Special

MmuINT0053299 @ mm9

Intron Retention

Gene
ENSMUSG00000044322 | Dsc1
Description
desmocollin 1 [Source:MGI Symbol;Acc:MGI:109173]
Coordinates
chr18:20248039-20253160:-
Coord C1 exon
chr18:20253018-20253160
Coord A exon
chr18:20248252-20253017
Coord C2 exon
chr18:20248039-20248251
Length
4766 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CCTATTTTTATCTATCCTAGCTG
3' ss Score
7.06
Exon sequences
Seq C1 exon
GTATGAGATGGTAGGAGATGAAGATAATTGGTTTGAGATTAACAAAATCACCGGAGACTTGAGAACTGTGAAAGTACTGGACAGAGAGTCGAAGTTTGTGAAAAACAACCAGTACAATATTTCAGTAGTGGCGACAGATACAG
Seq A exon
GTGAGTGCCATTTTCTAGAAGAAAAACATGAATATAGAATGTGTCTAGGTCAAATCTTAGTTCAGACACTGCTTCCTCTAAGGTTCTAATTAATAATCTACAACAATGTGTTCAGTATGATAGCTCATTTCAGTCCGATCATCCATTTAGTGCCCGGTACACCCCTCGGGCAGAGCCACAGGAGAGTGAATGATCAAAGTCTAATTTTGAGTACTGGTTTGTTTATTTCTGCTGAGGAATATAATTAAATCTCATAATGCCTTGTCTAGGGACTTTTTTTTTTTTAATTGTCCTAGTGAGGGTTACTATTGCTATGATGAAACACTATGACAAAAGCAAGTTGGAGAGGAAAGGACTTATGTTATTCACAGCTCCTTTTAACAGTTCATTGTCAAAAGCAGTGAGGGAGGAACTCACACAGGGCAGGAACCTGGAGGTGAGAACAAATGCAGAGGCCATGGAGGAGTGCTTGCTTATCATGCCTTGCTTAGCCTGCTTTCTTATAAACTCAGGACCACCAGCCCAGGGATGGCTCCACTCACCATAAACTGGTCCCTCCTGCATCAATCACTAATTAAGAAAATGCTCTACAGGCTTGTCTGTAGCCTAGCTTTATGGAGTCATTTTCCGAACTGGAGTTTCCTCTTCTCAGATGACTCTAGCTTGTGTCAAGTTGACATAAAACTCGCCAGGACACTTACCTTACAGGTCTTTTCATATATATGTTTTTGGTTTCCTGTTTTTATAGGATGTTCGTGTGTGCAAATGTGTGTGTCTCTGAGTCTATATATGTTTCTTGTGCTTTTACTTGGCTTCTTCTTTTCTGCTTATTTTGTCCTATTCTGTTTTGCTTGTATTATTATTGTTTTAGATGCCTGTTTGTTTTCTAAAGAGAGAAAGGTAAAGTATGGATTTAGGAGGGAGGGGAAGTGGGGAGGAGTTGGAAGGAGCTGGGGGAGAGGAAACAGTAATTGGAATTTATTATATGAAAAAAAATCTATTTTCAGTTAAAGAACAACCATGAACTAGTTCTACTCTATAGAGTGTTTCCTTCAAATACTGTCAACTGTCAAGTGATGATCCTGAAACTCTTGAAATAAACTCCTGCCTCCTGGAACCATATTAGATAGTTTAAATAAACATATGCATATTAATGTGCTACCAATGTTTGCTAGTGTACACATGTACTATTATGCAAAACATTATATAAATCTATGCCATAGAGATAAATGAAATAAAAGTTAAAATGAGTAATAAAGTATTACCCATGTAAGACAAATCCTCATAGAGATTTAAAAAATTATCATCTTGGGGTTTTCAGACAGAATTAAATTTTTTGCCTGTTTGATTAACTCAACAAGATTTCTGGTGTTTTTAGATGTACATGCTAAGCATGTAAAATGTATTGACAGACAGTAACATAGGCTATTTCTACACATTTCTTGAATTTCCTCAAATTAATAATATATAACAGTTCCCCAGATATTATTGGCTATCCAGCCTATTTTAGCTACAATGTTTTTTTTTTAAATATAAAAGTATGTGTTTGGGTATAGGTGTATGCATGTGAGTGCAGGTGACCCAAGAGGCCTTAGGAGCTGTGGGTGGTGTGAGCCACCTGTTACGAATGCTGGGACTTGAACTCGGATCCTCTGGAAAAGAAGTACCATGCTCTTCACCACTGAGCCATCTCTCTGGCCCTTTTGTTGGTTTTAAAGCAAGCAGTGTAGCTACTGAGAGACCAAAGGTTAACTGATGAAGACTGCTTCCTGTTTATGCAGACAGGACAAGCTGACTCATGACCACTCTGCCCATTAGAGCTTTTCTCACCTCTCAGTCCCGCTGCCTTTGGGATGGAAGTACCAGGTTACACATCCTCTTCATGACCATGGAAATGAGAAGTCATGAGATGAGGTTTGGTCTTTCTAATAACGAAAGCTTTACTGCTTTATATTCTGAGCATTAAAGAACTCTCCTATCAGCTAAGCTAATCCAGCTTTCAAAAGCTGAGCGCCCTTTTACTGTGAATGTCATTACCAAGTAAACTACCTGCATAGTACCTTTCTCTTTGATCCACACCTCAAATATACTCTGTGTTTGTTTTATAGAGTTATCTTACTATAAGTTCCAAAACTCTGCAGAATAACAGGTGGGCGGATATTAGCTGAGAAACATACTGATTTAATATACTTTACAGCTCTGGATAATGTGGTTTATTTTTTAAGTTTGCTATTCCTATAAGTAAAAATGAAATCTAAACAGCTTATACATATAATTATGCTGTGAAACAGGACTCTCTATCTACTTACATTTAGATGTTAAAATTCTAAGTGCAGGATCATGGAAACTAGGAGGCATGAGATGAGGAGTTGGTCCTTCTAATAATGAAAGCGTTACTGCTTACATTCTAAGAAGAGAGTCTATGGTATAACATTTTATTCCAGTAGAGAATGTTTAGATGTCTCTACACACTGAGAGAGTTTGGAGGCTTTTAGGGTAAAGCACAAAGAGGGGTGAAGCCCTGGCACTAGATGAAAGGAAAATAAATTCTTATTTAGAGAGGATAAAATTACAGAGAGCAAAATATAAGAAAGAAACTTTGTTGCTTAGTACTGAAAGATACGGAGGGTAAGCATGGTAGGGTTAGTATAAAAGAGCAAAGCTTAGGCAAAGCACGCCCCAGAGTCATACATTACCTAGCCATGCCCTAGAGAAGATGAGGATTCAAAACACATTTATGAGAAAATTAATGGTAATCATGTATTCATACATTTAGATTAATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGAACTTGTTTTGGTGCTCAAAGGTATTCCTAAATGATAATTTAGGAAGTCCTAATGGCCCCTTAGAATCTAGCTTATGTCCTTGTATTTCTCATGTGCATCATTCTTCTCTGTCAGGCTGATCTCCCTGCTATCTGTCTAGAGAACGCTGTTTTATGTATCTTACTCCTAGAACATGAGAGTAGCAGGGCTCCTCTAGCCCTACCCTGAAGCACATGTTCCTTAAATTATTCAAATGAATAGCCGTGACAGCTTCTGTGATTGTTCTCTGCTAGTCTTTGTTTGATTCATAATACTGCAATTTAAACATTATTATACACTGGAAATAAATATAATAATTATCACATATGCTGTACTGTTACTTTGAAAGTGTGCCTTCACTTGCTCTCATTCATATTTTTTTCTTCTAAGTTGGTTAACAGCTCAAATTCCCTCTACCCTCCACCCTACCACCTCTCCAGTAAACTGTCCCTTTATCAAGCATGAAGATGAAAATTTGGTACATATCTGTTTAAGGCATTTTAAATGTTATGTGTGTGTGTATGTGCGCGCACACCTATATGCATGGCCTTTAGAAAGGTAGAAAGCGGCATTGGATCCCCTGGAGCTAGAGTTACAGGCAGAACAAGGCTGATCTAAGGCTTTCGCAGAGACCCTGATTAAAGGACAGAGGGGACCTAGTTCTGTCTCCTTGCCCAGGGACAGATTTGGCAAGATCCAGTCTATGGCTGGGGCCAGGGTCTCAAAGGAGTTAAGGTTTCAGTTCTTGACAACTTGCTCCCCACCCCCACCCTCACCAGAGAGATCAGTCCCAAGACCTCTGTGGACAGCATTTCTGACACTTGAGGTATTCTACATTCACCATGTGCTTTATTAGCCTTCTGCTGAATTTGTCCCATTTCTTCCCTAACAACTGGATGTAAGATCCTTACTTCTTATTAGGCCTGCTTGGCGTAACACGTTGCTTGTGCAATAATTCCTGACCCCAGGTTTCCTATCTCCTCTAACCTTTCTTCTGATTTTCTCCTTTAGAAGCCTTTCATTGAAGAATAACCAGTTTGTCCATGTTACCCATTTATGACATGAATGTTAAGATCTAAATTGTGGTCCTGGGCAGGAGTAACATGACTCCTCCCCAGTAAGGCCCAGCTAACGTGTCATGGTTAGACTTGTTGTTCCTCTGTGGTTTGAGAAGCATGTAAACCTCCAGGTTCAGGCTGTGAAATTAGCTACTAAGGATTTGACAACTTTGATGTGTACTTGGTGCTTAGAACAACTGAGCTCAAACCTTATGAAAGACCTTCTTAGTTTTTAGCTTCTGAAAAAAAGTCTTAAAATTATTACTGAGTGGTTATCATATCAAAGTGGTAAGCATTTTCTTATTTGAACCCAAAAGTAACACACATGATGTTAGAAGCTAATGGGCATACCACAACTCAAGAAGAAATAGAAGAAATAATAAAGAGCTCTATTCATTCAGGTCTGACTTATAATATTGTGAGCTTCAGGATATGGAAAACAGTAATGACAGCTACTGACTTCAGAAGCTCTTTCTCGAAGGGCTATGGACTTAGATTTTAGTTGGTGCATATACTTCTTAGTTCTGTGGCTGGTACTCCCCACTCATTGACACTTATCAATCAACTGACAGGTAATTTAAAGTAAGCTGTTGAACTAGACAAATCTATGTAGCTGCCTCTTCATGATGTTCCATTTACTATAAATGGAAAATCAGGCTCTGGTGTCTTGGCAAATTTTCAGAGTTTATTTTCAACTCTGCTTTGACTAATAAACTTCCAAGTGACGTCGAGCATCTCCTGTTCTGTTTTTATCAGCATGTTTCAAACAGAGAATCATTAAATGACAAATATTGGTTAAATGTAGGCTTAAGTGAATCTCAATCTGCTATTAGAATAACCTATTTTTATCTATCCTAG
Seq C2 exon
CTGGCCGATCTTGCACAGGAACACTGGTAGTTCTTCTGGAAGATTTTAATGACCACCCACCACAGATTGACAAGGAAGTGACCATTTGTCAGCAGGAGAAGGATTTTGCTGTTTTGGAACCTATAGATTTAGATGGGCCAGATAATGGTCCACCTTTTCAGTTCCTTCTGGATAATTCTTCCAGCAAACTTTGGACTCTAGAATCACAGGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000044322-Dsc1:NM_013504:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.061 A=NA C2=0.056
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0002812=Cadherin=FE(51.6=100)

							
A:
NA

							
C2:
PF0002812=Cadherin=PD(14.0=18.1),PF0002812=Cadherin=PU(54.0=65.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000025187





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000042303
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr18:31134785-31139747 
LOW PSI
HsaINT0052267
(DSC1)
Human
(hg19)
chr18:28714748-28719710 
LOW PSI
HsaINT0052267
(DSC1)
Rat
(rn6)
chr18:11885050-11889687 
LOW PSI
RnoINT0051263
(Dsc1)
Cow
(bosTau6)
chr24:26304993-26312672 
BtaINT0052769
(DSC1)
Chicken
(galGal4)
chr2:105639455-105640873 
LOW PSI
GgaINT0101877
([1])
Chicken
(galGal3)
chr2:109114616-109116034 
LOW PSI
GgaINT0101877
(F1NJD7_CHICK)
Zebrafish
(danRer10)
chr20:7283939-7283951 
DreINT0145643
(si:dkey-30c15.12)
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"