Special

MmuINT0032443 @ mm9

Intron Retention

Gene
ENSMUSG00000024670 | Cd6
Description
CD6 antigen [Source:MGI Symbol;Acc:MGI:103566]
Coordinates
chr19:10865059-10865660:-
Coord C1 exon
chr19:10865406-10865660
Coord A exon
chr19:10865161-10865405
Coord C2 exon
chr19:10865059-10865160
Length
245 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACT
5' ss Score
8.63
3' ss Seq
CTAGCTCGGGTCTTCCGCAGGGC
3' ss Score
7.22
Exon sequences
Seq C1 exon
GACTTGAAGAGCTGCATGTTTCCCACATCCCAGCGGCTGACCCCAGACCCTGTGTGGCAGATGTCCCCTCTCGGGGCTCTCAGTACCACGTGAGGAACAACAGTGATTCCAGCACCTCCTCTGAGGAGGGCTACTGCAATGATCCCAGCAGCAAGCCACCTCCATGGAATTCCCAGGCGTTTTATTCTGAGAAGAGTCCCCTCACAGAGCAGCCCCCCAACTTGGAACTGGCTGGCTCTCCGGCAGTGTTTTCAG
Seq A exon
GTAACTGTGTGTCCTTCCATGCTCCCAACCCTGTGTCCAACCTGCCCAGAAAAGACATAGAGCCAAACCCTGAGCTGCTGGCTGGCTGTGTGACCTTGGACAAGTCTCCTTCCCTCTCTGGGCCTTCATTTCCTCATTTGTCCAGCTTCAGACTTGGCTCTCCTGAGTCTTCAGGGCTTCTGGCTCTGGGAGCTCATGTGCAGCCGGGCTCCTGGCAGAGAATAACTAGCTCGGGTCTTCCGCAG
Seq C2 exon
GGCCCTCAGCCGATGACAGCTCCAGCACCTCATCCGGAGAGTGGTACCAGAACTTCCAGCCACCACCCCAGCATCCTCCAGCAGAACAGTTTGAATGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024670-Cd6:NM_009852:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.968 A=NA C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000079172





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000046861
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr11:61018014-61018288 
ALTERNATIVE
HsaINT0031229
(CD6)
Human
(hg19)
chr11:60785486-60785760 
ALTERNATIVE
HsaINT0031229
(CD6)
Rat
(rn6)
chr1:226849808-226850045 
ALTERNATIVE
RnoINT0032265
(Cd6)
Cow
(bosTau6)
chr29:37936166-37936448 
ALTERNATIVE
BtaINT0034622
(CD6)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGCATGTTTCCCACATCCCAG

				
R: 
TGGCTGGAAGTTCTGGTACCA

				
Band lengths: 
305-550

			

		

	





	
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






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