Special

MmuINT0025649 @ mm9

Intron Retention

Gene
ENSMUSG00000024335 | Brd2
Description
bromodomain containing 2 [Source:MGI Symbol;Acc:MGI:99495]
Coordinates
chr17:34250122-34250777:-
Coord C1 exon
chr17:34250515-34250777
Coord A exon
chr17:34250427-34250514
Coord C2 exon
chr17:34250122-34250426
Length
88 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGG
5' ss Score
7.66
3' ss Seq
CAATTTCTTATTACCCGTAGGCT
3' ss Score
7.55
Exon sequences
Seq C1 exon
CTTCGGGCAGTTCATGAACAACTGGCTGCCCTGTCCCAGGGCCCAATATCTAAGCCCAAGCGGAAGAGAGAGAAAAAGGAAAAAAAGAAGAAACGGAAGGCAGAGAAACATCGTGGCCGAATTGGGATCGATGAAGATGATAAGGGGCCTAGGGCACCTCGCCCACCTCAGCCCAAGAAATCTAAGAAAGCAGGTGGTGGGGGTAGCAATGCTACTACACTCAGCCATCCTGGCTTTGGGACTTCCGGAGGAAGTAGCAACAA
Seq A exon
GTAAGGATTTAAGACTGTGTCTTACAGTATTGTACAAGCCAGCTTGCATGGTGTAAACTCATTACTGACAATTTCTTATTACCCGTAG
Seq C2 exon
GCTACCTAAAAAGTCTCAAAAGACAGCTCCACCTGTCCTTCCCACTGGCTATGATTCTGAGGAGGAGGAAGAAAGCAGGCCCATGAGTTATGATGAGAAGAGACAGTTAAGCCTGGATATCAATAAGTTACCTGGGGAAAAGCTGGGTCGAGTAGTACATATCATCCAAGCCAGGGAACCCTCTCTACGTGATTCAAATCCAGAAGAAATTGAGATTGATTTTGAAACACTCAAGCCGTCCACACTTAGAGAGCTTGAGCGATATGTTTTATCCTGCCTTCGAAAGAAACCCCGGAAGCCCTACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024335-Brd2:NM_010238:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=0.816
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF090735=BUD22=FE(27.2=100)

							
A:
NA

							
C2:
PF090735=BUD22=PD(13.1=40.8)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000025193





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000092990, ENSMUSP00000109879, ENSMUSP00000109880, ENSMUSP00000134608
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:32978389-32979827 
ALTERNATIVE
HsaINT1005383
(BRD2)
Human
(hg19)
chr6:32946166-32947604 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr23:7245837-7246313 
ALTERNATIVE
BtaINT0026724
(BRD2)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr16:73269-73357 
LOW PSI
GgaINT0123643
(BRD2)
Zebrafish
(danRer10)
chr19:7245130-7247210 
LOW PSI
DreINT0038110
(brd2a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CTAAGAAAGCAGGTGGTGGGG

				
R: 
CATGGGCCTGCTTTCTTCCTC

				
Band lengths: 
167-255

			

		

	





	
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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