Special

MmuINT0024171 @ mm9

Intron Retention

Gene
ENSMUSG00000026987 | Baz2b
Description
bromodomain adjacent to zinc finger domain, 2B [Source:MGI Symbol;Acc:MGI:2442782]
Coordinates
chr2:59797878-59800687:-
Coord C1 exon
chr2:59800078-59800687
Coord A exon
chr2:59798163-59800077
Coord C2 exon
chr2:59797878-59798162
Length
1915 bp
Sequences
Splice sites
5' ss Seq
CAGGTTATT
5' ss Score
3.49
3' ss Seq
AGTGCTTCTTTACTTCCCAGAAT
3' ss Score
7.33
Exon sequences
Seq C1 exon
GAACAATATAAGCAGACATTCCCATCACAAGGAAAGAAACAGGAGATGGGGAAGAGCCTGAAGAAGGTTATTGCAGCTTTGTCAAATACTAAAGCAACCTCTAGCTCACCAGCACATCCAAAACTACCACTAGATAACAACCACCCTAATCCATTTTTGACAAATGCACTTTTAGGGAATCACCAACCAAATGGAGTCATTCAAAGCGTCATTCAAGAAGCTCCGTTAGCACTAACTACCAAAACGAAAATGCAGAGTAAGATTAACGAAAATGTCTCAAGTAGCACCCCGTTCTCCTCACCTGTCAATCTGAGCACGAGTGGGAGGAGAGCCCCTGGCAGTCAGACTCCAGCGCTGCCCTCTGCCTCGCCCATCCTGCACAGCAGTGGGAAGGAAAAGCGGGTCAGCAATGACGCAACCCCGCTCAAAGCGCACCATCACCCCCATCCGGCGGCAGCGGCCGCGGCCTTGGTGGAACAGTTTAGAGGGACAGATTCAGACGTTCCCAGTAGTAAAGACTCTGAGGACTCAAATGAGGATGAGGAGGAAGATGATGAGGAAGAAGATGAAGAGGATGATGAAGATGATGAGTCTGATGACAGTCAATCAG
Seq A exon
GTTATTTTCTGCTTTAACTTTTAAAGTTTGTTTTTAAGTGTATGTACCAGAAAGTTTTCTAAAACATCGTGATTTTCACACTTAGACTCACCGCCACTCACTGATTTCTTACAGCCAATAAAACGTAAAATTGTTTCTGAAACTGTAAGTTAAATCTTAGATTGTGGTTCCCCTGGCATTAGTGACTAATTGTAAAGTGCTGGTGCATGAATCAAACAGTTTGATCAGGTTGCTGAGTTTCCATTTCATCATGACCACTTACACAGTGCAATTGTTATGTTTTCAAAACTAATTTTAAGCCAGGTGGTGGTGACTCATTCTCTCAATCCCAGCACTGTGGAAACACACAGGCAGATTGAAACCAATAATAATAATAATAACAACAACAGCTAATAATTTTGACCCATGTTAGCTGCATACACCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGAGGCAGGTGGATCTCTGTGATTTGGAGACCAGCCTGCTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTGGGCAGAGAAGCCCTGTCTGAGGTGGGGGGGGGGTGAGTGGGTGGATTATGCATTAATTTAGAATTTCACTCAATGTGTTTTGAGCATACCTTGCCCCTTTCTTGCTCCTCACCATGCCCCATCTCCTCCCGCAATGTCTTCTCCATTACCCTACCAAGGCCAGCTAGTGCTGCCCAGGTATTCTTGGGTGTGCTTTATTTTCTTCTGCTACCTATTAAAACATTACTACCTATCTTTAAAATGGAAAATTTTGCACCATGGTCATTTAAAAAACCAAAATCTTAAGTCCCTTTTGATTGCAGGATTTATTAAATGACATAGGGTCATCATCTTATGCCTTGACTTCATCTACTCTCTCTAGTGGTTTGGTTTGTTTTTTTATAAATAGAGATTGCTTTTAAATTCATAAAATGAAAGATAATTTAAAATATAAATACAGAAATGATACAAATATGTATGTATTAATGTTTGTATATGGATTTGTTGCTGTTCTGACAGGAATTTTTTAGTAACTAATGGGAATAGGAAAACAGTCCTTCTACAATTTAACATTCTAATATTGTACAATCCCGAAAGGCACTGTCTATCTGTATCAGGGCTTTTTAAAAGTAGCTTTCATCGAGCCCCAGTGCGGGCAATATACCAGACCAAACAGTGCCACCGAGATGCTGGCTGGGCACCTTTGTAGTACAGCCCTATGTTTACCCAGTGTTTAATCCACTCTTGTATGTCATATGTCTAGAGGAGTATGTGCTGACTAACATATGTATTAACTTCCCAGACTTCACAACCAGGGCAGACCTGCCTCCCTCAGCCTGTCTCTTGTCTTACCACAGTTATTCCTGTGAGCATAGTTTGTGAATCTCTCAAAACTTGATGAAGTCTTTACCTGAATTGAAAAACTACAGCTAAGAAAGCAAAGCACAAAACCAAAACTACTCCCTAGGGGGGAAACATTTTTTTTTTAACGCAGAATCACAGGTGGAAAGTTGACGGTAGTTCCAGGACAAGGGGCTGAGCAAGGAGCTACCACAGCGCTGGGGCCTGCCAGGGTCCCCTCTGTTACCCGCGGTTTCTCCATGGAGAGTAAAGTAATTCTGAAAACCTGAAGCAGAACTGCAGTATCAGTAGTACCAACCGTGTGGGGACTTTTCTATGATTTAAATGTTAAAACTGATGATTTGGAGAGAGATTTGAGGAACTGTAGTCTGCATACACTTTACTCCAATAGCTTGTAAGTTGGTAATTTTAATATTTGCACTTCCTCTTGGGAAATGGCTTCCTTGAGTCTTTGGTCACAAACGGTGGCTCTGAAATACTCTCCTAGGTGCGACCTGCCTGTGATTGGTTCTGACCTAGCTGTAACATGCAAGTGCTTCTTTACTTCCCAG
Seq C2 exon
AATCAGATAGTAATTCACAATCAGATTCAGAAGGCTCAGAAGACGACGAGGAGAAAGACCAGGAGGAATCAGATAGTGACACTGAAGGCGAGAAACCTGCCGTGAACCTGACCCAGACAAGCTCCTCTGCCAAAAGCCCTCCCTCCAGTCTCACAGCGCACTCAGCACCTCACCTCCACATAGGAAGCCCCCCAGGCTCTGCTCCTGCTGCCCTGTGCTCTGAGTCCCAGCCTCCTGCTTTTCTTGGCACTTCTTCTTCCACACTCACTTCAACTCCACACTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026987-Baz2b:NM_001001182:9
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.985 A=NA C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0334410=Daxx=PD(35.0=58.8),PF0334410=Daxx=PU(43.8=38.2),PF104464=DUF2457=PU(57.4=38.2)

							
A:
NA

							
C2:
PF0334410=Daxx=FE(53.4=100),PF104464=DUF2457=PD(41.9=59.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000108172





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000088443, ENSMUSP00000108167, ENSMUSP00000108169
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:159431157-159432756 
ALTERNATIVE
HsaINT0016853
(BAZ2B)
Human
(hg19)
chr2:160287668-160289267 
ALTERNATIVE
HsaINT0016853
(BAZ2B)
Rat
(rn6)
chr3:46028567-46030456 
ALTERNATIVE
RnoINT0024844
(Baz2b)
Cow
(bosTau6)
chr2:37044849-37047938 
LOW PSI
BtaINT0025119
(BAZ2B)
Chicken
(galGal4)
chr7:36095765-36097006 
ALTERNATIVE
GgaINT0050404
(BAZ2B)
Chicken
(galGal3)
chr7:38232628-38233869 
LOW PSI
GgaINT0050404
(BAZ2B)
Zebrafish
(danRer10)
chr6:11715580-11716877 
LOW PSI
DreINT0036889
(baz2ba)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GTCAATCTGAGCACGAGTGGG

				
R: 
TCGTCGTCTTCTGAGCCTTCT

				
Band lengths: 
356-2271

			

		

	





	
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"