Special

MmuINT0074006 @ mm10

Intron Retention

Gene
ENSMUSG00000026959 | Grin1
Description
glutamate receptor, ionotropic, NMDA1 (zeta 1) [Source:MGI Symbol;Acc:MGI:95819]
Coordinates
chr2:25296877-25297296:-
Coord C1 exon
chr2:25297148-25297296
Coord A exon
chr2:25297035-25297147
Coord C2 exon
chr2:25296877-25297034
Length
113 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGG
5' ss Score
7.13
3' ss Seq
TGAGGTCTCTGTCCCTGCAGCTC
3' ss Score
9.56
Exon sequences
Seq C1 exon
GTGCCCCCCGGAGTTTCTCTGCTCGTATCCTAGGCATGGTGTGGGCTGGTTTTGCCATGATCATCGTGGCTTCCTACACTGCCAACCTGGCAGCCTTCCTGGTGCTGGATAGGCCTGAGGAGCGCATCACAGGCATCAATGACCCCAGG
Seq A exon
GTGAGGCCTCTGGACTGCAGGTTGTGTGTGGGGTATCAAGAGGTTAAGAGGGAGGTGTCTGTTTCTTGTGGTGCTTGGGGAGCAGCCACAAGTTGAGGTCTCTGTCCCTGCAG
Seq C2 exon
CTCAGAAACCCCTCAGACAAGTTCATCTATGCAACTGTAAAACAGAGCTCTGTGGATATCTACTTCCGGAGGCAGGTGGAGTTGAGCACCATGTACCGGCACATGGAGAAGCACAATTATGAGAGTGCAGCTGAGGCCATCCAGGCTGTGCGGGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026959:ENSMUST00000114312:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.040 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0049715=SBP_bac_3=FE(14.3=100),PF0006021=Lig_chan=FE(18.4=100)

							
A:
NA

							
C2:
PF0049715=SBP_bac_3=FE(15.2=100),PF0006021=Lig_chan=FE(19.5=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)
chr9:137162740-137162845 
ALTERNATIVE
HsaINT0072513
(GRIN1)
Human
(hg19)
chr9:140057192-140057297 
ALTERNATIVE
HsaINT0072513
(GRIN1)
Rat
(rn6)
chr3:2513514-2513619 
ALTERNATIVE
RnoINT0067639
(Grin1)
Cow
(bosTau6)
chr11:105928442-105928556 
ALTERNATIVE
BtaINT0069125
(GRIN1)
Chicken
(galGal4)
chr17:1014612-1015368 
LOW PSI
GgaINT0126088
(GRIN1)
Chicken
(galGal3)
chr17:1405637-1406393 
LOW PSI
GgaINT0126088
(Q6R6I2_CHICK)
Zebrafish
(danRer10)
chr5:29017465-29018974 
LOW PSI
DreINT0075091
(grin1b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CCCGGAGTTTCTCTGCTCGTA

				
R: 
CCGGTACATGGTGCTCAACTC

				
Band lengths: 
242-355

			

		

	





	
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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