Special

MmuEX0041597 @ mm9

Exon Skipping

Gene
ENSMUSG00000028064 | Sema4a
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A [Source:MGI Symbol;Acc:MGI:107560]
Coordinates
chr3:88256893-88263023:-
Coord C1 exon
chr3:88262909-88263023
Coord A exon
chr3:88258601-88258768
Coord C2 exon
chr3:88256893-88257053
Length
168 bp
Sequences
Splice sites
3' ss Seq
GAAAGTGCCTGTTTCCTCAGAAC
3' ss Score
5.27
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
Exon sequences
Seq C1 exon
GGATGGGGTTGAAGATGGGGGTGGGAGGGTGGCGGGAAGGAGGCACTCGGAGACCGGAAAGCTGAGCGCCTGGCATTCCAGGGGGAGGGAAGCACAGCGGAATCCCGAGCTCCAG
Seq A exon
AACCATCTGGTGACCATCTCAGGCTGACCATGGCCCTACCATCCCTGGGCCAGGACTCATGGAGTCTCCTGCGTGTTTTTTTCTTCCAACTCTTCCTGCTGCCATCACTGCCACCTGCTTCTGGGACTGGTGGTCAGGGGCCCATGCCCAGAGTCAAATACCATGCTG
Seq C2 exon
GAGACGGGCACAGGGCCCTCAGCTTCTTCCAACAAAAAGGCCTCCGAGACTTTGACACGCTGCTCCTGAGTGACGATGGCAACACTCTCTATGTGGGGGCTCGAGAGGCCGTCCTGGCCTTGAATATCCAGAACCCAGGAATCCCAAGGCTAAAGAACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028064-'1-17,'1-15,12-17
Average complexity
C3
Mappability confidence:
100%=100=100%
Protein Impact





	

	
Alternative protein isoforms (Ref, Alt. ATG (>10 exons))





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=NA A=0.221 C2=0.002
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NO

							
C2:
PF0140314=Sema=PU(72.0=66.7)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000029700





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000029700f2240A, ENSMUSP00000103156, ENSMUSP00000114330, ENSMUSP00000118706, ENSMUSP00000119028, ENSMUSP00000123061, ENSMUSP00000125909, ENSMUSP00000128510, ENSMUSP00000128887
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:156154550-156154717 
ALTERNATIVE
HsaEX0057088
(SEMA4A)
Human
(hg19)
chr1:156124341-156124508 
ALTERNATIVE
HsaEX0057088
(SEMA4A)
Rat
(rn6)
chr2:187816510-187816677 
HIGH PSI
RnoEX0079301
(Sema4a)
Cow
(bosTau6)
chr3:14679058-14679228 
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr19:24769718-24769967 
HIGH PSI
DreEX0065081
(sema4ab)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GATGGGGTTGAAGATGGGGGT

				
R: 
GGATATTCAAGGCCAGGACGG

				
Band lengths: 
243-411

			

		

	





	
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"