Special

MmuEX0021078 @ mm9

Exon Skipping

Gene
ENSMUSG00000070594 | Gm4788
Description
predicted gene 4788 [Source:MGI Symbol;Acc:MGI:3646434]
Coordinates
chr1:141598376-141629053:-
Coord C1 exon
chr1:141628880-141629053
Coord A exon
chr1:141628107-141628283
Coord C2 exon
chr1:141598376-141598558
Length
177 bp
Sequences
Splice sites
3' ss Seq
TGTTCAAACTTTTTTTTTAGAAA
3' ss Score
8.56
5' ss Seq
AAGGTATTT
5' ss Score
7.64
Exon sequences
Seq C1 exon
GACTTCCTTGTGGACCTCCACCTTCAATTCCTCTTGGTACTGTTTCTCTTGAGCTAGAGAGTTACCAACATGGGGAAGAGGTTACATACCATTGTTCTACAGGCTTTGGAATTGATGGACCAGCACTTATTAAATGTGAAGGAGGAAAGTGGTCTGACCCACCAAAATGCATAA
Seq A exon
AAACGGATTGTGACATTTTACCCACAATTGAAAATGCCATAATAAGAGGAAAGAACAAAAAATCATATAGGACAGGAGAACAAGTGACAGTCAGATGTCAATCTCCTTATCAAATGAATGGCTCAGACACTGTGACATGTATTAATGGCCGGTGGATTGGAAAGCCAGTATGCAAAG
Seq C2 exon
ACTCAAGAGGGAAATGTGGGCCTCCTCCACCTATTGACAATGGAGACATCACCTCCTTGTCATTACCAGAATATGAACCATTCTCATCAGTTGACTATCAGTGCCAGAAGTATTATCTCCTTAAGGGAAAGAAGACAATAACATGTAGAAATGGAAAGTGGTCTGAGCCACCAACCTGCTTAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000070594-'11-13,'11-12,12-13
Average complexity
S
Mappability confidence:
50%=100=100%
Protein Impact





	

	
Alternative protein isoforms (Ref)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.017 A=0.008 C2=0.016
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0008415=Sushi=WD(100=91.5)

							
A:
PF0008415=Sushi=WD(100=91.7)

							
C2:
PF0008415=Sushi=WD(100=88.7)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000107620





     
                   









    
Main Skipping Isoform:
ENSMUSP00000107617





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000027612
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:196741875-196742051 
HIGH PSI
HsaEX6035717
(CFH)
Human
(hg19)
chr1:196711005-196711181 
HIGH PSI
HsaEX6035717
(CFH)
Rat
(rn6)
chr13:56992873-56993049 
HIGH PSI
RnoEX0020645
(Cfh)
Cow
(bosTau6)
chr16:5939070-5939246 
Chicken
(galGal4)
chr8:2646130-2646306 
HIGH PSI
GgaEX6043512
([1])
Chicken
(galGal3)
chr8:2672421-2672597 
HIGH PSI
GgaEX6043512
([2])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGGAATTGATGGACCAGCACT

				
R: 
GTAAGCAGGTTGGTGGCTCAG

				
Band lengths: 
251-428

			

		

	





	
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"