gene
ENSMUSG00000026923 | Notch1
Description
Notch gene homolog 1 (Drosophila) [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26313422-26317765:-
Coord C1 exon
chr2:26317668-26317765
Coord A exon
chr2:26316497-26317667
Coord C2 exon
chr2:26313422-26316496
Length
1171 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
CTCCTGTCCGTGTCCTACAGGAG
3' ss Score
10.06
Exon sequences
Seq C1 exon
GCAAGTCGGCTTTGCATTGGGCGGCCGCGGTGAACAATGTGGATGCTGCTGTTGTGCTCCTGAAGAACGGAGCCAACAAGGACATGCAGAACAACAAG
Seq A exon
GTAAGCAGACGGGCTGCTTAACCGCAGGCGCATGATGGGGACTCCGGGGCACCCATACGTTGACCACTTAGAGGTTTAAGAGTGTCTGGGACAACAGCAGCCTAAAATAACCCGTGCTCTTGCTGGAGAGGAGCTGAGGCGTAAGCAGCTGTCCCATGTCACGGTTACTTGAGCCTTGCCTTCTGTCCCCTTCTGTCCCTGGTGGCTGTGGTGACCCTAGGGGTTCAGGATTGGCCAAGGGGCAGGGATGGGGTGGCCCTGTCTCTTAAGGCCTGCAAGGCTTCTGGCTTGGTCCACCACTACCATGCTCCCTCCTTTGGGATAAGAAAACTGCTGAGCTGGGCTGCGTGTCTCCACCTCGCCTCCCAGTGTCTCTGTTTGTGCAGGGCTAGTTGCTTCATCAGGACTCTGCTTAGTTGCTCACAGGGCAGAGTTTGTGCCTCCCTTACCAGCTCCACTGCAGGCTGGGAAATGGAGCAGGAGTCAGGTACCTGGAGTTGCTGTTGGGCACAGGTTCTCCACAGTCCAGGGTGGGCCAGTGGTTATAGAGAATCCAAGCCTGATAGACATTCTGTTGTGGTGTATGATTATGTCTGCTGGACAGAGCAGACCTGGAAGGAGCTGAGATGCCCTAGCCACTGGTGACCCTTTGGCATGGTAGTACCTTCCCCATGGCCATTCACTTGCCTTAAAGGTCCCTGAGTCCCAGGATTGCAGTACTTGTGCCTGCATTTTGGGGAGGAAAGCAAAGGGCACACAGTTACATTCTGTTTTCGGCAGTCTGACTCCACACAGGGGAAGAAGCCCTATGTATTTATCCCACAGATCTCTGGGGTGTGAGGTGTTAAATCTAGGTTCTCTAAAAAAAGAACTCGGGACCAGCCATGTGTGCGTGCTAGCACCGAGAAGCTGAGGCAGGACGATACTGAGTTCCAAGTACGGCTGTGGGCCCTGAGTGAGATTCCTAGCAACATAGGAAGGCCCCACTATAAATACTCTCTGAGCCTGGTGGTCTAGGATGCTTGGGTCTAGATAGATCTCTCCAGATAAGAGAAGAGAAAGAGGCAGCACCTGCTTCCCTAGCCCCTCCCCCCAGGCCATCCATCATCAATGACTCAGCAAATTCTACACCTGCCCGCTCCCTCATGTACCTCCTGTCCGTGTCCTACAG
Seq C2 exon
GAGGAGACTCCCCTGTTCCTGGCCGCCCGTGAGGGCAGCTATGAGACTGCCAAAGTGTTGCTGGACCACTTTGCCAACCGGGACATCACGGATCACATGGACCGATTGCCGCGGGACATCGCACAGGAGCGTATGCACCACGATATCGTGCGGCTTTTGGATGAGTACAACCTGGTGCGCAGCCCACAGCTGCATGGCACTGCCCTGGGTGGCACACCCACTCTGTCTCCCACACTCTGCTCGCCCAATGGCTACCTGGGCAATCTCAAGTCTGCCACACAGGGCAAGAAGGCCCGCAAGCCCAGCACCAAAGGGCTGGCTTGTGGTAGCAAGGAAGCTAAGGACCTCAAGGCACGGAGGAAGAAGTCCCAGGATGGCAAGGGCTGCCTGTTGGACAGCTCGAGCATGCTGTCGCCTGTGGACTCCCTCGAGTCACCCCATGGCTACTTGTCAGATGTGGCCTCGCCACCCCTCCTCCCCTCCCCATTCCAGCAGTCTCCATCCATGCCTCTCAGCCACCTGCCTGGTATGCCTGACACTCACCTGGGCATCAGCCACTTGAATGTGGCAGCCAAGCCTGAGATGGCAGCACTGGCTGGAGGTAGCCGGTTGGCCTTTGAGCCACCCCCGCCACGCCTCTCCCACCTGCCTGTAGCCTCCAGTGCCAGCACAGTGCTGAGTACCAATGGCACGGGGGCTATGAATTTCACCGTGGGTGCACCGGCAAGCTTGAATGGCCAGTGTGAGTGGCTTCCCCGGCTCCAGAATGGCATGGTGCCCAGCCAGTACAACCCACTACGGCCGGGTGTGACGCCGGGCACACTGAGCACACAGGCAGCTGGCCTCCAGCATAGCATGATGGGGCCACTACACAGCAGCCTCTCCACCAATACCTTGTCCCCGATTATTTACCAGGGCCTGCCCAACACACGGCTGGCAACACAGCCTCACCTGGTGCAGACCCAGCAGGTGCAGCCACAGAACTTACAGCTCCAGCCTCAGAACCTGCAGCCACCATCACAGCCACACCTCAGTGTGAGCTCGGCAGCCAATGGGCACCTGGGCCGGAGCTTCTTGAGTGGGGAGCCCAGTCAGGCAGATGTACAACCGCTGGGCCCCAGCAGTCTGCCTGTGCACACCATTCTGCCCCAGGAAAGCCAGGCCCTGCCCACATCACTGCCATCCTCCATGGTCCCACCCATGACCACTACCCAGTTCCTGACCCCTCCTTCCCAGCACAGTTACTCCTCCTCCCCTGTGGACAACACCCCCAGCCACCAGCTGCAGGTGCCAGAGCACCCCTTCCTCACCCCATCCCCTGAGTCCCCTGACCAGTGGTCCAGCTCCTCCCCGCATTCCAACATCTCTGATTGGTCCGAGGGCATCTCCAGCCCGCCCACCACCATGCCGTCCCAGATCACCCACATTCCAGAGGCATTTAAATAAACAGAGATGTGGGATGCAGGACCCCAGCTTCCGTTCCCAAGCCCTGTTGGGAGTCCTTTCCAGTGCTTCAGGATGCTGGGGCGACCAAAGGAGCCTTTTAAAAAATGTTTTTATACAAAATAAGAGGACAAGAATTTCCATTTTTTTTTTTAGTATTTATTTATGTACTTTTATTTTCCACAGAAACACTGCCTTTTTATTTATATGTATTGTTTTCTATGGCACTAGGGAAAAACATATCTGTTCCAAGAAAATAAACTAGTTCTCAGAGCCTTGATTTTCCTGGTCAGGGTGAAGTTCCCTGTGTGTCTGTAAAATATGAACAAGGATTCATGATTTGTAAATGCTGTTTATTTATTGATTGCTTCTTTCCAAAATCGAAAAGAAAGAAAAAAGAACGTGACAGGAGAAGGGAAGCTGGAAACTGCCATGGCCAGAATTGCCCCTCCCCCACACTCACTGCCCCTCCCCCCAGCGTCACCTGGGATTTGCAGATGTGTTTAGAAACACGCCCAGACCTTGAACCTTGGGTTCATGGATTAGTTTTGTATCTAAAACAGGAAACAAGTCAGATGATGTGGTTTGTACACTTTCTGTAACCACCAGTGTGGACTTGAAGAAGTGTCCTCAGCATGTGCAGAGTCTACTACCCAGTACCAGTCGTGAGTCTGCAGGCTCCAGTGTTCTGTAGTAGTGTTTATGGGCCTTGGGAGTACTTCTCCCCTGCCCTGCCCCACTGTCCCCTTCCTGACAACTTGAGCCAGTAAGCCATGCAGGGTGTGGTGCCTCCTAGAGAAAACACTGCCTGGACTGTTCTGTGCATCCCTCCAAACAGCATCATCCAAATCCAACTGAGGACAGACGGACTGTCCCGGCCTGGGCCTGGGCTCCTAACACCTGACTGCCAAAGGGCTCCAATGTGCATTGTGGACTCGCCAGAGTAGCCTGCATTGAGACTCCAAGAAAACAGAAGCTATGTGGCCTCTGATCCCCAAACTGGCCTGGGTGGGGACATGCCTTGAGTGTGCTGGAATGTGGGTGGAGCCTGCTTCTGGGCCACCCCTCCTGGTTCAGGGCTGTGCTCACAGCAGATTCTTGCAGTATCAAGTATACGCCTGTGGCAGAATAAGTATCTGTAAATACATGTTTAAAGATGGATTTTGTTTAAAAAATCTAAAGGAACAAGTGTGTCGTGTGTCAAGCTGATGAGGACTGTCAGACTGTGGCTTAGCTCAGTGTGACCCAGACCTTGTGACCTGTAGCTGCCGAACCAGTAGCTCCTAAGAGCACAACCCAGGATGGCCCATCTGCTGCCCACCAAGTCCCTTTCCAGCCACTGTGTGCTGGGGGCTTTCGGGGGCAGTTGCCCACCTCCTCAGGGCAGCTCTTTCTGGCCTTTTGGGGGGCAGTGTCTGTGCCATGCCTAATAGATATGACCAGACGCATCCTAAGATGTTGATTCTTACTGTGTTGTATAAAATAAAGTGTAGTTTACAAAAAAAAGAAACGTAAAAAAAAAAAACTACATGCAAAACTGTAGGTAATGAAAATGATGTATTTTTTTCATCTTTTTTTGTTAACTAATTTGCAATAAAAATGATACTGATGGTTGTCCACATTTTGCTAAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923-Notch1:NM_008714:33
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.212 A=NA C2=0.784
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF127962=Ank_2=PU(31.1=84.8)

							
A:
NA

							
C2:
PF127962=Ank_2=PD(66.7=12.4),PF119363=DUF3454=WD(100=13.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000028288





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000099972, ENSMUSP00000109696, ENSMUSP00000128155
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:136497559-136498898 
LOW PSI
HsaINT0114833
(NOTCH1)
Human
(hg19)
chr9:139392011-139393350 
LOW PSI
HsaINT0114833
(NOTCH1)
Rat
(rn6)
chr3:3908593-3909759 
LOW PSI
RnoINT0102228
(Notch1)
Cow
(bosTau6)
chr11:103988329-103989562 
LOW PSI
BtaINT0102860
(NOTCH1)
Chicken
(galGal4)
chr17:7840512-7840747 
ALTERNATIVE
GgaINT0124461
(NOTCH1)
Chicken
(galGal3)
chr17:8528940-8529175 
LOW PSI
GgaINT0124461
(Q9W737_CHICK)
Zebrafish
(danRer10)
chr5:65002013-65003443 
LOW PSI
DreINT0105463
(notch1b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GAGCCAACAAGGACATGCAGA

				
R: 
CTACCACAAGCCAGCCCTTTG

				
Band lengths: 
358-1529

			

		

	





	
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"