Special

MmuALTD0013314-2/2 @ mm9

Alternative 5'ss

Gene
ENSMUSG00000047793 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:MGI Symbol;Acc:MGI:3045960]
Coordinates
chr1:95178846-95179565:+
Coord C1 exon
chr1:95178846-95178959
Coord A exon
chr1:95178960-95179011
Coord C2 exon
chr1:95179269-95179565
Length
52 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGC
5' ss Score
10.08
3' ss Seq
TGTTTGGTGCAACCCTGAAGAGC
3' ss Score
-0.46
Exon sequences
Seq C1 exon
TGAGTGACCCCTGCTTCTCTAGCCCCTGTGGGAGCCGCGGCTACTGCTTGGCCAGCAACGGGTCCCACAGCTGTACCTGCAAAGTGGGCTACACAGGCAAGGACTGCACCAAAG
Seq A exon
GTGAGGGCCAGGAGCTCCGGGAAGGAGGATGGAGGAGCAAGGGGGCCAGAAG
Seq C2 exon
AGCTCCTCCCACCAACAGCCCTCAGGGTAGAAAGGGTGGAGGAGAGTGGGGTCTCCATCTCCTGGAGTCCACCCGAGGGCACCACGGCCAGGCAGGTGCTGGATGGCTATGCAGTCACCTATGCCTCCTCGGATGGATCGTCCCGGCGCACAGACTTTGTGGACCGGAGCCGCTCCTCTCACCAGCTTCGGGCCCTAGCAGCCGGCCGCGCCTACAATATCTCCGTTTTCTCAGTCAAGAGAAACACAAACAACAAAAATGACATCAGCAGGCCTGCAGCACTGCTCACCCGCACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047793-29-27,30-27-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption when splice site is used (sequence inclusion)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.221
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0000822=EGF=WD(100=79.5)

							
A:
NA

							
C2:
PF0004116=fn3=WD(100=85.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000050832





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000132455
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr2:242004433-242004434 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr3:120786927-120786928 
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr9:5945264-5945265 
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGCTACACAGGCAAGGACTG

				
R: 
GGTGACTGCATAGCCATCCAG

				
Band lengths: 
147-199

			

		

	





	
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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