Special

MmuINT0012837 @ mm9

Intron Retention

Gene
ENSMUSG00000041936 | Agrn
Description
agrin [Source:MGI Symbol;Acc:MGI:87961]
Coordinates
chr4:155544175-155544520:-
Coord C1 exon
chr4:155544424-155544520
Coord A exon
chr4:155544340-155544423
Coord C2 exon
chr4:155544175-155544339
Length
84 bp
Sequences
Splice sites
5' ss Seq
AGGGTTAGT
5' ss Score
5.02
3' ss Seq
ACAACTCCACATGACCCCAGGGA
3' ss Score
3.83
Exon sequences
Seq C1 exon
TCCTGGAGAATGCTGGCTCCCGGCCCTTCCTGGCTGACTTTAATGGCTTCTCCTACCTGGAACTGAAAGGCTTGCACACCTTCGAGAGAGACCTAGG
Seq A exon
GTTAGTGGGGAAGGAGGGCTAAGGGAAGGGAGCTAACCTGACGAGGAGACGGTGACACACTCCCACAACTCCACATGACCCCAG
Seq C2 exon
GGAGAAGATGGCGCTGGAGATGGTGTTCTTGGCTCGTGGGCCCAGTGGCTTACTCCTCTACAATGGGCAGAAGACGGATGGCAAGGGGGACTTTGTATCCCTGGCCCTGCATAACCGGCACCTAGAGTTCCGCTATGACCTTGGCAAGGGGGCTGCAATCATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041936-Agrn:NM_021604:26
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0005418=Laminin_G_1=PU(34.8=82.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000101200f4306A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000075191, ENSMUSP00000091942, ENSMUSP00000101199, ENSMUSP00000101200
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:1050330-1050426 
LOW PSI
HsaINT0005697
(AGRN)
Human
(hg19)
chr1:985710-985806 
LOW PSI
HsaINT0005697
(AGRN)
Rat
(rn6)
chr5:173595575-173595658 
LOW PSI
RnoINT0015321
(Agrn)
Cow
(bosTau6)
chr16:52678385-52678486 
LOW PSI
BtaINT0015960
(AGRN)
Chicken
(galGal4)
chr21:2716950-2717272 
ALTERNATIVE
GgaINT0133400
(AGRN)
Chicken
(galGal3)
chr21:2701080-2701406 
LOW PSI
GgaINT0133400
(AGRN)
Zebrafish
(danRer10)
chr23:23948887-23950160 
LOW PSI
DreINT0027912
(agrn)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCTTGCACACCTTCGAGAGAG

				
R: 
TTGCCAAGGTCATAGCGGAAC

				
Band lengths: 
175-259

			

		

	





	
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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