Special

MmuINT0075605 @ mm9

Intron Retention

Gene
ENSMUSG00000024459 | H2-M5
Description
histocompatibility 2, M region locus 5 [Source:MGI Symbol;Acc:MGI:95917]
Coordinates
chr17:37124600-37125725:-
Coord C1 exon
chr17:37125450-37125725
Coord A exon
chr17:37124876-37125449
Coord C2 exon
chr17:37124600-37124875
Length
574 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAT
5' ss Score
7.88
3' ss Seq
TGTTCAACTCTTTCCCTCAGATC
3' ss Score
10.26
Exon sequences
Seq C1 exon
GCTCTCACGTCTTTCAGTGTGTGTATGGCTGCGAAGTGGGGCCAGATGGACTCTTCCTCCGTGGGCATGAGAAGCACGCATACGACGGCCGCGATTACCTCACCCTAAGCCCGGACCTGCACTCCTGGGTCGCAGGCGACACAGCTGCGCAGATCACGCTGCGCAGGTGGGAGAAGTCTGGTGTCTCTGAGCAAAGGCAATCCTTCTTGAAGGGCGAGTGTGTGGAGTCGCTCCGCACATACCTGGAGATAGGGAAGGAGACTCTGCTAAGAACAG
Seq A exon
GTATATGAGGCTGCCGGGAATCTCCTCCATCTGTTCTGGGGCTGGGGCTCACAGTCTCTCTGGAAGGGAGCAAAATGAGCTGGGCTAGAATACTGCTTCTTTTCTTTGCATCTGAAGAAGGAAGAGAGTTCTGGTTTTCCCGATCAAACACTAGACAGAGACTCTTGCGACTTTTTCTCGGGAGAGTTGAGATTGTCTCAGGAAGGAAAGAGAGAAGATCCCTAAACAGCTGCCCCTTTCAGTCTGCAGCCCTTTGTAAGCCATGCCCTTTCTCAGGCCATGTTCTCAGCCCACACCCAACCTCTTTGGAGTCTTGACTCCAATGATGCTAAGTCTCTCAGCCTTCACCCAGTCAAGACCTTTCTCCTTTCTTCCTTGGGAGTCCCGAAGTCCATCTTGTCATCCTATGTCTAGGGTTTCCCAAGGGGTCGATTATTCCAGATGCCTGAATCTAGAATACTGTATGGTGCTTAAATCCCTCAACTACCCATTCAATTTCCAAGATGGTCCATAAACATTGCTTCAGTTCAGGGAAGAATTCAAGATTCCTGAATTGTTCAACTCTTTCCCTCAG
Seq C2 exon
ATCCTCCCAAGGCACATGTGACCCATCACCCCAGACCTGAAGGTGAAGTCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCTAACATCATCCTGACCTGGCAGTGGGATGAGGAAGACCTGACTCAGGACATGGACCTCATTGAGACCAGACCTGCAGGGGATGGGACCTTCCAGAAGTGGGCATCTGTGGTGGTACCTTCTGGAGAGGAACAGAGATACACATGTCATGTGCAACATGAGGGGCTAACCCAGCCCCTTGTTCTAAAATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024459-H2-M5:NM_001115075:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.007 A=NA C2=0.124
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0012913=MHC_I=PD(49.2=94.6)

							
A:
NA

							
C2:
PF0012913=MHC_I=PD(15.6=7.6),PF0765410=C1-set=WD(100=92.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000131365





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000131365f1561A
          









    
Other Skipping Isoforms:
ENSMUSP00000134912, ENSMUSP00000135262
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr6:29895230-29895827 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr23:27843408-27844711 
ALTERNATIVE
BtaINT0001476
([1])
Chicken
(galGal4)
chr16:77301-78223 
LOW PSI
GgaINT0123603
(DMB2)
Chicken
(galGal3)
chr16:54373-55295 
LOW PSI
GgaINT0123603
([2])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CCAGATGGACTCTTCCTCCGT

				
R: 
ACTGCCAGGTCAGGATGATGT

				
Band lengths: 
343-917

			

		

	





	
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"