Special

MmuINT0074007 @ mm10

Intron Retention

Gene
ENSMUSG00000026959 | Grin1
Description
glutamate receptor, ionotropic, NMDA1 (zeta 1) [Source:MGI Symbol;Acc:MGI:95819]
Coordinates
chr2:25296548-25297034:-
Coord C1 exon
chr2:25296877-25297034
Coord A exon
chr2:25296710-25296876
Coord C2 exon
chr2:25296548-25296709
Length
167 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGC
5' ss Score
6.39
3' ss Seq
GACCCTGACTCTGCCGGCAGCAA
3' ss Score
5.78
Exon sequences
Seq C1 exon
CTCAGAAACCCCTCAGACAAGTTCATCTATGCAACTGTAAAACAGAGCTCTGTGGATATCTACTTCCGGAGGCAGGTGGAGTTGAGCACCATGTACCGGCACATGGAGAAGCACAATTATGAGAGTGCAGCTGAGGCCATCCAGGCTGTGCGGGACAA
Seq A exon
GTGAGCAGGCAGACCAAGGGCCGCCCTGGCTGGGGGGGACAGTAAAGGGACAGGAAAAGGGGAGCCCTCTCACCCAGCAAACACAAGTGAAGACTGTCTTCTGCAGTGTGAGCAGGGTGGGGTGAACAGGCTACACGGGGCTCCTTTGACCCTGACTCTGCCGGCAG
Seq C2 exon
CAAGCTCCATGCCTTCATCTGGGACTCAGCTGTGCTGGAGTTTGAGGCTTCACAGAAGTGCGATCTGGTGACCACGGGTGAGCTGTTCTTCCGCTCCGGCTTTGGCATCGGCATGCGCAAGGACAGCCCCTGGAAGCAAAATGTGTCCCTGTCCATACTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026959:ENSMUST00000114312:15
Average complexity
IR
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:
PF0049715=SBP_bac_3=FE(15.2=100),PF0006021=Lig_chan=FE(19.5=100)

							
A:
NA

							
C2:
PF0049715=SBP_bac_3=FE(15.8=100),PF0006021=Lig_chan=FE(20.3=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000109949





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028335, ENSMUSP00000109946, ENSMUSP00000109947, ENSMUSP00000109951, ENSMUSP00000109953, ENSMUSP00000109956, ENSMUSP00000109957
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr9:137163004-137163168 
ALTERNATIVE
HsaINT0072514
(GRIN1)
Human
(hg19)
chr9:140057456-140057620 
ALTERNATIVE
HsaINT0072514
(GRIN1)
Rat
(rn6)
chr3:2513185-2513355 
ALTERNATIVE
RnoINT0067640
(Grin1)
Cow
(bosTau6)
chr11:105927712-105928283 
ALTERNATIVE
BtaINT0069126
(GRIN1)
Chicken
(galGal4)
chr17:1014294-1014453 
LOW PSI
GgaINT0126089
(GRIN1)
Chicken
(galGal3)
chr17:1405319-1405478 
LOW PSI
GgaINT0126089
(Q6R6I2_CHICK)
Zebrafish
(danRer10)
chr5:29014079-29017306 
LOW PSI
DreINT0075092
(grin1b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CAGGTGGAGTTGAGCACCATG

				
R: 
ATGGACAGGGACACATTTTGCT

				
Band lengths: 
242-409

			

		

	





	
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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