Special

MmuINT0115831 @ mm9

Intron Retention

Gene
ENSMUSG00000031860 | Pbx4
Description
pre B cell leukemia homeobox 4 [Source:MGI Symbol;Acc:MGI:1931321]
Coordinates
chr8:72390367-72394081:+
Coord C1 exon
chr8:72390367-72390502
Coord A exon
chr8:72390503-72393927
Coord C2 exon
chr8:72393928-72394081
Length
3425 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
GTCGGTCCATCTATCCACAGGTC
3' ss Score
10.48
Exon sequences
Seq C1 exon
GCGCAAGCGGCGGAATTTCAGCAAGCAGGCCACAGACGTGCTGAATGAATATTTCTATTCCCATTTGAGCAACCCTTACCCCAGTGAAGAGACCAAAGAAGAGCTGGCCAGGAAGGGTGGCATCACAGTGTCCCAG
Seq A exon
GTGAGCCCTTCTGCCCCGGGGATGGGGTGGGGGTGGGGCCTCAGACTCCTGGAGGAGTTACTTAATAATGTATGAAGGAGACTCCTGGGAAAGTTACTTAATGTATGGGGAGGACTCCTAGGAAAGTTTGTTAATATGGGAGGAGGGAAGACTCCTGGGAAAGTTATTGCTGTGTGGGGAGGACCCATGGGGAAGTTCCTTACTGTGTGGGGAGGACCCGTGGGGAAGTTCCTTACTGTGTGGGGAGGACCCGTGGGGAAGTTCCTTACTGAGTGGGGAGGACCCGTGGGGAAGTTCCTTACTGTGTGGGAGGACCCATGGGGAAGTTCCTTACTGTGTGGGGAGGACCCGTGGGGAAGTTCCTTACTGTGTGGGAGGTCCCATGGGGAAGTTCCTTACTGTGTGGGGAGGACCCGTGGGGAAGTTCCTTACTATGTGGGAGGACCCGTGGGGAAGTTCCTTACTGTGTGGGAGGACCCATTGGGAAGTTCCTTACTGTGTGGGAGGACCCATTGGGAAGTTCCTTACTGTGTGGGGAGGACCTGTGGGGAAGTTCCTTACTGTGTGGGAGGACCCATGGGGAAGTTCCTTACTGTGTGGGGAGGACCTGTGGGGAAGTTCCTTACTGTGTGGGAGGACCCATGGGGAAGTTCCTTACTGTGTGGGAGGACCCATGGGGAAGTTCCTTACTATGTGGGAGGACCCATGGGGAAGTTCCTTACTGTGTGGGAGGACCCATGGGGAAATTCCTTACTGTGTGGGAGGACCCCATTGGGAAGTTCCTTACTATGTGGGAGGACCCATTGGGAAGTTCCTTACTGTGTGGGGAGGACCTGTGGGGAAGTTCCTTACTGTGTGGGAGGACCCATGGGGAAGTTCCTTACTGTGTGGGGAGGACCCGTGGGGAAGTTCCTTACTGTGTGGCCCTGGTCAGGTGCCTCAGCCTGGCTCTGCTCCAATCCCGGCTCTGCGCTGTGAATTAGAATTTTGGTGGGGACTCTGCTCCCTCTCCTAGAAGAGGAGTGCGAGAGTGTCATGGCACCTCAAGGTGCTGGTGTGAGCTCTAGGAGACTGGCAGCTCAGGCTCCTGGGACCCGTGTGGTTGCAGCAGGACAGATATGTAGTATGAGCTCTGCTGGGTGAGTGAGAAACCTGACCCTGTTTGGCAACAATCACCTTTGCCTTTCTTGGAATTGGAGGCAAAGGAGAGAGTGACTAGAGGCCATAGTGCTAAGAGAACATTCCTGAAGTTTCAGAGTGAGTGGCGGGAAGGCAGGGCCAGCACTGGAGCCAGGAGTGCAAGCCCCACAGGCTGCAGCATGGGGTCACTCAGCCACAGCTCCTCTGACATTAGTCACTGCAGCCCTGTCACATGCCATGTTCCTCCTTGCTTCACAGTTGGAAAGGGTGAGTGTCCTGCCCTTAGGCACTGCCCTCAGCCCAGGCTGTTCTAGTTATGTCTCCGTGACAGAGCCCAGGGTCCTATTCCTCAGGGAGCAGTCGGACGTCCTCACAAGGCCAGAGCTGAGGGCAGGGTCTGCACCTCTGGTCAGAGTGTAAGCCTGGGAGCTTGGGCACTATGGACAGTGTGAACAACAGGCAGATCACCCCACCCTTCTGCCCCTGGCACCATGTTGCTGGTGCCAGGTCCTCCAGGGAACAGAGTAAGCAAGGTTCAAAGGCCCTGCTACATCCAGGGCCACTCCTATTGGGTGACCTGGGCCCTGTGCTAGAAGCTTCACTCCACTTTGTCACATCCCCTAGTCGGTGACAGGATCTACTAAAGTGGCCTGCCATATTAGTTAAGAGAGGTTTTGAATTTGGGGTACAGAGGAGTAGGCCATGAGGTGCACCTCAGCAGAAGTCAAGAGAAAGGAAACACCATTAGGGCACCTCAGGCTGAGGAAACCCCAAGGGCAGCTGAGCCAAGGGTGAGGTAGGGTCTCTCTGTGGAGATGAGTTTCCTGCCGGCCACTGAACCCTCTCAGCAGTGCTCAAATCCACACTGAAACTCTGATCTTTGTCTAGAGCCATGAAGAGTTGAGTAGCCTGTGTCCAAGCTATAGAGGAAGGTCACTTGAACCCAGGAATCCAGTCCATCTGGGTAACACAGTTAGATCCTTATGTCAAAAAGAAAATACAGGACTGGGCCTGGTAGAGCATCCCTTCAGTCCCAGCCATCAGGAGATGACAGGCATCTCTGTGAGTTCAAGGCTAACCTGGTTTACACAGAGAGTTCCAGGACAGCCAGGGCTATACAGAGAAACTCTGGGGGGGGGGGAGAGGAGGGGGAGGAGGAGGAGGAAAGTAGTAGTAGTGGTCATTGTCATAGACATCGTCATAGACGTAGTCATGGTACTATAGTGGAGTTAGAGAGCTGGCTCAGAAGTTAAGAGTACCGACTGCGCTGGGCATGGTGGCGAACGCCTTTAATCCCAGCACTCAGGAGGTAGAGGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGAGAGAGGCAGAGAGGCAGAGAGGCAGAGAGGCAGAGGCAGAGGAGGCAGAGGCAGGCGGATTTCTGAGTTCCAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCAAAAAAAAAAAAAAAAAGAGTACCAACTGCTTTTCTAGACTACCTGGGTTCAATTCCCAGCACCCACATGGCAGCACACAGCCATCTTTAACTTTAGTTCCAGGATGTCCCATGCCCTCTTCCCACCTCTAGCAGCCCCAGACATGCACAGGCACACATGCACATGCATGCATGCAGGCAAAGCACGCAAGCACATCTAACAAAATGAAAGCACCTTAGAGAGCACTAAGCACCTGGTGGAGGTGTGGCCCTCCCTGCAGGACAGGACAGAGCCCTGCAGTTACCTGGGGCCTTTTCCCTGTTTTGTTCAATTGGGTGAAGTTGTTTAGCTGGATCTCACTTCAGCCTAGGCTGGCCTTGAATTTACAGCAGTCCTCCTGCTTCAGCCTCTCAGAGTCTATGCTAACAAGTATGAGCTATTAAGCTGGTACCATTTTGTTTGTTTGTTTGTTTGTACTAGAGTTGGTATTATTATTTTTTATATTTGTGTATTTATTTGTGGGGGGTGTACGCGTGTGTGCAGTCTCCTCTTGCACCAATCCGTGCATCGATCACTGTGCGTGTGTGGTGCCTGTCACTGAAGAAATGGAGAGATCTGAGGACAGCTTTAGCAGTTATTCCCCTCTCCTGCCACTGTGTGGCTCCTCGGAATTGAACTCAGGTCATCAAACTTGGCACCTTTAAGCCATCTGGATCAGCCCCTGAGAGGAAAGGTCTCTAATCGAGTCTTCATACGGTTTGTCCCCAGCATGGCCCACACCAGAACAATGTCATTGTCGGTCCATCTATCCACAG
Seq C2 exon
GTCTCTAACTGGTTTGGCAACAAAAGAATCCGGTACAAAAAGAATACAGGGAAGTTTCAGGAAGAAGCCACCATGTACACAGGGAAAGCATCCACAGTCACCAAGGCCCGGCGTCCCAGGGGTCAGAGCAGCTGCCAGTCCACACCCAGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031860-Pbx4:NM_001024954:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.302 A=NA C2=0.510
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF040917=Sec15=PD(0.1=0.0),PF083976=IMD=PD(26.8=71.7),PF0004624=Homeobox=PU(75.0=97.8)

							
A:
NA

							
C2:
PF0004624=Homeobox=PD(21.7=25.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000080219





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000122281
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr19:19565090-19569448 
ALTERNATIVE
HsaINT0120879
(PBX4)
Human
(hg19)
chr19:19675899-19680257 
ALTERNATIVE
HsaINT0120879
(PBX4)
Rat
(rn6)
chr16:21306170-21308823 
ALTERNATIVE
RnoINT0107851
(Pbx4)
Cow
(bosTau6)
chr7:3679226-3682693 
ALTERNATIVE
BtaINT0108062
(PBX4)
Chicken
(galGal4)
chr17:9817757-9818454 
Chicken
(galGal3)
chrUn_random:30305796-30306441 
LOW PSI
GgaINT0001717
(PBX4)
Zebrafish
(danRer10)
chr3:52798490-52807095 
LOW PSI
DreINT0110770
(pbx4)
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"