Special

MmuINT0075628 @ mm9

Intron Retention

Gene
ENSMUSG00000067235 | H2-Q10
Description
histocompatibility 2, Q region locus 10 [Source:MGI Symbol;Acc:MGI:95929]
Coordinates
chr17:35607034-35607590:+
Coord C1 exon
chr17:35607034-35607124
Coord A exon
chr17:35607125-35607320
Coord C2 exon
chr17:35607321-35607590
Length
196 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TCACCGTGCGCCGCCCCCAGGCT
3' ss Score
8.48
Exon sequences
Seq C1 exon
AGACGCCCCGGATCCCAGATGGGGGCGATGGCGCCGCGCACGCTGCTCCTGCTGCTGGCGGCTGCCCTGGCCCCGACCCAGACCCAGGCAG
Seq A exon
GTGAGTGCGGGGTCGGGAGGGAAACAGCTTCTGCAGAGAGGGGCGGGGGCGGCACCAGGGAAGCCGCGTCCCCGCGTCGCCCACCGGACCCTCCGCCCCTTCTTCACCCGAGCCCCGCGCCCTGCTCCCCTCCCGGCCCGCGCACCCGCCCGGGGTCCGGAGAGGAGGTCCGGGTCTCACCGTGCGCCGCCCCCAG
Seq C2 exon
GCTCACACTCCATGAGGTATTTCGAAACCTCCGTTTCCCGGCCGGGCCTTGGGGAGCCCCGGTTCATTATTGTCGGTTACGTGGACGACACGCAGTTCGTGCGCTTCGACAGCGACGCGGAGACTCCGAGGATGGAGCCGCGGGCGCCTTGGATGGAGCAGGAGGGGCCGGAGTATTGGGAGCGGGAGACACAGAGAGCCAAGGGCAATGAGCAGAGTTTCCATGTGAGCCTGAGGACCCTGCTCGGCTACTACAACCAGAGCGAGAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000067235-H2-Q10:NM_010391:1
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=0.000 A=NA C2=0.319
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0012913=MHC_I=PU(0.1=0.0)

							
A:
NA

							
C2:
PF0012913=MHC_I=PU(50.3=98.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000040179





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000066419, ENSMUSP00000134163
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:31271869-31271998 
LOW PSI
HsaINT1015531
(HLA-C)
Human
(hg19)
chr6:31239646-31239775 
HsaINT0076438
(HLA-C)
Rat
(rn6)
chr20:4677530-4677728 
Cow
(bosTau6)
chr23:27715075-27715380 
Chicken
(galGal4)
chr16:75376-75524 
Chicken
(galGal3)
chr16_random:100083-100254 
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CGACCCAGACCCAGGCAG

				
R: 
GGCTCACATGGAAACTCTGCT

				
Band lengths: 
249-445

			

		

	





	
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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