Special

MmuINT0053487 @ mm9

Intron Retention

Gene
ENSMUSG00000056632 | Dsg3
Description
desmoglein 3 [Source:MGI Symbol;Acc:MGI:99499]
Coordinates
chr18:20691876-20695468:+
Coord C1 exon
chr18:20691876-20692130
Coord A exon
chr18:20692131-20695325
Coord C2 exon
chr18:20695326-20695468
Length
3195 bp
Sequences
Splice sites
5' ss Seq
TATGTGAGT
5' ss Score
5.56
3' ss Seq
ATGTCCTTGTTCCTGACCAGTGG
3' ss Score
7.05
Exon sequences
Seq C1 exon
CTACATCAGCTCTTCTACAAGCCCAGCAGCAAGTGTCTCCAGGAGTGTACAATGTCCCAGTCATCGTGAAGGACAATCAGGATGGGCTGTGTGACACACCAGAGAGCTTGACCCTGACAGTGTGTCAATGTGATGACCGGAGCATGTGCAGAGCCCCTATCCCGAGCAGAGAGCCTAACACATATGGGGAGTCATCCTGGAGGCTGGGGCCTGCTGCCATTGGCTTGATCCTGCTAGGACTCCTGATGTTGCTAT
Seq A exon
GTGAGTAAGCAGACGTGTTCTTCAGGGTCCATGGCAGTGATGTCATTTACAAAAGCCACTGTGCTCATCTGTACAATGTGAGAAGTGTCATTCTCTAAGCCGATGACGAGCAAAGCTGAGGGAAATTGCAGGAAGATTCTGAAATGTTTAGCCTGTCATTTAGTAACAATTTAAATATAACAAAATGGGTCATATATGCAAATATTTTGAAAAAACAGGGTTGGGGGACTAGCTCAGTCAGTAAAGCATTTTCTCCACAAGCTGAGAACCTGAGTCCAGTCTCCAATAGGCACCTGAAAAGCCAGGTGCAATGGAGAATGCTTGTATACCAGCCATAGCAAGACTTGGGAGGCAGAGATAAGCTAATGCCTAGAGCTCACTGGCCAGCTAGCCTAGTCTACTTGGCAAAGCTCTGGGCATTGAGAGCGCCTCCCAAACAAAAAGTGGACAACACTAAGGGATGATACTCGTGGCTGCCCTCTGGTCTTCATCCAGGTGTGTGCTCATAATTACATTCCACACATATGAGGGAGGGTGGACATGAGAGAGAGAAATTATAAAGCTATTCTACATTCAGTCAATAATGTTCATACTTAAAGCTGTGCCTTTATGCATAAACGTGGGCTTTCTAAAATGAACATAAATATCTCAAATGCATATGCAAATCTTGTGAAGCCCTAATATAAAAGGATGCTGGTCAAATAACATTAGAGAGGGCCTGCATTAGGATCCACATCCAGGATGCACATTAATAGAACTTCAGGTCTGAGGTTCTATTGTTTAATCCAACAAGTCCTCAAAACAGAGTTTACCCCTCGTGTGCATCCCTCTAAAATGCCCACACCTGGGCTGCAGAGATGATGCAGTAGTTAGGAGCACTTGTTTCTCTAGCAGAGGACCCAGGTTCAATTCCCAGCACCCTCGTGGAGGCTCACAATCACCCATAACTTCAAGACTCACATGCTGTACTTATTCATACATATAAAAGTACTTTTTAAAAGCATTTTAATGTTCACACATAATAGTGAAGACATTTAGGGAAATTACATGTCTGTACTACCTTTTAATAAACATGCATTTTATTTTATTCAATAGATAGACTTCTGGAAATTTTCATTTTCGTCAATATTTTGTTAATCAAATGGTTCTCTGAATGTGAGAGTCCTCTACCCTCTATTTAAGGGAACTTTGAAAGGAGTTGCACAAATAAGTGATCCTTAACAAATTCACAATAATTCCCTAGTTCACTACTGAATCATAAAATATTAACGATAAAACAAATTCCCATGATAGCATATTATACTTCCACTGTCTTTAGAAATGTCATTTAGGGGGTAGAAGGATGGCTCAGTTATTATGAGCATATAGCTCTTGCAGAAAACCTGAGTTCAGTTCCCAGCACATATTTTGAATGGCCAATAACTCCCTATAAACACAGCTTCAGGGGATCCAATGCCTTCTTCTTCTTGCCTTCAGAGACATGTGCAATCAGATATGCATACCTACACAGAGACACACAATTAAAAATAAAACATTTTAAGGATAAATATGAATAAATACAATTTTTATAAGCCCTGTATTAAATTTCAAGATCAATTACATTCCATCTATTTTATAACTTGACCTAATTATATAGTAATCTAGGACTGATCCAATTTGCATAATTATGTAGTTCATTCTACCAATGCTAGCAGGTCTTCATAGCATCCATCACTGTCTTTTCCATCTATCAGACAACCATGATGGACGCACCATTTATTTCCTTTTTGAGCTGATGAGTTAGCTGAGCAAAGAAAGATCACATAAAGCATTTGGGGTTCCAGAGCTGGAGTGCAGTGCATCCAAAGCTCAAACCCTAGAAGTCTAATTTAGAGACTGTGTTCCCTAAAACCCTTCAGTAAACTACTTGACTTGTAAGTGGGCAGGTCAAGCATAGGGTTCATGTGGCCTTGACAGGGCAGAGAAGGTGAGCCATTGACATCAGAGAATAATAAACACCTGCTTTCAATAATTAGTATTTCTGGAGCTGGCGAGATGGATCAACAGCTCAGAGCCCTGGCTGCTTTTCCAGAGGACCTGGATTTGAATCACTGTACTCACATGGTAGTTTTGGGTTTTTTGTTTTGTTTTGTTTTGTTTTTTTGGTTTTTTTTTGTTTGTTTGTTTGTTTTTTTAGTTTTTCAAGACAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAGATCCGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGCACCACCATGCCCGGCTCACATGGTAGTTAACAACTGCCAGTAACTCTATCCAATTCTGGGGAATCTGACACCTTCTCCTGGCCTTTGCATGCACAAGTCATACACATGGTAGGTAGAGATAGATGCAGGCAAAACACCCATGCATATGAAACAAATATTTTCAGATGAATGTTTCTTAGCCCATTAGCAGAGTGATGCAATGACTGAAAGATCTTCTAAGCTAGGGACTCTCACTTCACAATTAAAAGTGCACTGATAAGGCCTCTGAGCTTAAGAGCACAGACTCTGCAGACAACCCAAGTTCCAGTTCTTAACACCTCGCACCCCCAATCCTCACATGCATCACACACACACACACACACACACACACACACACACACATATATTCAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGGACACTGACAGCCATTGACTAAACCATCGCTAGTTGCTCTTGTACTTTGTTGGTCAATTACCATTTACTAAGAAATTACTAAAGACCAGATTGCTGAAGTGCTGTCACAATCACCTAAAATCTTGGCTAAGGAGGTATCTCACTTGTGTGTGTATTTATGGGAACAATACATACACTCAGTATATATAAATACAACAGCAATTATAGTAATAATAATTTTTAATATGTATTATGGAAAAGGATTAAGATCCTCCAATAAATGCCCCTGCCTCCTCCTTTAGCTCATGATCATTGGAAAATTACTGTGTTTCACTTACTAAATTGTATGCTGTAGACACCAATTTTGCTTCCATTAAATATATTCCTTTAATGTTTAAACTATTGTGTTGCCTTTGTAACATTTTGGCAATTGCCATGTCAAATAGTTTCCAATGAATTTAACCATTCTCCATGTCCTTGTTCCTGACCAG
Seq C2 exon
TGGCCCCACTTCTGCTTCTGACCTGTGACTGTGGGTCAGGTCCCATTGGAGGAGCAGCGACAGGTGGCTTTATCCCAGTGCCCGATGGTTCGGAAGGTACAATTCATCAGTGGGGAATCGAAGGAGCTCAGCCCGAAGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000056632-Dsg3:NM_030596:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.070 A=NA C2=0.250
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000064718





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000111508
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr18:31469350-31472283 
LOW PSI
HsaINT0052442
(DSG3)
Human
(hg19)
chr18:29049313-29052246 
LOW PSI
HsaINT0052442
(DSG3)
Rat
(rn6)
chr18:15658521-15661894 
LOW PSI
RnoINT0051413
(Dsg3)
Cow
(bosTau6)
chr24:25984327-25987424 
BtaINT0052923
(DSG3)
Chicken
(galGal4)
chr2:105760864-105762759 
ALTERNATIVE
GgaINT0094727
([1])
Chicken
(galGal3)
chr2:109236875-109238770 
LOW PSI
GgaINT0094727
(F1NHU4_CHICK)
Zebrafish
(danRer10)
No conservation detected
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"