Special

MmuEX0041583 @ mm9

Exon Skipping

Gene
ENSMUSG00000057969 | Sema3b
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B [Source:MGI Symbol;Acc:MGI:107561]
Coordinates
chr9:107500005-107502189:-
Coord C1 exon
chr9:107502134-107502189
Coord A exon
chr9:107501908-107502047
Coord C2 exon
chr9:107500005-107501506
Length
140 bp
Sequences
Splice sites
3' ss Seq
TTTACATCTTTTGTCTCAAGACT
3' ss Score
5
5' ss Seq
CAGGTGTGC
5' ss Score
6.46
Exon sequences
Seq C1 exon
ACGGTTCCGGAGGCAAGACATAAGGAATGGCGACCCCAGCACCCTATGCTCTGGAG
Seq A exon
ACTCTTCTCACTCTGTGCTGCTGGAGAAGAAGGTGTTGGGTGTGGAGAGCGGCAGCGCGTTTCTGGAGTGTGAGCCCCGCTCGCTCCAGGCGCATGTGCAGTGGACCTTCCAAGGTGCAGGGGAGGCAGCTCACACCCAG
Seq C2 exon
GTGCTGGCTGAGGAGAGAGTAGAGCGCACTGCGCGGGGGCTGCTGTTGCGGGGGCTGCGGCGCCAGGACTCTGGCGTGTATCTTTGCGTCGCGGTTGAACAAGGCTTTTCACAACCACTGCGTCGCCTGGTGCTGCATGTGTTGAGTGCGGCGCAGGCTGAACGACTGGCACGGGCAGAGGAAGCAGCCGCTCCTGCACCTCCTGGCCCTAAACTCTGGTACCGGGACTTTCTGCAGTTGGTGGAGCCAGGCGGTGGCGGAGGTGCAAACTCCCTGCGAATGTGCCGCCCGCAGCCCGGGCACCACTCTGTGGCAGCAGATTCACGTCGTAAGGGTCGCAACAGACGGATGCATGTCTCTGAGCTCCGTGCTGAGCGTGGACCACGTAGTGCAGCTCACTGGTGACTCGGCTGTCCCCACAATGGGACGAGGCTGAATATGACACTCCAAAGAGGGGCAGACAGATGCCAGGAAGACAAATGAGTTATGGCTGGGCCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057969-'25-32,'25-30,26-32
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact





	

	
Alternative protein isoforms (No Ref, Alt. Stop)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.250 A=0.000 C2=0.418
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0143720=PSI=FE(29.7=100),PF0768612=V-set=PU(0.1=0.0)

							
A:
PF0143720=PSI=PD(14.1=19.1),PF0768612=V-set=PU(48.9=97.9)

							
C2:
PF0768612=V-set=PD(48.9=34.1)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000073152





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000099588, ENSMUSP00000099589, ENSMUSP00000099590, ENSMUSP00000099591, ENSMUSP00000130861
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr3:50275705-50275844 
HIGH PSI
HsaEX7002004
(SEMA3B)
Human
(hg19)
chr3:50313136-50313275 
Rat
(rn6)
chr8:116355048-116355187 
ALTERNATIVE
RnoEX0079266
(Sema3b)
Cow
(bosTau6)
chr22:50656389-50656528 
HIGH PSI
BtaEX6095189
(SEMA3B)
Chicken
(galGal4)
chr12:2656812-2656942 
HIGH PSI
GgaEX6009854
([1])
Chicken
(galGal3)
chr12:2487174-2487304 
HIGH PSI
GgaEX6009854
([2])
Zebrafish
(danRer10)
chr8:26568496-26568635 
HIGH PSI
DreEX6050303
(sema3b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GACATAAGGAATGGCGACCCC

				
R: 
AGAGTTTAGGGCCAGGAGGTG

				
Band lengths: 
257-397

			

		

	





	
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"