Special

MmuINT0075675 @ mm9

Intron Retention

Gene
ENSMUSG00000054128 | H2-T3
Description
histocompatibility 2, T region locus 3 [Source:MGI Symbol;Acc:MGI:95959]
Coordinates
chr17:36326546-36327096:-
Coord C1 exon
chr17:36326995-36327096
Coord A exon
chr17:36326816-36326994
Coord C2 exon
chr17:36326546-36326815
Length
179 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TCACCACATGCTGCCCCCAGGCT
3' ss Score
7.28
Exon sequences
Seq C1 exon
ATACAACTTCAGATTTCCCTAACATGAGGATGGGGACCATGGTGCCTGGCACCCTCCTGATCCTCCTGGCTGCCTCACAAGGCCAGACCCAGACCTGCCCAG
Seq A exon
GTGAGTGCTGGATGAGGAGGGAAACAGCCTTTTAGGGGAGGGGCGGAGGTCCACCCTCCACCAGACCCTCCACCACTTCTCCACTCAAGGCCCTAGACCTGAGTCCTTCTACTTCCCTGACCTGCGCACCTGGCCGGGTTCTGGGAGAAGGTCACAGTCTCACCACATGCTGCCCCCAG
Seq C2 exon
GCTCACACTCGCTGAGGTACTTCTACACCGCCTTGTCCCGACCTGCAATCAGCGAACCGTGGTACATAGCTGTGGGCTACCTGGATGACACTCAGTTCGTGCGCTTCAACAGCTCAGGGGAGACTGCGACATATAAGCTAAGTGCGCCATGGGTGGAGCAAGAGGGGCCCGAGTATTGGGCGAGAGAGACAGAGATCGTCACAAGCAATGCACAGTTTTTCCGCGAGAATCTGCAGACTATGCTGGACTACTACAACCTGAGTCAAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054128-H2-T3:NM_008208:1
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=0.122 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

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

							
A:
NA

							
C2:
PF0012913=MHC_I=PU(95.7=98.9),PF107444=Med1=PU(12.4=25.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000099736





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000025312, ENSMUSP00000134469, ENSMUSP00000134547, ENSMUSP00000134607
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:29942627-29942756 
LOW PSI
HsaINT1015517
(HLA-A)
Human
(hg19)
chr6:29910404-29910444 
HsaINT0076428
(HLA-A)
Rat
(rn6)
chr20:2057963-2058196 
Cow
(bosTau6)
chr23:27863162-27863482 
LOW PSI
BtaINT0026334
(BOLA)
Chicken
(galGal4)
chr16:59718-59834 
Chicken
(galGal3)
chr16:345925-346041 
GgaINT0123704
(F1NED2_CHICK)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CACCCTCCTGATCCTCCTGG

				
R: 
ACGATCTCTGTCTCTCTCGCC

				
Band lengths: 
252-431

			

		

	





	
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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