Special

MmuALTA0002686-2/2 @ mm9

Alternative 3'ss

Gene
ENSMUSG00000004892 | Bcan
Description
brevican [Source:MGI Symbol;Acc:MGI:1096385]
Coordinates
chr3:87800907-87801777:-
Coord C1 exon
chr3:87801667-87801777
Coord A exon
chr3:87801006-87801278
Coord C2 exon
chr3:87800907-87801005
Length
273 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
GCTTTGACCCCTGTCCACAGAGG
3' ss Score
8.36
Exon sequences
Seq C1 exon
TTCTTCCATCAGTGTGCAGAATGATTCCACTGCTTCTGTCCCTGCTGGCCGCTCTGGTCCTGACCCAAGCCCCTGCCGCCCTCGCTGATGACCTGAAAGAAGACAGCTCGG
Seq A exon
AGGATCGAGCCTTCCGCGTGCGCATCGGTGCCACGCAGCTGCGGGGCGTGCTGGGCGGTGCCCTGGCCATCCCATGCCACGTCCACCACCTGCGGCCGCCGCACAGTCGCCGGGCCGCGCCGGGTTTTCCCCGGGTCAAGTGGACCTTCCTGTCCGGGGACCGGGAGGTAGAGGTACTGGTGGCTCGTGGGCTGCGCGTCAAGGTAAACGAAGCCTACCGGTTCCGCGTGGCGCTGCCTGCCTACCCCGCATCGCTCACGGATGTGTCTCTAG
Seq C2 exon
TATTGAGCGAACTGCGGCCCAATGATTCCGGGGTCTATCGCTGCGAGGTCCAGCACGGTATCGACGACAGCAGTGATGCTGTGGAGGTCAAGGTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004892-2-2,2-1-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact





	

	
Protein isoform when splice site is used (Ref)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.008
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0768612=V-set=PU(11.4=51.6)

							
A:
NA

							
C2:
PF0768612=V-set=PD(87.9=98.4),PF073547=Sp38=PU(56.0=33.6),PF0019312=Xlink=PU(0.1=0.0)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000088491





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr1:156616593-156616936 
HIGH PSI
HsaALTA0000919-2/2
(BCAN)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr3:14236380-14236754 
HIGH PSI
BtaALTA0004279-4/4
(BCAN)
Chicken
(galGal4)
chr25:499049-499050 
Chicken
(galGal3)
chr25:885651-885652 
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TCTTCCATCAGTGTGCAGAATGA

				
R: 
GACCTTGACCTCCACAGCATC

				
Band lengths: 
205-478

			

		

	





	
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
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






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