Special

MmuINT0075670 @ mm9

Intron Retention

Gene
ENSMUSG00000053835 | H2-T24
Description
histocompatibility 2, T region locus 24 [Source:MGI Symbol;Acc:MGI:95958]
Coordinates
chr17:36154186-36157505:-
Coord C1 exon
chr17:36157405-36157505
Coord A exon
chr17:36154483-36157404
Coord C2 exon
chr17:36154186-36154482
Length
2922 bp
Sequences
Splice sites
5' ss Seq
CCCGTAAGT
5' ss Score
9.09
3' ss Seq
AAATCCTATTCTAACCTCAGGGT
3' ss Score
5.53
Exon sequences
Seq C1 exon
AAGTCTAGTTTCTCAGGACAGTGGAAGCTTAAAGCTTGATCCTGACACCATGTGGGCTCTTATCTTCTGGCTTCTGAGTCACCCCCAGGACGGCGGAGCCC
Seq A exon
GTAAGTAGGGTTGTGTGCTGGGTAAATTTAAGACCGGAAAACCTCCAACCTCGAACCTTGGGCCATTTTGCAGAAGACTAGGTTTCAGTTAGTAGCTCTGTCTTCAAACTTGCTATGTAGACCAGGCTGGCCTTGAACTCAAAGGAGTTGGGACTAAAGGCATGCACCGCCAAACCAGCCCTTTCCTTACATTCTAATGTGGTTTTGAGTATTTGCTTGTATGTGTGCATAACATGCCAGAGGTCAGAAGAGGGCATGAAGCTCCCTCCAGCTGGTGCTCAGAACTATACCACAGTCTTCTGGAAGAACAGTAAGTGCTCTTAACAGCTGGGCTGCCTTCCCTACTTCTGCGAACTACATGTTTACTTATAAAGTATACACTGTGCACACTGTTGTGTAAATTTATCCATATGCATGTTTGTGTGTGCTCATGTGTAGCCTGCAACCCATAGTATAGCCCAGATGTGGAGGTCAGAGGACAACCTAATTTGGATCAGGTCTCCTTCCACCATATGGGTGGCAGCAGGTGCCTTTACTAGCTGAGCAGTCTGTCTCCCTGGCATCATCATTTGTTAAAGTCCTGGTTCTTTCTGCCAGCCCCATGCTCCTGGACATAAGATTCAGGCTCAAATTATATTTACAAATACCTTGGCCATATAGCTAGGCTCTACTCTGACTAGATTATAACTAAAAAATACCCATTTATTTTAAGCTGCATTTTGCCACGTGGCTGATTACTTGTGCTCAGGTACCACGTGTCCATGTGTCTGTCTCCTCACCTTTTTCCAGGCTCCTCTCTCTCCCGGACTCCTCCTCTCCCAGAATTCTTTCTCCTCCCAATGTCCCACCTCTATTTCCTGCTTAAGCTGTAGGCTTTTAAATTGACAGGTAAGGCATCCACAATACACAAGATGATCTCTCTACAGTCATTATCATTATCATCATCATTAATAATAATTATTGTATTATAGGATTCTATTTATGTGACCCTCAAATTCATGATCCTCCTGCCTCACACATACATGTATAATTATGTATTTCTGCTAGCTGGTTATAATGGTTGATTTCGTGTGTCAATTTGACTAGAACACAATATTCAGTTGAAATGGAGCTGGATATGGCATCTCACACCCATGATCCTGTAATCATTTGGAAGACTGAGTAGGAAGATTACTGAGTTCTAGGCAACCCTCCACCCAACCCCAGAAAAATAACTACTGTAGATATTTCAGGATGTGAGTGGCTTCCTCGTCCTCCTAAACAGGGACCACCCAGGGCAACCTGGAAATCCTGCCTGGGTGTGTATCCACTGTGTATCCACTGATAAAGACAAAAGCCAGGAGGCAGAGGCTGAGGACTTGGAAGGCAGGCGGATCTCTCTGAGTAAAGGACAGCCTGATCTACAGAGTGAGTTCCAGGACAGCCAAGGCTCCCCACAAAACAAAACAACAACAACAAAATGCAGTTCAATACACACTAGAATTTGATACAATACAATGAAATCTTATTTGGCTATAAAATGAAATTCTATGCCCTTTTTAAGCAAAATTAAATTATGATATTGGGAGAGATGGATAAAACTGAAAGAAGCAAACCTCAGAAAGACAAATATACATCTTGTCTCTGGAACTCCAGTTTACAATTATTATTATTTTGTATGTGCTGAGTATAATGGTGCACACCTGTGATCCCAGCATTGGGAGGTGCAGGCAGAAAGATCAGAAGTTCAAGGCCAGCCTCAGCTACATGAGACCCTGTCTCAAAAATAAAGATTAAAAAACAAACATATTTTTTAAAAGCGGGGGTGCTGGAGAGATGGCTCAGCAGTTAAGAGCACTAACTGCTCTTCCGAAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTTACAACCATCTGTAATGAGATCGGATGCCCTAGTCTGGAGTGTCTGAAGACAGCTACAGTGTACTTACATATAATAAATAAATAAATCTTTTTTAAAAACCATAAAATTATACACGCATGTGTATATGTGCTTTTAAATATATGGGAGGACTGCAAAACAAAATGGAAACATGGAAGAGATCTTAGAGGAGGCAGGTGATGATACAGAACATGTGATAAAACAGAAGCAGCAGAGCCGGGTTTAACTAGGAAAGAAATGGAAGCAGCTGGAGGAGGGTGAGGAGTATGGGACAGAGCAGTGAGAGGAAGAGCACATGGTAGAAAGTCTAATGGCAGAGGCCACTGAGATAGTTTTCTGGTATCAAAGTCTAATGACAGAGGCTGCAGAGGGGGTCCAAATGGTAGCAGAGTCTAATGGCAGAGGCTGCAGAGGGGGTCCAAATGGTAGCAGAGTCTAATGGCAGAGGCTGCAGAGGTGGTCCAAATGGTAGCAGAGTCTAATGGCAGAGACAGCAAAAGTGGTTCAGCTCCCTGCACCCCCAGCACTTAGAATACAAAATAACCCTGTAGCAAGCATAATGCACATATACAAATATGATAAGATGAAACCCATTACTTTGTATCCTAACTTCTTTAATTAACCAAAAACAAAATCAAAACTCTGATACGGGAGAGCAAGTTACTGCAGCTTCATCTATGCGCGACACACAGACAGTGCCCTTGAGGGGCCAAAAGGCATCAGATCCCCTGGAGCTGGAGGTACAGATGGTTGGGAGAGGACACGTGGATGCTGGGAATTGAACTCAGGTCCTCTATAAGAGTGACCAATGCTCTTAACCACTGAGCCATCCCTCCAGCCCCTTACACTCACACTTTGTTGGTTCTCTGAATTATCCCAGTGAGCAGTATGGAATCCGATTCTCTTGGCTGGTGGGTTGTTATGAAGTGTTCTCATTTATGTTTGTGTGCCCTGTCTCTTCTAGAGCTGGGCCCTCACTCGGTACCTCACACTAAATCCTATTCTAACCTCAG
Seq C2 exon
GGTCGCACTCTCTGCATTACTGTTACTCAGCTGTGACTGAGCCGGGCCCGGGAGTTCCTTCATTTTTCGCCAGTGGCTTCTTAGATAACCAGCCCTTCATCCACTACGACAGCAGGAGCATGAAGGCAGAGCCTTGTGCTGACTGGCTGAGGGAAAATGCACAGTACTTCACTCATGAGACTGAGGTTTTCACCAATCGGATGAAGATTTTCCAGTTGAGCCTGAGAAACATTCGGCAATACTACAACAGCTCTGGTACCCAGAGTCAGAGAGCAGATGGCTTCCGCCAGCAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000053835-H2-T24:NM_008207:1
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=0.033
 
                        

				
Domain overlap (PFAM):

					





						

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

							
A:
NA

							
C2:
PF0012913=MHC_I=PU(52.9=99.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000109389





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000067933, ENSMUSP00000133476
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr6:31324735-31324752 
HsaINT0076434
(HLA-B)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr23:28299574-28302426 
ALTERNATIVE
BtaINT0007561
([1])
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
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






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