Special

MmuINT0053335 @ mm9

Intron Retention

Gene
ENSMUSG00000059898 | Dsc3
Description
desmocollin 3 [Source:MGI Symbol;Acc:MGI:1194993]
Coordinates
chr18:20119431-20124383:-
Coord C1 exon
chr18:20124129-20124383
Coord A exon
chr18:20122071-20124128
Coord C2 exon
chr18:20119431-20122070
Length
2058 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGT
5' ss Score
7.97
3' ss Seq
CTCTTTTTTGGACTTTACAGAAA
3' ss Score
7.99
Exon sequences
Seq C1 exon
TGCTCTGCCAATGGATTCACCACCCACACTGCCAACAACTCCAGCCAAGGCTTCTGTGGTACAATGGGGTCAGGAATGAGGAATGGTGGGCAGGAGACCATCGAGATGATGAAAGGACACCAGACCTTGGACTCCTGCCGTGTGGCCGGGCATCACCATACCCTGGACTCCGGCAGGGGAGGACACATGGATACTGACAACTGCAGATACACATACTCAGAGTGGCACAGTTTCACTCAACCCCGACTTGGTGAA
Seq A exon
GTGAGTTTCCTTAGATGTTTTACTCTGAAGTAAAGAACAATCAGACACTGATATTAATGTACATTTCCAGAAACTGCTTTGCCACAGTGTTTATGAGTTTCCTCTTGTTAGTCACTTAAAAATGCTTTGGTTTTGTTATAGTCTTTAATTTTTAAATATTTTGATTCCTCTGTCACATTCATTCAGTTTCTAGACCCTTATAAGATCCAGGGACGCCAGGCGTAGTGGTGCATGCCTTCTAATATCTGCCCCTGAATGGTGTATCTTTTAGGTGTATCTCTATCTTATAAACTCCTTGGATAAGAAAAGAATGTGAAGAAAAATTCTAGTTCCTCACAAATAGACCTTTTCCAAATTAAATTTGTATTTTGCTATGAAAACATAAACTTCTAAATGCAGTTTTATGTTAAAGACTCCACACTTTACTGAGGTGCAGCTTTAGCTTAGAAAGCTGCACAATTAAGTTAAGCCAGACATTATTTACTTAGTTTACTTTTCTTATTTACTCTAAGTGCATCACTTACGGTGAATCGAGGAATCACCCGCGTAGACAATGTACAGGGAAATGACCCAGTTCATGGGGACATTTAAAATTTATTCTTAGTAATTTTGAAATATACAGCACACCACTATATGGATTGTTTTCAATACATAAAGCATACTACCAGATATAAAGGGCCTTATCTAGAAAGAGGCAATGATGAGGAAGAAAGGGTTCAATGAGTGGGTCTCAGTCTAAATCAGCAGTGTTAGGATGCTTTTAAAAATACAAATGCTTTTGTTTCATTCTAGGAGAGTCTAATTCCACTGCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATACAAAGTCTCACATGTGATTTGTATGTCAGGGAGGGTAGGGTAGGGGTCCTGTTTAAACATTCTTCTCAATGATTCATGCCTGAATCAGAGGGAACTTATGTGCTCTTAGCAAATATTGTACCAGACATGGTTAATTCTGTGATGGACAGAATATGGGTAATATTCTAGAAGAGGGTTCTTGGTCACTGCCTATATTATTATTATTTTTGTCTTACATTGTCACATTAAAGTTTTTACATGTTTTATATTTAAAGATGGCATTCATGTGAGATTATAAGAATTGTCAAAGCTCCAGACACTCATTTAGGAACGCCCTTCAGTGTTATAACTGGGAGGAGAAGCTAGCAAGGTCATGGATAAAACAGTTGGTAGCAGCCAGCCAGGAGCTGAGGATAAGGGAAAGGCTGTGCAGGTCAGCATAGGGAACCTTGAAGATTGGCAGACGTGCCAGTGAAACATAGTACTGAGGGTAAGGGAAAGAGGGTAGCAGGACATTGTACTGAGGGTAAGGCAAAGGCGGTCAAAGGCTTGGCTGCCTCAGAGCTCAAGTGTAGCATCTGCAGTGTGAGTTAAATGGATGATATTAATTTCATTGATTTTTCTGGGGATATATCTCTGGCTTTTGGATATGTTGGAATGCAGAATTTTTTTTTATGTTCCTCATCACTGCACAAGATAGAGGTTTAGTTCATGGTCATTGTATCCTTACGAGTGATGGGCACGAGTAGTATACTTCCATCCATTGCTCTTTCTATAATTAGTTTCCTGAAATAACAAAGTGATATTGGAGGAGAGGTTGACTTAAAAGTAACACAAGTTAGTAAACTAAAGTTATTTTAAACCAGAACCATTTGGTATTCACCTACAGATTCTAACCATTTGATATATTGTCTCCATCATGTGAACTGACCTCAATATAAGATGTAACATTTGGGGATAAATATTTAATTATGACTTAAGTGTACTTAGATATAACATTTGTAGACCTACTTTTATTTTGATGAATTATTAAAAATGACAACTATACTGATTTATGATATGGCTGTAATATAGACCAATCATGTGCATTTTTTGTGTGTAGGACTCCATTAGAGGACACACTGGTTAAAAATTAAACATAAAAGGTAAATAAAATAAATTTTCTGTTCATATGTTGAAGTTGTTTTAAAAAAATAATACAATCCTCTTTTTTGGACTTTACAG
Seq C2 exon
AAATTGCATGTGTGTAATCAGAATGAAGACCACATCCCATCCCAAGACTATGTCCTCACCTATAACTATGAAGGCAGAGGGTCTCCGGCCGGCTCTGTAGGTTGCTGCAGTGAAAAGCAGGAAGAAGAGGGACTTGACTTTTTAAACAACTTGGAACCCAAATTTCTTACATTGGCAGAAACATGCACAAAGAGATAATGCCAGTGGGTTACAATTTGAGATAGCCTTATCAGACATTCCAGAAATTTGAAACAATGATACTGTAAAACAGACTCAGTACTTATACAAAATGGTCTTGAGTTATGCTGGCTTGACATGTGATATTCTGAGTGTAGTCTAGTGTAAAATTGACACATATTCGGAAGAAACCATTTGTGAAATTCTGATCTTTTCCAGGAGTTTTGTGCTGTGTGTAACTCTCCTGCAAGGTGAGGCAGGAACTGTGCTCCAGTTCCTGGTCTGTTATAGGGTCACGAGATCCTGGCTGTGTGCAGGGCATGTATCTTCAAGTACAGCTAAGGTATACCTACATTGTGTGGCTAAGAGCTTCTGCACATATTATTTTCTCCATTTTACAATCTCCCCCCTATCAATTTGCGTTGTTAATGCAGTTTGTTGCTGACCACTTTTCAAAGAGTACAAGTGTTAAAACAGAGGACCAGAAGCGCTCAAGCTGTAGTAGTAGAGTTAAGTAAGGTCCACAGAGAACTCACCCTGTCAGGAGGATATTTTCCAAACAAATGAAACTATTAGTCTGAAAACAGTTAAGTTGTACCACTATCACATCCTTCTAAGGATGGTTTAAGAAACAAACAAAACACCAAGGAAGGATGTTTTAGGACAGAACAAACTTATGATGCATTGCATTAAAACTTTTGCAGAGGTGAAGATCGAGGGCCTGACTCTTTATAATTTCTATCAAATACTTTATTGGACATTGGAAACAAACTTTTGTACGCTGGCCTAATGTGTGCCAATTTTCTGTTTCAGCACCTTCTGAAGCCAGTGTTTATTTGCAACCAAAGTATGCACTGGAATGACATTTAAAATACAAAGGAAACAACAAGGAAAATGACAATGATTGAAAATAAGGCTGGGGATGGCTTATCTTGTAAAAAGAAATCAGGATCTTAAAGGAGTAGACTTCCTTCTGCCAGGCTACAGTGGGCTGTGTGACACCTAAAAGTGTCAGCTTCTGCCTGCTTGAGTAATTTGTTTAAATTTAGAAACATATATTGTAGTTTTAGTGGGGAAGAAAGAGACAGCCACATGGAAGAGTAGATTCATTTTGCAGGATATATATACATTTGTGCATTCAAACATTAGCAGCCAATTACGAGATTCAGCCCTCTACACTGCTGGAGCCTACGGCTTCCTGGCCTGCAGTTCACAGAAAGGATGTGGTTTTCTTGGGACCTAGTGTTGACAGATGCTGAAATACATGCTCTACCGCTCTTTTCTTCTATGTCTTCTCTCCTTTTCTTTTTTTTTTCCTTTCTTTTATTCTATTCTGGGGTATTGGATTACCTCTGCGTATTGCCTGGCCTCAAAATCTTAGTCCTCCTGTTGCAGTCTCTGGATATTAGAATTATAGGCAGATACTACCATTCTTGTTATTGAAGTAGAGCCAATTGGTCTTGTCCTTTAAAGTTGGAGCCTTCATGGTGCTGGGAGATAGTGGGAAAAATGTTGTTACCTTCATGTGGACTCAGAATCATAGCTTTGTTTCCAGAACCCACTCAGACTTTATGTGAAAGTAGCTCTGGCAGCCGTCCAGAGAGTCAGCCCTTCTTTTTCCTGTCTGCCAAGGCTGCTTGAAAGCCCTGCAGCAGATTCACTGAGCTGGCAAATCTTCCAGAAACTCTATAATCCTTCAGAGTGACTTTATTTTTATTTTTATCAGTTTGCTTTGTTAGAGGGGATTTATCACTTACAGAAGAACCAGGAATTTTGGATCTATGCAGGAAAGACCTTTTTCAGACCTCTTCTCATCTGGAATATGAAATCAGGAAAGTGGGCTGCAATGGGGGATGTAACTCAGCCTGGCATGGACAAAATAAAGGAATTGAGTCCAAGCTTTGCGTAAAACAGGCATGATGACAACATGCCTGTAGCCACAGCACTTAGGAGGCAGGGAGCAGGAAAATCGAGGGAGTTCAACATTCTCCATAATTATGTAGAAGCTTGAGGCCAGTTTAGGTTACATGTGGTGAGTCTTTGGATGGGCCAGAATTGTTATACTGGTCAAACTACATGTGCATCTAAGATTTTGATTAGATTTTAATTTTTTTCCTGTTTTTATTTTACCCCAAGGGTTACTTTCATGATAGACTTTTGAAACAATCAATTTGTTTTTTGTTCACAGCATCATATAATATTATACTCTTCTCACATGTATAGGTGAAAATTGTGCTATTTTAGTGTGTAAGAAAAATCATCTCTCCTTTTGTAACACTTTCCTTCCCTCCCCTGGGTTTTTATGTAAATGTACAGTCCATTTTTTTCTTACATTTATAAGGAAGAAGTTAACTGTCTAAAGAACAATTGGAGTTTATTTTTCAATGTTATAAACAACTTTAATTTGACAATTAAATTGCTTTTGAACCTTGTCAAATAAAAACAAACAAGCGTTGAATGTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000059898-Dsc3:NM_007882:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.239 A=NA C2=0.200
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0104912=Cadherin_C=PU(46.8=68.2)

							
A:
NA

							
C2:
PF0104912=Cadherin_C=PD(51.6=97.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000111514





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr18:30994373-30996790 
LOW PSI
HsaINT1011889
(DSC3)
Human
(hg19)
chr18:28574339-28576756 
HsaINT0052303
(DSC3)
Rat
(rn6)
chr18:11755644-11758359 
LOW PSI
RnoINT0051298
(Dsc3)
Cow
(bosTau6)
chr24:26447760-26447841 
LOW PSI
BtaINT0052805
(DSC3)
Chicken
(galGal4)
chr2:105634357-105635130 
LOW PSI
GgaINT0101881
([1])
Chicken
(galGal3)
chr2:109109516-109110289 
LOW PSI
GgaINT0101881
(F1NJD7_CHICK)
Zebrafish
(danRer10)
chr20:17050369-17056184 
LOW PSI
DreINT0141999
(si:ch73-74h11.1)
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"