Special

MmuINT0025669 @ mm9

Intron Retention

Gene
ENSMUSG00000026918 | Brd3
Description
bromodomain containing 3 [Source:MGI Symbol;Acc:MGI:1914632]
Coordinates
chr2:27312429-27315348:-
Coord C1 exon
chr2:27314977-27315348
Coord A exon
chr2:27312558-27314976
Coord C2 exon
chr2:27312429-27312557
Length
2419 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
CACCTTGTTGCTTGTTACAGAGG
3' ss Score
6.79
Exon sequences
Seq C1 exon
AAAAAGGGCGTGAAGCGGAAAGCAGACACAACCACACCCACAACATCTGCCATCACTGCCAGCCGGAGTGAGTCTCCCCCACCACTTTCAGAGCCCAAGCAAGCCAAGGTAGTGGCCCGAAGGGAGAGCGGGGGCCGCCCCATCAAACCTCCCAAGAAGGACCTGGAAGATGGTGAGGTCCCACAGCACGCGGGTAAAAAGGGAAAACTGTCCGAGCACCTGCGGCACTGTGACAGCATCCTCCGGGAGATGCTGTCCAAGAAGCATGCTGCCTATGCGTGGCCCTTTTACAAGCCAGTGGACGCGGAGGCGCTGGAGCTGCATGACTACCATGACATCATCAAGCACCCCATGGACCTCAGCACGGTCAAA
Seq A exon
GTAAGTGGGCTGTGCCCATGTCAGAGTCAGTCGGCTCCTTATGGCCCTGGTAGCCCTGCTTGGCTGAGCTGCACTCTGTGACCTCCTGCTGGTCCTCTTCTGTTGGTGCCTCTTGTCCCTGAGAGCTGGGCCTGCCCACACTGGACCTCGGGGACCAGGACCTGTTAGTTTCTGAGTCTGCACCCTCCATTGTCACTTATCCTGGTGGAACATAGAGCCGTAGTTTAGTTCTTTCTGTCCCCCAGTTCTGTATCACCAGAAGGGGGCTCTTAATGGTGTCTGCTTCAGAGACTAATGCAGAGGCAGGTAGATCTCTATAAGTTTGAGACTTACAGCCTGGTGTGCAAAACAAGTTCCAGGACATTCAGGGCTACATAGAGAGGCCCTGTCTCGAACCCCTGATGTGTAGGTACATCACAGCAGAGATGGGGAGTCTGGTGGCCAGCAGAGTGGCCATCTTTGATCTTGGCCTTTACGTAGATAGGGAAGTATATATAGAGAAATGGACAAAGAACAGAGGCCACAAGCTCAGCTGTGCTATCCCCACACCGGCGTTTCCTAGAGTCTGTGTCTTGTTCTGGTTTTTGTGGTGTCCAGCCAGGTCACGGCTTGGCGGGTGTAAAGGTGGGCTTGAGTTTGTGAGAAGACCCTGGGAGATGATAATGCAGTTGAGCTTGGCTCTTCCTAAAGGAATCTCTGCTGACTCCCAGGTAGTTGCTTATTTCATCCAGGCGTCCTTTCAAAGGCAGTGGCTTCAGCTGAAGAATCATGGTGCCTGAAGCAGAATCTCCCAGTTGAAGCCTTTTGTCCTAGATAGTAGTGAGTATGGGGACAGGTAGACCTAGCCACCTAAAAAGTGTTTATACCTGTGTTCGTTTGAGTAAAAAGTGAAGAAAGCAGCTGGGCCTGTCCAGCAGGGCTGGAGTGAGGAAAAGAGCCCTGGGAAGGAACCACGTTGTCCCAGAGCTGCTGGTGGCCTTGGTTTACTCTGCCTGGCCACTGCTGTGCAGTTGCGTGGAGTTCCAGTTGCAGCTGGAACTTTGGGGGCTCCAGTGTTTTGGCTGTACTGGGACAGAATAATTCCGTTTGGTCGCTCTCTCATCTGTCCAAGATGAGGCACCTTTGGGAGTTCAGTTGACTGGGAAGTCGCCATCTGCTTTGTTCAGGCCTGACAGAGAGGCTGTGTGCTTACACAGGTGACGCTTGCATGGCTGAGCCCGACTGACACAGTCTGTGCGAAGACTTTAGCAGAAGAGCCCGAGACTAAAGACTGAAAGACTAATAAAGGCTATACAGTAAAGGGGGAAGTACTGACTAGGCTATGGATGTCATTTCTGTTTTAGGTCTGTGTACGAGTGTTGGCCTGCATGTGTGTATGTGCACCATGTGCATGTCTGCTACCCACTGAGGTGTTGGATACCCGGCAGCTGGAGTTATAGATAGTGGCCGCGTGGGTGATGGGAACTGAACCCAGCTCTTTTGCAAGAGTAACAGTTGCCCTTAAACACTTTACCATCTTTCCAGCACCCAGTACAGTATAGCTTTTAATGATAAAGCTTAAGGGGGGATTGTCCCGGCATGTATCATGCTAGTTCCAGGAGTTGTCCAGGTCCATATCACACCAGTTCCAGGAGGCATTTCTCCAAGCAGCCATCTGCTGAGACATGAGTGTCTTTGGGCACAAGGGCCAGGCCTGTTACTGAGATCCCTCCACTGTGTAGGAACACATATCCAGTCAGGGGTTGGGATGGATACTTAGCTCCCCACACAAGACAGGAACCCTATACCCTTATAAGCAGCTTTTGCCAGCCCAGTCCCCACCGGTCTGCCCTGCCCAGCTTTGTGTGCCTGTGTGACCTTGCCCAACCTGCAGCTGCTGGGACTGCTTGGGCTAGACTTCAGTGGAGTTTGAGGGGCTTTGCTCCAGGGTGGTCCCCGTGATTGTCAGCATTGGCTTCACAGACCTGTACTGCCCTGCCCTCCACCCCTGCACAAGGTCAGAGCTGCCTCTGGGCCCAAAACATAAGCAGCAGGTTGGTAAGAGCGCCTGGATTCCTCCCAGGAAAAGCTGTCTTCTGTGAGCTGAATGGACTTCCCAAGATTGGGATTGAAATTCCCCTAAAGCTCCCCGCACCAGAACCTTCTGCGACACGCGCCATGCCATGTGGAACTGAAAACTAAATGAGGGTGGGGTTGGTGTGAACCTTTCTCCCAATTGTTCTTCCATTCAGTGGCTCTGTCCTTAAAGCCAGATGCTTCTTGTTGGATTTCTTACTCCTTCCCCGAGGGCTCCCGCCTCTGACAACCCTAAGCTAATTGCCAGATGCCTGACTGGCAGTTGGCTTGGTTGCAATGGGATGTTCTGAGGATCTAAGTCTATCCCTTGCATGGTCTGCTCACACCTTGTTGCTTGTTACAG
Seq C2 exon
AGGAAGATGGATAGCCGAGAGTACCCAGATGCACAGGGCTTTGCTGCTGATATCCGGTTAATGTTCTCGAATTGTTATAAGTACAACCCTCCAGACCACGAAGTGGTGGCCATGGCCAGGAAGCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026918-Brd3:NM_001113574:6
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.661 A=NA C2=0.244
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0043920=Bromodomain=PU(52.8=37.9)

							
A:
NA

							
C2:
PF0043920=Bromodomain=PD(44.9=93.0)

						

					

				








    
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)
chr9:134045422-134048082 
ALTERNATIVE
HsaINT0018493
(BRD3)
Human
(hg19)
chr9:136910544-136913204 
ALTERNATIVE
HsaINT0018493
(BRD3)
Rat
(rn6)
chr3:6006805-6009208 
ALTERNATIVE
RnoINT0026400
(Brd3)
Cow
(bosTau6)
chr11:104872860-104875084 
LOW PSI
BtaINT0026730
(BRD3)
Chicken
(galGal4)
chr17:7165305-7168729 
ALTERNATIVE
GgaINT0123972
(BRD3)
Chicken
(galGal3)
chr17:7847603-7851027 
LOW PSI
GgaINT0123972
(BRD3)
Zebrafish
(danRer10)
chr21:18234896-18234980 
LOW PSI
DreINT0038121
(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"