Special

MmuEX0004315 @ mm9

Exon Skipping

Gene
ENSMUSG00000041936 | Agrn
Description
agrin [Source:MGI Symbol;Acc:MGI:87961]
Coordinates
chr4:155550513-155551259:-
Coord C1 exon
chr4:155551065-155551259
Coord A exon
chr4:155550743-155550943
Coord C2 exon
chr4:155550513-155550661
Length
201 bp
Sequences
Splice sites
3' ss Seq
CTTCTTACCATCTCCTGTAGAGA
3' ss Score
7.12
5' ss Seq
CGGGTAAGC
5' ss Score
9.14
Exon sequences
Seq C1 exon
ACCGATGTGGGCAGTGCCGGTTTGGATCCTTGTGCGAGGTGGAGACTGGACGCTGTGTGTGCCCCTCTGAGTGTGTGGAGTCAGCCCAGCCCGTATGTGGCTCTGACGGACACACATATGCTAGTGAATGTGAGCTGCATGTCCACGCCTGTACACACCAGATCAGCCTATACGTGGCCTCAGCCGGACACTGCC
Seq A exon
AGACCTGTGGAGAAACAGTTTGTACCTTTGGGGCTGTGTGCTCAGCTGGACAGTGTGTATGTCCCCGTTGTGAGCACCCCCCACCTGGCCCTGTGTGCGGCAGTGATGGCGTCACCTACCTCAGTGCCTGTGAGCTCCGAGAGGCTGCCTGTCAGCAGCAGGTACAAATTGAGGAGGCCCGTGCAGGGCCGTGTGAGCCGG
Seq C2 exon
CTGAGTGTGGCTCAGGGGGCTCTGGGTCTGGGGAAGACAATGCGTGTGAGCAGGAGCTGTGTCGGCAGCATGGTGGTGTCTGGGATGAGGACTCAGAAGACGGGCCGTGTGTCTGTGACTTTAGTTGCCAGAGTGTCCTTAAAAGCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041936-'22-24,'22-23,24-24=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact





	

	
Alternative protein isoforms (Ref)





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0005016=Kazal_1=WD(100=81.8)

							
A:
PF0764810=Kazal_2=WD(100=66.2)

							
C2:
PF0764810=Kazal_2=PU(16.7=14.0)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000101200f4306A





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000071229, ENSMUSP00000075191, ENSMUSP00000101199, ENSMUSP00000101200, ENSMUSP00000101200f4307A, ENSMUSP00000101200f4308A
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:1043823-1044023 
HIGH PSI
HsaEX6027655
(AGRN)
Human
(hg19)
chr1:979203-979403 
HIGH PSI
HsaEX6027655
(AGRN)
Rat
(rn6)
chr5:173601995-173602155 
HIGH PSI
RnoEX0008009
(Agrn)
Cow
(bosTau6)
chr16:52684661-52684861 
ALTERNATIVE
BtaEX0002872
(AGRN)
Chicken
(galGal4)
chr21:2728248-2728448 
HIGH PSI
GgaEX1007057
(AGRN)
Chicken
(galGal3)
chr21:2712970-2713170 
HIGH PSI
GgaEX1007057
(AGRN)
Zebrafish
(danRer10)
chr23:23870361-23870561 
ALTERNATIVE
DreEX0012160
(agrn)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GTTTGGATCCTTGTGCGAGGT

				
R: 
TAAAGTCACAGACACACGGCC

				
Band lengths: 
299-500

			

		

	





	
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"