Special

MmuINT0053362 @ mm9

Intron Retention

Gene
ENSMUSG00000050272 | Dscam
Description
Down syndrome cell adhesion molecule [Source:MGI Symbol;Acc:MGI:1196281]
Coordinates
chr16:96862345-96865676:-
Coord C1 exon
chr16:96865386-96865676
Coord A exon
chr16:96862522-96865385
Coord C2 exon
chr16:96862345-96862521
Length
2864 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGC
5' ss Score
5.06
3' ss Seq
CATCGTGGCCCTGCTTTCAGGTA
3' ss Score
9.19
Exon sequences
Seq C1 exon
AACCCCAGTTCTCCAAGGAGCAGGAGCTCTTCGCCAGCATCAATACCACCCGAGTGAGGCTGAATCTGATTGGCTGGAATGACGGCGGCTGTCCAATCACCTCATTCACTCTTGAATACAGACCCTTTGGGACCACGGTCTGGACCACAGCTCAGCGGACCTCCCTTTCCAAGTCCTACATTCTGTATGACCTGCAAGAAGCCACGTGGTATGAACTGCAGATGAGAGTGTGCAACAGCGCCGGCTGTGCGGAGAAGCAAGCCAACTTCGCCACGCTGAACTACGATGGCA
Seq A exon
GTAAGCTCACGGCTTCATGGCGTTCCTGTTTGTGGCTCGGGGATGTGCACACGTATACTATTCACTCTCCTACGAGACACTTATCATTACCACAGAGTGAGCAGTGCCTCCATAGCACTTTAGGGTTTGGGCCACTCAGTCCCCTCTCTGCGGGCTCCCTAGTCCGTTGTACACAGATGACTACCAGTGTGTGTCTAGAGTGAAGGGACTGAAGACTAAGGGGAACACCCTGGGGAGTCTTAGTCTTAGAACTCCCAGGAGTGGCTTCTCTCAGGGCTGAAGGACTCTGCCTCATGGTTCTGTTGCTTTGCAGATGACTGTGAGCTAACACTGCTTTTGTTGTCTCCCACCCCTTCCCCATCCATCCCAATCCACACAACTTTCTTTTTGCTCTCATTACACCCTTAAAATGCACGTGCACAGCAGTTTTCCTTGGCAAGGGAAGTTAGGTTAGTCTCACCAGAAGCAGGGGCACCGAGGGGGATAGAATGGGGGATGGGTCAGGCTGGGCCCGTGCTCACACGCATGCATACCTTTATGCACATCCTAAAAGCTAGGGAGTCTCTTGATCTCTGCTGCCCCAACTAAATCGTTTAAATTTTGGGTACCTAAACAACACCCAGCCCAATGAAGCTGAGGCAGCCGATCAATCTTAACAATCAGCCAATGGGTCTTCCTTACAGCACATCCATGCTGATTTCTGTAGCCCCACAGAAACCCTCACTTATGGAAAGGCAACCACAGGCTCTGAGTTCTGATCACCAACAGTGACTCATCAAGCTGTTTGGAGCTGTGGACAAGCTCCCCGCTCAGCCTTCTGTCCATTTCGCACTGCTCCAAAGGGACTATGGTCCCAGGTAGGCCCTGAGTTGTGCTTCTCTCTCTGGCATACCGTGTTAATCCTCTGGCTTCCATCTCTTGCCAACAATCATTGCTTCTAAAGCCTATCTCAGATAGAATCAGATTCCTCTTGCCTCTGCAGCTGAACTCTTGGCTGTAGGAAGTACTTCCAAGAGAAGTCCTTCTGGTATTGGGCTCTACCCAATGGGCTGTTGTAAAGCCCTGGCTCTTGGACAGCAGCTGCCTCTCCTCTTCAAGGGTCCAGGCCCCTCTTACATGGCCTCTCTCTGTTTTGTGTGTGTGGTTTATTTAGAGAAGTCTTTGTCCTAAGAATCATGCACAAGCAGAGCTACATTCATATCTAAGGTTTTCCACCAAAGGTGCCTGATTGTCTGTTCTTACAAAATGAAAGGCTAAGACCATCTTCTATCAAGTGCATTTAAATGCTTCACCCAAGCCCCCTACAAGCACATGCCCAGTTGGACAGTCAGTGTATGTGTCACTTTGGACACCTATACTCTGGACCCAGGCCTGACAGAGAGCTTGCCACACATGGGTGGCACGTTGACACCTGGTCATGTCCCAGATAGTCTTCAGACTTTAATTATTCAGCTTCTGAGACAATGTTCAATGTTCTCACTTCACTCAGAACCATATTAGGAAGGTGTGTATGTGTGTGTGATTCTCTTTCCTGAAATCTGAAATAATTTCATGGCACAGAGATGTAAGAGTACATATTTGTTTTTGAAAAAGGTGGTAGACCTATCTAGTCCATACCATGGCCGTGTGGCTTTAGTATCTCTTTGGCCACTGTGCTTGTTTTCATATTAGGAAAAACACACATTGAAACAAAACCACCCTGATAGTCACTTCAGGCAGATTCTCAGCTCCCACCTCTTTATCTGAATCACCTCTATTTCCTTCACCAAAACTTTCTGTGTGTCCTTATGGTGTCCTGTTCACAGACCAGCCTCAAGCACCGATTCTGTGCCTCTTTCTTGGAGTCTGGATATCTGTAGGCTTGGGTTTGCTTCCCAAGATGCTGTGATACTAAAAGAACTCACTCTGCTTAGCTCCAGCAGAGGTCAGAGAAGGGCAGGGGTTGCATTTTCATGGCTCCAGTTACTAAACAAGATCATCTTTTTGCTCTTGGGATAATATATATACATATATATTTTTTCCCCTTAAGCCCTAGCTTTCTAGTCTGCATAGAAAAGACAGTGGGAATGGAACCGCTTATGTAATGGACGATTGTAAAAATCACAGATGTCTGCACCCTTGTGTTCAGCCTCAGGGTGGAAAGCATCTTAGCAGCCCAGAGTTCAGTCAACTTCTATTTTGTTTCTTACCGCTCCAAATAACCTAAGTTTTGTAGCATAATAACAAGGCCCCCGCCAGCGACACGCTTTTCGGTGACCTAGATAGACCCCCCCCCTTTGAAATGTTGCCCTTCGCTCCTTCTACCCTAAACTGGGAATTTTAAAAAGCAGCTGTGAAACTGGGGTTGAAATCAAGAGAAAAATCAAAAGAACAAAAAGGTCGTCTATGCTTCTTTAGGCTCAGGAACCCTACATCCTCCCCAAAGGGGGTCTTCTGTCCAGCTGACAAATCTATTGTTCTTCCTTTCATAGGCAGTGTTCAAAGAGCCTTTAGCAAAAGCACCATGATTGACAGCCAAGTGGGCATTGGATTTCAGGTGAATCCAGGTAGCTTTTGTGAGCCCTGAGCCCAGGCACCATACTGTCAGAGGGTGGCATCTTAGAATGTTCTACCAAAAACAAACAAACAAACAAACAAACAAAGCGAAGTCCTTTACAAAGATGTGCTAGGGTGAGTTGTAAGTTTGGGCGAAGGGAAAGTTGAGAAAGTCAGCCCACAGAGATTCAGGGAGCTGGTCCTCTCATTTCTCATCACACAGACACCCCTGGATCACACCGTGCGGTCTCTCTGTAACCCATCATCCCTAAAAACTCCACCACGCCGTCGCCATTAATAGCCATCTAACATCGTGGCCCTGCTTTCAG
Seq C2 exon
GTACAATCCCTCCACTCATTAAGTCAGTTGTCCAAAGCGAAGAAGGGCTGACAACCAACGAAGGGCTCAAGATCCTCGTGACCATCTCCTGCATCCTGGTCGGGGTTCTACTGCTCTTTGTGCTTCTGCTGGTTGTGCGGAGGAGACGGCGAGAGCAGAGGCTGAAGAGGCTGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000050272-Dscam:NM_031174:26
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:
PF0004116=fn3=WD(100=82.7)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000056040f4734A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000056040
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr21:40075214-40078686 
ALTERNATIVE
HsaINT0052332
(DSCAM)
Human
(hg19)
chr21:41447141-41450613 
ALTERNATIVE
HsaINT0052332
(DSCAM)
Rat
(rn6)
chr11:37053226-37056064 
LOW PSI
RnoINT0051325
(Dscam)
Cow
(bosTau6)
chr1:141712967-141716303 
LOW PSI
BtaINT0052829
(DSCAM)
Chicken
(galGal4)
chr1:107639750-107644982 
ALTERNATIVE
GgaINT0111567
(DSCAM)
Chicken
(galGal3)
chr1:111728614-111733846 
LOW PSI
GgaINT0111567
(DSCAM)
Zebrafish
(danRer10)
chr15:6169566-6171049 
LOW PSI
DreINT0060113
(dscamb)
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"