Special

MmuINT0109835 @ mm9

Intron Retention

Gene
ENSMUSG00000015468 | Notch4
Description
Notch gene homolog 4 (Drosophila) [Source:MGI Symbol;Acc:MGI:107471]
Coordinates
chr17:34714893-34718117:+
Coord C1 exon
chr17:34714893-34715077
Coord A exon
chr17:34715078-34717864
Coord C2 exon
chr17:34717865-34718117
Length
2787 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
GGCTCCCTCTGTGTCTCCAGTGT
3' ss Score
7.56
Exon sequences
Seq C1 exon
GCATAGAGATCTCTGGCCTGTGCCAGAATGGAGGCCTCTGTATTGACACGGGCTCCTCCTATTTCTGCCGCTGCCCTCCTGGATTCCAAGGCAAGTTATGCCAGGATAATGTGAACCCCTGTGAGCCCAATCCCTGCCATCACGGGTCTACCTGTGTGCCTCAGCCCAGTGGCTATGTCTGCCAG
Seq A exon
GTAAGAGGTCTAGAGGAGTAGAGATGGGGGCAGGGGGGGGGTAGTGAAGATCTAGTTTATCCAGTTCTCTTCCTTTAAGCCAGGCACCCAACCACCCACTGGGTCAGGCCATGCCACCTCATAAGAACTTCCCTATGCTGTGTTTTCACTTCTTCTTTTCTTTCCCCCACCTTGATACCAACATCAAACTCCTGCAACCTCTGCCTCCATATTTGCCCTTCTGATGGCTCAGTCTTTACCCCATTACCAAAGGGGGTAAAGGGCCTATGTCATCCCTGCAGGACTTATTTTCCCACCTGTCTCTCCCTCGCTGGTCCAGGTCGCCATCCAGGAGAGGAAATGTTGGGATTATAGCAGAATCCGTTTAAATCCTGTGCTCAAAAACTCACTTTTTTTTTTTTAAATTTTTGTGTGTATGAATGTTTTGACCGGATGTGTACCGCATGCATGCCTGGTACCCATGGAGGTCAGAAGATAGATTCAGATTCCCTGAAACTGGAGATGCTGATAGTTGTGAAGTACCATGTCGATGCTGGGAATTGAACCCCAGGCCTCTGCAAAAGCAAAAAATACTCTCCACCAGAGGTATTTCTCCTGCCCCTAGAAACACAACTTTTGATCCCCTGGCTTACCACTGACTTAACTTTGCAGTCACTATCTCCAACTTCTTATAAAAATAATTTATTTAATTTTATTTTATGGACATTGGTGTGAGGGTGTCGGATCCTCTAGAACTGCCATGTGTGTGCTGGGACTGGAACCCAGATCCTCTGTAAGAGCAGCCAGCCCTCTTAACTACTGAGCCATTTTTACACACACACACACACACACACACACACACACACACACACACACAACTTTTTTATTTTAAATTACACGTGTGACTCTCTATGTGTGGGTATGTGTACATAAGTGCTGGTGCCCACAAAAGCCAGAGGCATCAGATCCCCTTGGAGCTGGGTTGCAGGCAGCCGTGTGCTAACCTGTGTGGGTTCTGGGACTGGAGCCTAGGCCCTCTGCAAGAGCAACGTCTGCTTTTGTGTTCCTTTGCTTCCTGTGTTGGGTTTTTGAGACAGGGTTTGTCTGTGTAGCCCTGGCTGTTCTGGAACTCACTCTGTGGACCAGGCTGGCCTTGAACTCAGAGATCTGCCTGCTTCTGTCTCCCCAGGGGCTGGGATTAAAGGCACATGCTATCACCACCCAGCTTGCTTTTATGTTCTTAACTGCTGAGCCATCTCTCCAACTCCCTACCCCTACCCACCCTTTTCTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCCTCCTTTCTTCCTTTCTTCCTTCCCTCCTTCCTTCCTTCCCTCCCTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCCTCCCTCCTTTCTTCCTTTCTGAGGCAAGGTCTCATGTAGCCCAGGCTGGCCTTGAACTCCTTTATGTTGCTTTGGATGATCTCAACTCTCCTGCTTCCGGGTAGTCGGTGCTGGGACTGTAGGTATACACCCCCCACACCTACTTTAGACAGTTCAGGGGATCAAACCCAGGATCACGTGTGTGCTGGGCTAACACTCTACCCACCACCATCCCCAACCTTTACAAGCCTTTCCAGACATAGAGAACCCGGGTAGGGATGACCCTGTTTCAAATGTGAAGAGAAGAGTGTCCTGACAGTGAACCTCTGTACTCTCATTCACCCTCCTCCAGTGGGTTCCAAAATGCCCTCCATTCAATCCTACCACTCTCTGGGCCACTCCCTGAATTCTCTTGACTCTCAAAGCCTCCCTTCTGGCTTGCTGTCCGGCAGAAGCATAGTACTTATGACTTTGGGCTAGCAAGCAAAAATCACAGTGTGGCTCTGGACCGAGCCAGTCTTTCTTTGACCCAGATGTCACTTCACCTTCTTGGCAAACCATTTCGTTATCTGTGGAATGGAGATGAAGTGAGATAGTATCTCTTCAGGGTTGCTAAGAGGATGGTTTAAGGCTATGCACACAGATTACACAATCAATGCCAACCCTCTCTCCCCTCTGGTTATAGACAGTGCTTCCTAGAAATGCAGACTAATTTTAATTTTTACCTGTACTACTTAAAATGCCACCTGGCCAGCTAGGAAGATGGCTTCGCCAAGACCCCTAGCCAGAAGATTCCCCAAAAACCCAAGTCCACAGATGGCAAGACAAAGGCAGAAACAGACAAATAGCCTGGCCTAAATGGCAAGTTCCCAGCCAATAAGAGGCCCTGTCTCAAACAAAAGGCCAGAGGACTAACAGGGAAAATGTCCTCCGATCACTACACACCAAGCATATGCGCATTCGAGTACATACACTGCATGACACAAGTACGTAATCATCAGATGGCCACACACCATGCACACGCACACAGAGGCAGGAATGATCCAAGTCGATAATCATCAGACACCTATGATTCAATGCATGAGAAAGGCTGGAGGGTAAGTTGGTACGAAAAAGAAGTGTCCCCCCAAATGAGGCAATGCTTAGTGGCCACATTGTTTGGGACTAAGGATTTTGCTCTGTCACTGAACAACTGCATGTCAGGTAGTACTCAGAGAGGCTGCAATGGATGAGTGAGAACTTCAGCTGTGGAGGTAGGAGGCGGGAGGTGGGAGGCTGGCAGACCACCTTGAGCTCCACACATCCACTGGCTCCCTCTGTGTCTCCAG
Seq C2 exon
TGTGCCCCAGGCTATGAGGGACAGAACTGCTCAAAAGTACTTGACGCTTGTCAGTCCCAGCCCTGCCACAACCACGGAACCTGTACCTCCAGGCCTGGAGGCTTCCACTGTGCCTGCCCTCCAGGCTTCGTGGGACTGCGCTGTGAGGGAGATGTGGATGAGTGTCTGGACCGGCCCTGTCACCCCTCGGGCACTGCAGCTTGCCACTCTTTAGCCAACGCCTTCTACTGCCAGTGTCTGCCTGGGCACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015468-Notch4:NM_010929:18
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=WD(100=46.8),PF0000822=EGF=PU(67.7=33.9)

							
A:
NA

							
C2:
PF0000822=EGF=PD(25.8=9.4),PF0000822=EGF=WD(100=36.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000015612





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:32204390-32210751 
ALTERNATIVE
HsaINT1025124
(NOTCH4)
Human
(hg19)
chr6:32172167-32178528 
Rat
(rn6)
chr20:4343645-4346449 
ALTERNATIVE
RnoINT0102309
(Notch4)
Cow
(bosTau6)
chr23:26987909-26991198 
LOW PSI
BtaINT0102941
(NOTCH4)
Chicken
(galGal4)
chr17:7833067-7833211 
ALTERNATIVE
GgaINT0124449
(NOTCH1)
Chicken
(galGal3)
chr17:8521495-8521639 
LOW PSI
GgaINT0124449
(Q9W737_CHICK)
Zebrafish
(danRer10)
chr3:53282351-53282481 
LOW PSI
DreINT0105515
(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"