Special

MmuINT0053315 @ mm9

Intron Retention

Gene
ENSMUSG00000024331 | Dsc2
Description
desmocollin 2 [Source:MGI Symbol;Acc:MGI:103221]
Coordinates
chr18:20196554-20200078:-
Coord C1 exon
chr18:20199936-20200078
Coord A exon
chr18:20196779-20199935
Coord C2 exon
chr18:20196554-20196778
Length
3157 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TCTTACTGCTCTATGTCTAGATG
3' ss Score
7.37
Exon sequences
Seq C1 exon
GTACAGAAAGTTAAGTGACCCAAGAGGGTGGGTCACTGTTAATGAAGATTCAGGATCGATCACTATTTTCCGAGCGTTGGATCGAGAGGCTGAGACTGTCAGAAATGGCATTTACAATATTACAGTCCTTGCGTTAGATGCAG
Seq A exon
GTAAGAAATCTGCTTTTAAGATAGCTACCTCCATTTTTGATTGTATGCGTCCTCAGTTTTAAAGTAAATTACATATTTTGAATGTCATGGTGCTCTGGATCAGTCCTTTTAGATGTAACACAAAACACCCTGCTAACAAGCCCTGCAACTAGCCCAACAACATACCTGTTCATCTTTTGAGACAAGAACTCACTGTGCAGTCCTTGCCAGTTGGGACCTCTTTGTGTAGAACATATTGGCCTTGAACTCATATAGATCTGTCTTCATCTGTCTCTAAGTGCTGAGACTAAAGGCCTTTGCCATCATGCCCAGCCTACCAAACATATAGTTTTAAAACTGGCTTCATATACTGTTAATTTATTTTCCCTCAGCATAACATATAATTAGAAGTGTGCTGTCATTTATTAACCCATCAGCTAACAGACTCTTTAGTATTAGATGTAACTATAAGATAGCATCTTCTAAGATAGGGCCAATGAGATGGCTCAGCTGGTTAAGGTCCTTGCTACCAAACCTGAAGACCTGCACTTGATTCTCAGACACAAGGAGAGAATGGACTTCTGCAAGTTGTCTTTTGACCTCTACTGTCGATAATAATAGTTAAACACATTCCGTAAAAATTAAAAGAAAAACCAATTTGGTATAAGAAACAGTTATAATATATTAATGATAGTCCTTAGAAAGTGGGAAATCTACTTTAGAAAGATGTATTAATTTATCTTGTAACATTCAGGAATGTTCATAAGAAGGAGGAGGTATTTAGTCACATAATACACTTAGAAAACATAACATTTTACAGGAAACTAACAGTATACTTGGGGTCTAGATTTAAGCACATTGTATAAAAGGAATCAGTCACAGTTAATGTGTGTTAAATGAGAGAGGCCAAATGTCAGTTCACGTTGCCCACTTTGGTTTCTGTTGCTATGATGAAATGACCTTATGGAAAGCAACATGGAAAAGAAAGGGACTTTTTAAATTCATGCATCCACGTTGTAGTCCATCATTCCAGGCAAGTGAGGGCAGACACTTGAAGCAGGTAGTCACCTCCACAGTGAAGAGTGGAGAGCGTGAAAGCATGTGTATCTAGTGCTCAGTGACCTCTCTCTACTCTACAGCCCAGGGCTCAACATCCAGGGCTGATGCTATTACTAAGTGGCTGGGTATACTTACCTCAGTTAAGGCAATCAGGACCACCCCACAAACCCCCTCTGCACAGACATGCCCACAGGCCAATGGGATTCCACTCCTGACAAGCTGACAGGTAAACTAACCCCACACCATATAAGAACCTAAAATATAACGTTATATTTTGTGCATCTTAAAAATTCAGAAAAATATGAGCACAGTGATTGTGCATATAAGACCTATTTAGTGTGTGAAGTATAATTTTGTTATAAGATATATTTGTTTGGGTGTGGTGCATCCTGGCAATTACAGTACTTGGATATTGGAGGCAAGAGAATCAACTCAAGGGCAACCTCAATTACACAGTAGATTTGAGGCTAACCTGGGCTACCTGAGATACTTTCAAAAAGAACTTGAAAAACACAAGCTATAATTGAATTTAGTACATTTGCACTAAATTTAAATATGCAGTTATAAGAAACATAACTCATTATGCTCTAAACAGCAAAATTAAATTTTATAAGTGACACTGGAAGATGATTTAGATGTTACAACTCTTTCTCAGTTAACGCAAACATTCTCAGAAGTGAATCTTCTCAAATATTGTTTCTTTGCTGATTGATCCTTCCTCTTCTAGATGATATTAGATATTAGATGAATTTTTGCTGTTTGTTTTTTTTTAAACCAGGATTTGAGGTGTGATTTAATTTCTGTTTAACAAATCACCTTCTTTGTGTCCTTGAAGATCTTACATGTGCTTGTTTCAAAGCTCTGATGTAGGGTAAATGCATCTTCCAACTGGTGCTTCTGTTGTTTCTGTTAACACTACTCATTAGGACCTATCCTAGCATTAACAGGGGGTATCTGATAGACTCCGCCTTTGGAGTCTCCCCTCCTACCTTACAATATTTTAACTGGAAGGCAGTTTTGTAGTGACCTGCACATACATGTCTGGTCTGTGAATCAGACCAGTTCTTAGCCTGGTTGCCTGGTGTGTGTAGCCTGTGATGGCTACACAAGACCCAGCCCCTGTGACAGAGGGGCCTTAGCTAAAGTTTTGGTTCCCAGGCAAGCTTAGTTTCCATTTGCTTAGGTTGGCAGCTGCATATAAGACATGCCGTCAAGCTCTTGTGGTGAGGTTTTTGTTTTTCCTTTTCCTCCATCTGCAGTGTCCAAATCCTCCTTCATATGTGGAAAGAACAAATGGTTTAGACAGGACTCCTAGTTTCATGCTTGGCTTTAAACTTCATAACCTCCTTCCCCTGTGATTACTCCATTTTTGTATGCCCCAGACTTCCTGATGCAGTGCCCTGTTTAGAGTTATCAGAAGGATTTACATATATGAATGACAGGTTAATTACAGAAGTTACACCCACAGTCCTAAGTTCCGTTTATTTAGTCTATAGATGACGGCTATTTATGAGGCTACACCCATAGCGATAACGTCTACATTTGAAAATGTCTCAATACCCTTGAACCATTTGTGGTTAAATTTTCTAAATACATATCTTCTACGACTCAACTTCCTTCTTCCAAAACCTAAGTATGTATGCCAAACTCTAGTCTAGTTCTCTAGTCTAACATTTATAAGTTCTCTAGTCTAGCCTTCAAGGGTTCTTAGCTCTTGCCTGTGTCAGTTCCCACCTCCTTATCCATTTTCTCCACATCACTGGTACGTGTGACATGCTGCCCACACTTTTAAGCTTAGTATGCATACTCCTTCTATACGTTTTTGTCTCTTCAAAATCAACTAAAGCTTCTCTGTCAACATTTTTCATTCCTAATGAACATGATCTAGTGAATAGACAAAAATATCTAAGTAGCAGTTATTATATGTATAGTCAATCCACTTGGAAGCAATAAGATTTTTCTTTTAGTGTTCCCAGCGTTGTTGCTCATGACTGTATTTGTTGCAGTAACCTATGCATTATAAGTGGTTAGTAAATATAGATATTAATTTTCATTGTAGGATTTCCTAGCAAAAAATAAAAGAAAGAAAAAAAATGTGTTCTTACTGCTCTATGTCTAG
Seq C2 exon
ATGGGAGAAGCTGTACTGGAACTCTGGGAATCATACTTGAAGATGTGAATGATAATGGCCCATTCATACCCAAGCAGACAGTGGTGATATGCAAGGCTACCATGTCCTCTGCTGAAATTGTTGCAGTTGATCTCGATGATCCAGTGAATGGCCCACCATTTGATTTCAGTTTGGAGAGCTCTGATTCGGAAGTTCAGAGGATGTGGAGGCTAACAAGAATCAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024331-Dsc2:NM_013505:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.020 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

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

							
A:
NA

							
C2:
PF0002812=Cadherin=PD(14.0=17.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000074702





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000042905, ENSMUSP00000116063
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr18:31074908-31079846 
LOW PSI
HsaINT0052282
(DSC2)
Human
(hg19)
chr18:28654874-28659812 
LOW PSI
HsaINT0052282
(DSC2)
Rat
(rn6)
chr18:11834271-11837410 
LOW PSI
RnoINT0051279
(Dsc2)
Cow
(bosTau6)
chr24:26364580-26370704 
LOW PSI
BtaINT0052785
(DSC2)
Chicken
(galGal4)
chr2:105639455-105640873 
LOW PSI
GgaINT0101877
([1])
Chicken
(galGal3)
chr2:109114616-109116034 
LOW PSI
GgaINT0101877
(F1NJD7_CHICK)
Zebrafish
(danRer10)
chr20:7281999-7283951 
LOW PSI
DreINT0060055
(dsc2l)
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"