Special

MmuINT0071494 @ mm9

Intron Retention

Gene
ENSMUSG00000073402 | Gm8909
Description
predicted gene 8909 [Source:MGI Symbol;Acc:MGI:3704134]
Coordinates
chr17:36304871-36305467:-
Coord C1 exon
chr17:36305389-36305467
Coord A exon
chr17:36305237-36305388
Coord C2 exon
chr17:36304871-36305236
Length
152 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
CTCCGCTTCTGCCCGCGCAGCCA
3' ss Score
7.05
Exon sequences
Seq C1 exon
TTCCCAGATGGGGCAATGGCACCGCGAACGCTGCTCCTGCTGCTGGCCGCTGCCCTGATACTGACGGAGACACGCGCGG
Seq A exon
GTGAGTGCGGGGGTCGGGAGGGAAACGGCCTCTGCGGGGAGGGGCGGGGACGGCACCGTGGAAGCCGCGTCCCCGTGTCGCTCACAAGACCCTCCGCCCCTTCTACACCCGCATCCCAAACCTTACGCCCTGCTCCGCTTCTGCCCGCGCAG
Seq C2 exon
CCACCGAAGGTCCCGGGAGGAGGTCGGGGTCTCACCGCGAGCCGCCCCCAGGCCCACACTCGATGCGGTATTTCACCACCGCAGTGTCCCGGCCCGGCCCACACTCGATGCGGTATTTCGAGACCGCCGTGTCCCGGCCCGGCCTCGGGGAGCCCTGGTTCATCTCTGTCGGCTACGTGGACGACACGCAGTTCGTGCGCTTCGACGGCGACGCGGAGAATCCGAGGATGGAGCCGCGGGCGCCCTGGATGGAGCAGGAGGGGCCGGAGTATTGGGAGCGGGAGACACAGATCGCCAAGGGCCATGAGCAGGGTTTCCAAGGGAGCCTGAGGAACCTGCTCCACTACTACAACCAGAGCGCGGGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000073402-Gm8909:NM_001081032:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.102 A=NA C2=0.453
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0012913=MHC_I=PU(50.3=94.7)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000133663





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000036092, ENSMUSP00000094947
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr6:29942627-29942756 
LOW PSI
HsaINT1015517
(HLA-A)
Human
(hg19)
chr6:29910404-29910489 
HsaINT0076428
(HLA-A)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr23:28505906-28506218 
LOW PSI
BtaINT0026327
(BOLA)
Chicken
(galGal4)
chr16:59718-59834 
Chicken
(galGal3)
chr16_random:12067-12074 
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GATACTGACGGAGACACGCG

				
R: 
GGCTCCATCCTCGGATTCTCC

				
Band lengths: 
258-410

			

		

	





	
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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