Special

MmuINT0075497 @ mm9

Intron Retention

Gene
ENSMUSG00000073406 | H2-Bl
Description
histocompatibility 2, blastocyst [Source:MGI Symbol;Acc:MGI:892004]
Coordinates
chr17:36220641-36221194:-
Coord C1 exon
chr17:36221105-36221194
Coord A exon
chr17:36220911-36221104
Coord C2 exon
chr17:36220641-36220910
Length
194 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
TCATCGCGCGCCGCCCCCAGGCC
3' ss Score
7.76
Exon sequences
Seq C1 exon
AGATGCCCTGTATTCCAAATGGGGCAATGGCGCAGCGAACGCTGTTCCTGCTGCTGGCGGCCGCCCTGACTATGATCGAGACTCGCGCGG
Seq A exon
GTGAGTGGTCGGGAGGGAAACGACCTCTGCGGGGAAGGGCGGGGACGGCACCGTGGAAACCGCGTCCCTGAGTCGCCCACCTCCGCCCCTTCTACACCCGCATCCCGAGCCCCTCACCCTGCTCCCCTTCCTGGCCTGCGCACCCGCCCGAGGTCCCGGGAGGAGGTCGGGGTCTCATCGCGCGCCGCCCCCAG
Seq C2 exon
GCCCACACTCGATGCGATATTTCGAGACCGCAGTGTTCCGGCCCGGCCTCGGGGAGCCCCGGTTCATCTCTGTCGGCTACGTGGACAACACGCAGTTCGTGAGCTTCGACAGCGATGCGGAGAATCCGAGATCTGAGCCGCGGGCGCCGTGGATGGAACAGGAGGGACCGGAGTATTGGGAGCGGGAAACACAGATCGCCAAGGACAATGAGCAGAGTTTCGGATGGAGCCTGAGGAACCTGATCCACTACTACAACCAGAGCAAGGGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000073406-H2-Bl:NM_008199:1
Average complexity
IR-C
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=0.209
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0012913=MHC_I=PU(5.6=45.5),PF0110318=Bac_surface_Ag=PU(3.8=27.3)

							
A:
NA

							
C2:
PF0012913=MHC_I=PU(50.3=98.9),PF0110318=Bac_surface_Ag=PU(54.5=93.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000134155





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000025333, ENSMUSP00000133277, ENSMUSP00000133426, ENSMUSP00000133982, ENSMUSP00000134121, ENSMUSP00000134524, ENSMUSP00000134693
  



Associated events







Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr6:29855608-29855731 
HsaINT0076475
(HLA-H)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr23:28333689-28333999 
BtaINT0000917
([1])
Chicken
(galGal4)
chr16:75376-75523 
Chicken
(galGal3)
chr16_random:100120-100254 
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CCGCCCTGACTATGATCGAGA

				
R: 
TGCTCATTGTCCTTGGCGATC

				
Band lengths: 
244-438

			

		

	





	
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"