Special

MmuINT0025662 @ mm9

Intron Retention

Gene
ENSMUSG00000026918 | Brd3
Description
bromodomain containing 3 [Source:MGI Symbol;Acc:MGI:1914632]
Coordinates
chr2:27305777-27308594:-
Coord C1 exon
chr2:27308353-27308594
Coord A exon
chr2:27306070-27308352
Coord C2 exon
chr2:27305777-27306069
Length
2283 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
GGCTCTGTCTTCTGCCTCAGACA
3' ss Score
8.36
Exon sequences
Seq C1 exon
CTGAAGGCCGTGCACGAACAGCTGGCTGCCTTGTCTCAGGCCCCAGTGAACAAACCAAAGAAGAAGAAAGAGAAGAAGGAAAAGGAAAAGAAGAAGAAAGACAAGGACAAAGACAAAGAGAAGGAGAAGCACAAGGCCAAGTCTGAGGAGGAGAAGAAGGCCAAGGCAGCCCCAGCAGCCAAGCAGGCCCAGCAGAAAAAGGCTCCCACCAAGAAGGCCAACAGCACAACCACAGCCAGCAG
Seq A exon
GTGGGTGGTCGCCTGCCAGGCCCTCAGACTACCTCAGGGCCCCAGGACTGCCAGATCTGGGACATGGAGCCGTGGCTTTGGGGAAGAAGAGGGTTCTCTGTAGCTAGGTGGGAGCATGAGCTGCTGTCAGCAGGTGAGCGGGTAGGCAGTGGAAGCTGGGTACAGAACTTAGGGGAGGCTAGCAGACAGCTTCTTTGGGTGGACTTAGACTACTGGGGGGAATGCTGAGAGGATGCGTGTAGACTGCCAAGTGCCCTTCTTTGGTAAGGCATCCTCAGAGGAAGGGGTCACATAGTGGCCATTGTGGAGGACAAGTTCTTGGGCAGAGGTCATGCAAGCAAGGACACTGCTTTGGATTGGTGGCGCTGCAGGAGGTGGCAGCAGTGAGGCTGATGGCTTAGAGGGCTGCTTGGGAACGGGCTGGGAAGGCTTGAGTGCCTAGGTTCAGGAGAACAGTGTGTGCAGCCCTGGAGCCATGCAGGGAGGGCTCTGTTCCCACCTGCCTTCCCCTCTCCTTGTTCTCTCCCTTGGAAAGGATATAGAAATCAGGATTAAATCCGCATGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTACACAGAAAAAACCCTGCCTCGGAAAAAAAAAAAATCAGGATTTTTTTCATACTATCTTTGTCTGGATTTGGAATCTGTATAATGCTGATCCCCAGAATGGTACTGTATAATATTTCAGAGTAATTAGGGACAGTTTTTGAGAAGACTATTTACCTCTTTTCTATTTTCTGGCATTGAGTATGTTGGGAGACTCCTCCACTCTACATTCTGTGGCCTGGCTTTAATGTATACATCTCTCTGCAGGTCTGAGGTGTCTTCATGGGCAGTTGACATATGGTCGAGACTCTTTGTCAGTATCTAGTCTCTTCTAGAGAACAGTCCTTGACAGGAAGCCTTCCCTATTGTCAGTTTTGGTTTTTGGTTTTGGTTTTGGTTTTTTGAGACACCTCTTGTCACTTTTAGTCTTTTGTTTTGTTTTGTTTGGGACAGGGTTTCTCTGTCCTGGAGCTCACTGCTCGCAGGATGGCCTCTAACACAGATCTGCTTGTCTCTGCTTCCTGGGTGCTGGAGTCAAGGTGTGCACCACCATGTCTGGACCTGCTTTTAAAAGTATTTATTTTTATTTTATGTATTGCCTGCATGCATAACTGTATACCATGAATATGTGTCCCCCTCAGAAGCCAACAAAGGATATCAGCTCCCTGGAACTGGAGTTATGGGTAGTTGTAAGCTGCTGTGTGGGCGCTGAGATCCAGGTCTTCTGTAAGAACAGAGCTCTTGGCCACTGAGCCATCTCTTCAGCCCCCCCCCCCCCCTTTTAAACTCTTTAAAATTACTTGTGGTGCTGAGTAGGCACAGTGCCACACATTGTTCATCCAAGCACTGAGGAGTCAGAGACGATCTCTGTGAGGTCCGGGCCAGCCTGGTCTACAGAGTGCATTTCAGGCCAGCCAGGGCTATATATTGAGAACCTGTCTCAATAAATAATTAGAAAATCGTGTGTGTGTGCATACCACAGTGTATACGTGGAAGTCAGAGGACAGTCTACAAGAGAGGACTCTCCCTTTGCAGTATGTATATACTGGGGATTGAACTAGGGTTTACAACCCCTCATCTACCAAGCTGTCTCCCAACCCTGTAGCCTTCTTTGTAAAAATACAATATAGCCATGTTTGGCTTTCCCCGCCATCTCAGAGACAAGGTTTTACTACCATCTTGCCTGTTGAGTTTGCATGGTGTGTTTTACCAGCTTGGTAACTTTGTCACTGAAGGCCTTGTTTCTCATGTGACCATCTCTTCCCTTTCTGTCAGCCACTCACACTCAGTGACTGACGCATTCGGACTGCATCGACCATGCCATCACGATCTCTGTCCCTGGCCTTTTCTTTTCCTTTCCAAATTTTAAATAGTATGAATGTGGCGATCTGGTTTTGACTTGTTAGGTTTGAGAGGTGGTAGGTAGTTCCTGACTGAACCCTGGGCCAGGAAGCAGCTATTCCCCGAAATAGGGTCTTGCCTATCTCTGGCAGGCAAACTAGACACCCTCAGTTTGCCCAGCTCTTGTTCCTGAGGAACCTTAGTTAACCTCTAGGGAAGAGAAGGGTCTTTAGTGAAGGAGAAAGGGGCTAGGTGGTGGGATAGGTAACTGAGACTCAACGCCACATGGCTCTGTCTTCTGCCTCAG
Seq C2 exon
ACAGCTCAAGAAGGGCGGCAAGCAGGCATCTGCGTCCTATGACTCAGAGGAAGAGGAGGAGGGCCTGCCCATGAGCTATGATGAAAAGCGACAACTTAGCCTTGACATCAACCGGCTGCCCGGCGAGAAGCTAGGGCGTGTGGTGCACATCATTCAGTCTCGGGAGCCCTCGCTTCGGGACTCAAACCCAGACGAGATTGAGATTGACTTTGAGACCCTGAAGCCAACCACGCTGCGGGAACTGGAGAGATATGTCAAGTCTTGTTTACAAAAAAAGCAGAGGAAACCATTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026918-Brd3:NM_001113574:10
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=0.926
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000109574





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028282, ENSMUSP00000076918, ENSMUSP00000114422, ENSMUSP00000115755, ENSMUSP00000128812
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:134036325-134040033 
ALTERNATIVE
HsaINT0018496
(BRD3)
Human
(hg19)
chr9:136901447-136905155 
LOW PSI
HsaINT0018496
(BRD3)
Rat
(rn6)
chr3:6000134-6002536 
LOW PSI
RnoINT0026403
(Brd3)
Cow
(bosTau6)
chr11:104864149-104868474 
LOW PSI
BtaINT0026733
(BRD3)
Chicken
(galGal4)
chr17:7162888-7163409 
ALTERNATIVE
GgaINT0123975
(BRD3)
Chicken
(galGal3)
chr17:7845186-7845707 
LOW PSI
GgaINT0123975
(BRD3)
Zebrafish
(danRer10)
chr21:18232850-18232942 
LOW PSI
DreINT0038115
(brd3a)
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
  • 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"