Special

MmuINT0012826 @ mm10

Intron Retention

Gene
ENSMUSG00000041936 | Agrn
Description
agrin [Source:MGI Symbol;Acc:MGI:87961]
Coordinates
chr4:156173543-156174090:-
Coord C1 exon
chr4:156173785-156174090
Coord A exon
chr4:156173681-156173784
Coord C2 exon
chr4:156173543-156173680
Length
104 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGC
5' ss Score
5.97
3' ss Seq
CTTAGACTGCGTTTCCCCAGGAC
3' ss Score
7.52
Exon sequences
Seq C1 exon
AGAGTGTTGCTCCTGGGGTTTCCCCTACATCTGCATCTATGACCACCCCAAGGCATATCCTGAGCAGGACACTGGCGTCTCCCCACAGCAGCCTTCCTCTGTCTCCCAGCACTACTGCCCATGATTGGCCCACCCCATTACCCACATCACCTCAGACCGTAGTCGGCACCCCCAGGAGCACTGCAGCCACACCCTCTGATGTGGCCAGTCTTGCTACAGCGATCTTCAGGGAATCTGGCAGCACCAACGGCAGTGGCGATGAGGAGCTCAGTGGCGATGAGGAGGCCAGTGGGGGCGGGTCTGGGG
Seq A exon
GTGAGCAGGGCCTCAGGGATGTGTGGGCAGGTTTGAGGGTGATGTGGGGGCAGAGCCCAAGAGTGGCTCCTCCCCGGGGCTGGGCTTAGACTGCGTTTCCCCAG
Seq C2 exon
GACTTGAGCCCCCGGTGGGCAGCGTTGTGGTGACCCACGGGCCACCCATCGAGAGGGCTTCCTGTTACAACTCACCTTTGGGCTGCTGCTCAGATGGCAAGACACCCTCACTGGACTCAGAAGGCTCCAACTGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041936:ENSMUST00000105574:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.990 A=NA C2=0.559
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0139015=SEA=PU(0.9=2.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000137931





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000071229, ENSMUSP00000101199, ENSMUSP00000101200
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr1:1046736-1046819 
LOW PSI
HsaINT0005686
(AGRN)
Human
(hg19)
chr1:982116-982199 
LOW PSI
HsaINT0005686
(AGRN)
Rat
(rn6)
chr5:173598973-173599076 
ALTERNATIVE
RnoINT0015310
(Agrn)
Cow
(bosTau6)
chr16:52681951-52682029 
ALTERNATIVE
BtaINT0015949
(AGRN)
Chicken
(galGal4)
chr21:2723532-2723641 
LOW PSI
GgaINT0133390
(AGRN)
Chicken
(galGal3)
chr21:2707662-2707771 
LOW PSI
GgaINT0133390
(AGRN)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CTCTGATGTGGCCAGTCTTGC

				
R: 
TGGACAGTTGGAGCCTTCTGA

				
Band lengths: 
250-354

			

		

	





	
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types





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