Special

MmuINT0032447 @ mm9

Intron Retention

Gene
ENSMUSG00000024670 | Cd6
Description
CD6 antigen [Source:MGI Symbol;Acc:MGI:103566]
Coordinates
chr19:10872166-10873117:-
Coord C1 exon
chr19:10872806-10873117
Coord A exon
chr19:10872469-10872805
Coord C2 exon
chr19:10872166-10872468
Length
337 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGT
5' ss Score
8.94
3' ss Seq
ACTTCATCACCTGCCCACAGAGC
3' ss Score
8.36
Exon sequences
Seq C1 exon
AGAACCAAGCAGTGCGGTTAGTGGATGGTAGCAGCCGCTGTGCTGGCCGAGTGGAGATGCTGGAGCATGGTGAATGGGGTACCGTGTGCGACGACACGTGGGACCTGCAGGATGCACACGTAGTGTGTAAGCAACTGAAGTGCGGCTGGGCAGTGAAGGCGCTGGCCGGCTTGCACTTCACCCCAGGCCAAGGACCCATCCACCGCGATCAGGTGAACTGCTCTGGGACTGAGGCTTACCTGTGGGACTGCCCGGGACGGCCAGGAGACCAGTACTGTGGTCACAAGGAGGACGCAGGAGTGGTGTGCTCAG
Seq A exon
GTCAGTGAGCCTGGAGGGCAGGATATGTTTACCAGGGGTTCTGTTTGGCCTGTGCTTCTTGTGTATATCCACAAAAATGACGGGTGTTAATAAAGTGATCGTAACCATTCCCCCCACCCCCACCCCCACCCCCATGCAGCTGCTTCTTCCTGTCCACAGCCCATGCTTTGAGCAGCCAGGGTCTAGAGAGGGCCGTAGCAGTTGGGGTGGACAAAGGGGTCACAGATGCAAGAGAGAAAACATGTAGGGCTATCTGGGTTCTTCTCTGCATTGATGCTCTAGGTCGGCAGGGTTTTGGGCCCAAAGCATTTAGCTTGACTTCATCACCTGCCCACAG
Seq C2 exon
AGCACCAGTCCTGGCGCCTGACTGGAGGCATTGACTCCTGCGAAGGGCAAGTGGAAGTGTACTTCCGGGGTGTCTGGAGCACGGTGTGTGACAGCGAGTGGTACCCATCTGAGGCCAAAGTGCTCTGTCGGTCCTTGGGTTGCGGATCAGCAGTGGCTCGGCCCAGGGGGCTGCCACACTCCCTGGACGGTAGAATGTACTACTCCTGCAAAGGACAGGAGCCCGCCCTCAGCACCTGTTCCTGGCGGTTCAACAACTCCAACCTGTGCAGCCAGTCGCGGGCAGCCAGGGTTGTCTGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024670-Cd6:NM_009852:4
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:
PF0053013=SRCR=WD(100=92.4),PF054546=DAG1=PU(11.8=8.6)

							
A:
NA

							
C2:
PF0053013=SRCR=WD(100=92.2),PF054546=DAG1=PU(24.1=27.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000079172





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000046861, ENSMUSP00000108676
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr11:61008846-61009571 
ALTERNATIVE
HsaINT0031233
(CD6)
Human
(hg19)
chr11:60776318-60777043 
ALTERNATIVE
HsaINT0031233
(CD6)
Rat
(rn6)
chr1:226857295-226857584 
Cow
(bosTau6)
chr29:37927048-37927651 
LOW PSI
BtaINT0034626
(CD6)
Chicken
(galGal4)
chr19:4224814-4225695 
GgaINT1026424
(SSC4D)
Chicken
(galGal3)
chr7:6871285-6872496 
GgaINT0045276
([1])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AAGCAGTGCGGTTAGTGGATG

				
R: 
AGGAGTCAATGCCTCCAGTCA

				
Band lengths: 
345-682

			

		

	





	
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"