Special

MmuINT0025652 @ mm9

Intron Retention

Gene
ENSMUSG00000024335 | Brd2
Description
bromodomain containing 2 [Source:MGI Symbol;Acc:MGI:99495]
Coordinates
chr17:34253853-34256845:-
Coord C1 exon
chr17:34255551-34256845
Coord A exon
chr17:34254157-34255550
Coord C2 exon
chr17:34253853-34254156
Length
1394 bp
Sequences
Splice sites
5' ss Seq
CAAGTACGT
5' ss Score
8.4
3' ss Seq
TCTGCTTCCCCTTTTTGCAGGCT
3' ss Score
11.13
Exon sequences
Seq C1 exon
ATTCTCCACTGCGGCGGCCTCGCAGCCAAGAACCTTTCGCCCGCCCCGCCCGCGCGACCCGTCCCACTCTGCGCCCCGCCCGCGCCGCCAATGGAAAAGCTGCAAATGGCGCGACCAGCCTGCCGCGGGCGACCGGCAGAAATTCGGTGTGTGCAAGCCCGGGAAGGCTCCGTCAGACCTGGAGGTGGGGACAGCGTGTTGCAGGCCCCGGGGAGATGGCGCCTACACGCCGTTCGGCCTCCATCTCTCCCAGGGTTCGCCAAGCCACGGCGCAGCCAATTGGCTCGGAGACATGGCGGGGTGCCTTTTCGCCTTGGCTCTCTGCGGCACTCTGCTGCCGATAATCGACGCCTTGGAACTGGAGTTTGTGACGTCATCCTTCGAGCGGACCAATAGGAAAGGCTCCCGCGAAGAGGCGGGCCTGCCCCCTCGCCTTTGCTTCTCCAGGCGCGTGAGCGGGCGAGCACGCGCGGAGGGGGCGGGGGAGCTCGCGAGCAGGGTGGCGCGCATGAGCAGCGAAGCTCCGCCCCTCCGGCTATATATAAAGCGCTGGCGCGGGGCTCGGCGGCGCCATTTCGCGCTGGAGTGGAGCAGCCTCTAGGACGAGCTGGAGGATTGCGCCTACTGACCCAGCGTCTCGGAGCCTCTGCGGGCCGCCAGTACAATCCACGTCCATCCGCTTGGAAATGGACTTCGTCCCGGCCCGCGACCGCTCCCGGCGGACAGTGCAGACCCCATAGAAGCCCCCGAGGCTCCCCTTTCTCGGGCCCCGCCCAGTCCTCGGTGTCTGTCCACCCCTCTACTCCGCCCTCAAGAGGATTTCAAAGATGGAGGCGGCGGCTCTCTGAAACCCCTTTTTGGTGCTCATCCGCCTCCATCGGAGGTCTGACGCGGCTCTCGTGACCCCCCGGCGACCGCGGCGGGAAGAGGGGACCCCTGTCCACCGGCGGCAGGCCGAATTGACGACGGTGTCCAGTTTCGGGGACTGCCGGGTTTGCAGACTGCGTTCTCCTGTGGCTCGCCGGCCGGCAGAGGCCGCCGCCATTTTCCTGCTGTCGCCGCCTGCGGAGCGTGCAAAGCTGCCGGAGTTGCGGGGAGGACGGCGCAGGAGACAGCGTTCCCGCCGGTCCCGCAACGAGGCTGACGCCTGGAGGGCCAAGGGCAGCGGCCTTCCCCCCACTTCCCGGGTTATGCTGGGCCCGGCGGTGAGGGGAGCCGAGGCTACCCGGACTTCACGCAGCTGAGCGGCGGCGGTTCCCTGAGGTCAAGATGCTGCAAAACGTGACTCCCCACAA
Seq A exon
GTACGTCTCCGCCAACCGTGTGTGGGAGGGGGGTTGGGGGGCGGCGTTCCGGGGAGCGGCGGGCGGGCGAGGCGCGCTTCCGCGCCGCAGCTGTTGACGCGAGCTCGCGGAGGGGGCTGCGACGGTTTTGAAGCGGTGGCGGCGGCCCAGGTACTGCGTCTGAGCAGCCTGTCGGTTTCCGCGACGCGGAGACCCATTCGGCCAGGACGAGTTGGACTGCAGGGTGGTGGGGGTGTGTGCGCAGATCCAGCCTTGATTTGTCATCGTGCTTGTGGGGGGTCTTCTTGGCTGCTTCAGTGCCCGTGGAGTTGCCATGGTGACAGCTTGAGGGTTTGCCAGGGGGATTCCCACAGGGTGGAGGGGTCATCACGCCCAAGACTAGGTTTCTGGTACATAGGTACAGGCTGCCGTTGAAGGTCTTATTTCCTTCAGCGGTGGGTGTGTTTGGATAACGTTGAGCTTCATTCAGTGGGGAGGAGGGTGGTTCGGAGACTCAGGGCTCAGTTCACTGCAGATGTAAACAATGAGATCTGAGTCTAGTGTCTTAGCCATTAGGAAACACCTGGTCTAGACTAACCACAGGGAGCCTGTGTGGTGATGGGAACCTCTGTTAGCCTTTAGTCTGAGGGACAGTGGGAGTCGCTAGGGACACTGTTTTTGTAAGGGGGGGGGGCGTGCTATCTAAATTAGGACTTGCTGACGCTGACCTTGACTGTAGGGTGCTTTTTGTTGTGCCTTTTGAAGGAGACTTGTTTGGTTGATACTTGATGGAGGTCTGGCAGTTACTATAGAAGGGATATTTGACATGCTTCCTTTCGTTTAGTTGAGGTTAGGTTGGTTTTGTCTGGTTCCTATTATGGTCTTGAAGCCCCCCCAGAGATTGAAAAAGATAGTATGATGAGTTCTTTTAGGTGTGTTGATATTAAGATTTATTCTTCCTTTTCTTCACTGTCCTCTCTGTCTCAACCACCATGGCAACCATTAAGTCCCTAGTGAGGATGAAGCTTCACTTTCTTAGCTCCACCCATTTTTGTTTCAGATCTTCTCCATAAGGCTAGAGTTGTCATGTGACATTGGTTTTGTATTTATTTTAACCAAGCAGCTCGTCAAACTACCCAGTGTAAGCTAAAGATGGACAAAAACTATTGTTAACTCTTTGCTGGTTGCAATTCACTTCACTGCTTTTTATTTATTTACTTGTTATGGAGACAGGGTTTCTCTGAATAGACCAGGCAGAAATCTGTCTGCCTCTGGCTCCCAAGTGCTGGGATTAAAGGTGTATGCTACCACTGCCCAGCCAGTCTGGCTTTGCAGGGTTGCATAGTGCAAGTTAGCAACATTTTCTTGATCTTTCATGTTATTACCACATCTAATTCTGCTTCCCCTTTTTGCAG
Seq C2 exon
GCTCCCTGGGGAAGGGAATGCAGGGTTACTGGGGCTGGGCCCAGAGGCAGCAGCACCAGGGAAAAGGATTCGAAAGCCTTCTCTGCTGTATGAGGGATTTGAGAGCCCCACAATGGCTTCTGTACCAGCTTTACAACTGGCCCCTGCCAATCCACCACCCCCTGAGGTGTCCAATCCCAAAAAGCCAGGACGGGTAACAAACCAACTGCAGTACCTGCACAAGGTAGTGATGAAGGCTCTGTGGAAGCATCAGTTTGCATGGCCATTCCGGCAGCCTGTGGACGCTGTGAAGCTGGGTTTGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024335-Brd2:NM_010238:2
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=1.000 A=NA C2=0.387
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0043920=Bromodomain=PU(31.8=26.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000025193





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000025193f1531A, ENSMUSP00000092990, ENSMUSP00000109880, ENSMUSP00000117359, ENSMUSP00000128835
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:32972928-32974461 
ALTERNATIVE
HsaINT1005386
(BRD2)
Human
(hg19)
chr6:32940705-32942238 
Rat
(rn6)
chr20:5262831-5264172 
Cow
(bosTau6)
chr23:7240089-7241651 
LOW PSI
BtaINT0026714
(BRD2)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr16:81310-81436 
Zebrafish
(danRer10)
chr19:7235716-7238046 
ALTERNATIVE
DreINT0038100
(brd2a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GTGTCCAGTTTCGGGGACTG

				
R: 
GTAACCCTGCATTCCCTTCCC

				
Band lengths: 
356-1750

			

		

	





	
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"