Special

MmuINT0012839 @ mm9

Intron Retention

Gene
ENSMUSG00000041936 | Agrn
Description
agrin [Source:MGI Symbol;Acc:MGI:87961]
Coordinates
chr4:155543329-155543990:-
Coord C1 exon
chr4:155543879-155543990
Coord A exon
chr4:155543446-155543878
Coord C2 exon
chr4:155543329-155543445
Length
433 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
TTACCCCGTGTCTCCTGTAGGTC
3' ss Score
12.17
Exon sequences
Seq C1 exon
GAGCAAAGAGCCCATAGCCCTGGGCACCTGGGTTAGGGTATTCCTGGAACGAAATGGCCGCAAGGGTGCCCTTCAAGTGGGTGATGGGCCCCGTGTGCTAGGGGAATCTCCG
Seq A exon
GTGAGTATCCAGGACATGAGGAAGGTCTAGACCTCCCACACCCTGTTCCCACCACCTCCCTTCCTCCTCCCCGGGGGCTTCACAGACCCTGATAGCCACCTCTCACAGAACTATTTTCTCTGTCTGCCCTGTGCCTCGGTCTGTCTCCTTTTTGCTCCCACTGCTCTCTGGCTCTTGCTCTGCAACCCCCCCACCTGCTCTCCGGATGTCAGAAATCCCGCAAGGTACTGTTGACCTCTTACCCAACTCAACTCACCATCTTTTGTAGCCATTCCTAGAGTAGCCCTTTCCCACTAAGGCCCAATCTGCCATTTCCGTGGGATTAATACTGCCTCCTAGGTAGTTTGGGGTAGGTGTGGGGCATCAAGCAATTGGGCATACTCCAGCCAAGTGGGCGGATCATACAGGACCCTTTACCCCGTGTCTCCTGTAG
Seq C2 exon
GTCCCGCACACCATGCTCAACCTCAAGGAGCCCCTCTATGTGGGGGGAGCTCCTGACTTCAGCAAGCTGGCTCGGGGCGCTGCAGTGGCCTCCGGCTTTGATGGTGCCATCCAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041936-Agrn:NM_021604:28
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.195 A=NA C2=0.026
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0005418=Laminin_G_1=FE(28.0=100)

							
A:
NA

							
C2:
PF0005418=Laminin_G_1=FE(28.8=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000101199





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000101200, ENSMUSP00000101200f4306A
          









    
Other Skipping Isoforms:
ENSMUSP00000075191, ENSMUSP00000091942
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr1:1050838-1051252 
LOW PSI
HsaINT0005700
(AGRN)
Human
(hg19)
chr1:986218-986632 
LOW PSI
HsaINT0005700
(AGRN)
Rat
(rn6)
chr5:173594702-173594911 
LOW PSI
RnoINT0015325
(Agrn)
Cow
(bosTau6)
chr16:52677548-52677992 
LOW PSI
BtaINT0015963
(AGRN)
Chicken
(galGal4)
chr21:2715645-2716110 
LOW PSI
GgaINT1030943
Chicken
(galGal3)
chr21:2699775-2700562 
ALTERNATIVE
GgaINT0133402
(AGRN)
Zebrafish
(danRer10)
chr23:23950613-23961552 
LOW PSI
DreINT0027914
(agrn)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCAAAGAGCCCATAGCCCTG

				
R: 
GGCACCATCAAAGCCGGAG

				
Band lengths: 
218-651

			

		

	





	
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
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






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