Special

MmuINT0032874 @ mm9

Intron Retention

Gene
ENSMUSG00000021279 | Cdc42bpb
Description
CDC42 binding protein kinase beta [Source:MGI Symbol;Acc:MGI:2136459]
Coordinates
chr12:112546319-112549777:-
Coord C1 exon
chr12:112549698-112549777
Coord A exon
chr12:112546409-112549697
Coord C2 exon
chr12:112546319-112546408
Length
3289 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
GACACCTTTTCTTTTTACAGACC
3' ss Score
10.11
Exon sequences
Seq C1 exon
GGCTCAAACTTCCAGATTTCCAGGATTCTATCTTTGAGTATTTCAACACTGCTCCTCTTGCACATGATCTGACTTTTAGA
Seq A exon
GTGAGTATTGCGTTTTGAAAGCAAGTATGAAATTTTGAAATAATAGTAGTAGTATGTAGGCCGGGTGTGGTGGCACATGCCTTTAATCCCATCACTCAGGAGGCAGAGGCAGACAGGCCAGCCTGGTTGATAAAGGAAGTTCCAGGGCAAGGCAGGACTAAATAGAGAAACCTTGTTTCAAAGCTGAAGGTCCAACACTCATTGAGAGTTGGCCCAGGTGACATCATGGGCTGGGAAGTCACATGTGTGAAGGTGGAGAGCTCTGCAGGTGTCAAACTGTTCCTGGAGTCTAAGCGGACTGAGAAAAGGCTCAACCTTTTCGGGGCCTCTGGCTGAGTAGTGTGTGTTTGAGATAAAATTTAAAACACAAGTAATGATAGTCATGTTGCCGTTTCTAATGTGAATATATAGCTTGGGTTCAGTGATTAGTGGGAAAAGTGGGTTATAAGTGATTCAGTACCAAGCAGTTTACCAAGACCCTGCCTGGTCCTGCTCGTCAGGGTGACCAGTGTGTGACTGCTTGTCTGCTTAGATTGCCTTTGTAGTGGGGATGAGCCCATTCCGCCCTTCACACAGGTGAGCAGCCCAGTAAATGTCTTCTAGTTCCTGCAGTGCACATACACAGAGGCGTGGAGTAGGCTGGACTACGGCTTAGTGACAGGGCACATGCCTCGCTCAGGCTTGATCCCCAGGACTGAAGGGGACGGGAGCTGGAAGAATGAGTGAGTGTGCGCGCGCATGGCGTTAGCGGAGCTTCTGCTAAAGCACCTGATGGTGGTGTTGACCCACCAGCCCAGTCAGAGTGGGGCATACTGAGCGTGCACATACTGAGCGTGCACGCCCTCACCTGGTGTGTGCTCCGCTTGCACACTTGCTTTTTCTCTGCTTGACTCCCTCGCTGACAGCTTCTTAGCTGATAGTGGTTTACAGACAGCAGCGACCCAGGACACCTCACCCTCACTCCCCCCTGGCACTCAGGTTCTTCTCCGTGAACTTCAGTGCCATCCTAAGGCTGTACCAGCAGTGAGTTTCGGCTCAGAGTAGACCTGCCTGTGTCCTGGACAACTGCTCTCCCTGTTCACGATGTACCGGAGGCCACTGGTGGCATTTAATCATCAGGCGCCATCTAAATGGCCTGTCTGTCCCACTTAGGACAAGGGGAATGCCCACACTCTGGGTTTACATCATGTTCCCTGTGCGTGGTGTGCGCGTGGTGTGTGTGTGGTGTATGCGTGGTGTGTGCGAGGTAGGAGGCAGTGTTGGCATTGTCTGAACAGGAGACAAATTCTTTTCTCTTCAGAGTTCACTTTGCAAATGCATCGCTGGGTTGAAGTGGCAAGGGCGTGGCGCCCCCACCCCCAACCCGTTTGTAGGTAGTAGTCACGGGTGACCACGTGGGGATGTTGTAACACTTCCAGGGCACCAGGGGGGCGTTCAAGTCACTCAGCTGTTTGACTTGACTCCACAGCGGTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGACTGGCCTCAAACTCAGGGATCCACGTGCCTCTGCTGGGGTTAAAAGTGTGACCACCACGCCCAGCAAGTCCTCAGTTCTTAAGCAGATCCATTATAAAAGTAATTTCTCACCTTGGACAAACCTTATCAGGGGGTAAATGGAAGAGCTGGGTGACTGTCACAGCATGGACGAGTTAGACATGGAGGCGGAGCAGCACGCCTCGTTCGCTGTCCAGCATGTTGCCCATGTCTAGACCCTGTTCAACACTGTTCACCTGAGTGTGGATGTGTTTCCTAGGAGAGAGCACCCTCAGCTGCATTGGGGTCCGAGCTCTCCTGGGAGCTCTTTCCCCTGCCAGATTAAACATGCTGCTGAATGCTAGAGCCGGGTCTCCATGGAGCCTCATTGGACTTTCTTGCCAGGGTTTACTGGGTGGGAAATGATCATTTGTGTTCCTCCTGTCTGTTACACCAAGGACTCGCTCTCTTCCTCATCTGCATCTTCTCTGCTAGCCTTGTGGGAGGACGTAAGTGACTGCAGTTCCCCTTCCGCGGGCTGCTCGGAGACAGTGCCCCGCGTGCCCTGACTTCTGAGTCTGCGTCCTTTGATTAACAACTAAGGAAACGGCTTTCATGCCGCTAAAACTGACTCCATTGGCTTGCTCTTCACTTACCAGCTGGATCGCTGACCTGTTTAACTTGCCTTGTGGGTGGTACTCATAACTACTAGCTCTGCTCACTACCTAATTAATGTCCCTGTCCACAGAGGTCCTTTACCAACTCCACCACTGCAGAATGCAGTTGTACCTGTGCTGTGTGTGACCCCTAGTCTCTCCTCCCCTCAGAATGTGGAGTCCTCCTCAGGGTCTGATCCGCAGCTGTCGGAAGGTGTGCACGGTGCTTTTGGATCAAAAGCAGGACACAGTTCAGCTGTAGACTTGTAGGCGCTTCTGCACATTTCCGAGTACTTTTGTGCACTGGGAGTAGCCAAACACTGCACCCACGCAATGTTGTATGAGGGCTACACCCGCAGAGAGGTTCACTCCAGAGAGCCAATCGTGAGGTGCCTGTGAGTGCAGGGATTGTTAGAGGAAGACCCTGTGTTCGCTGAAGTGCCAGCTCTAGCTGTCAGGGCCCTGAGGGAGCGGTAGATTCACGTGATTTCTGGAAGGAGGGAGGGAGGTTAAGCGTCTGGGCCGTCTGAGGACCGCCTGAGGGTGATTTTCCTAGTTGCTTTATTTTTTTTTATATATATATATATTTTTTTTAAAGATTTATTTATTATTATATGTAAGTACACTGTAGCTGTCTTCAGATATACCAGAAGAGGGCATCAGATCTCGTTACGGATGGTTATGAGCCACCATGTGGTTGCTGGGATTTGAACTCTGGACCTTTGGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCTAGTTGCTTTATTTTTAAGAGATAGGTTTTTACTGTGTGGCCTTTGCTGGCCTTTAGAGCTCATTCTTTAGTGCAGGTTGGCCTCAGACTCAGTGCTGATTAGAGGCGCGCACTACGCCTAGGCCCTGGTTCCTAGTTTATAATGGCTGGAGGCGAGACAGCCTATGTTACAGGGTGGCCAGGCACCATCTTCCTATTGACAATAATAGTGACTTGCCAGTCCCTGTAAATGACGGAATACTTGTGAGGAAACAGTTCGTGGTGAGACCTGGGGGCAGGGTACAGGGGACCCCAGGCCCTGACAATATACTATTGTCCAGGAAAAATGACACCTTTTCTTTTTACAG
Seq C2 exon
ACCAGCTCAGCTAGTGACCAGGAAACACAGGCTTCAAAGATGGACTTGTCCCCATCAGTGTCTGTAGCCACGAGCACAGAGCAGCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021279-Cdc42bpb:NM_183016:21
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.043 A=NA C2=0.933
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000042565





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000042565f957A
          









    
Other Skipping Isoforms:
ENSMUSP00000042565f955A
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr14:102954689-102959630 
ALTERNATIVE
HsaINT0031684
(CDC42BPB)
Human
(hg19)
chr14:103421026-103425967 
LOW PSI
HsaINT0031684
(CDC42BPB)
Rat
(rn6)
chr6:135762987-135765978 
ALTERNATIVE
RnoINT0032648
(Cdc42bpb)
Cow
(bosTau6)
chr21:69293256-69296243 
LOW PSI
BtaINT0035053
(CDC42BPB)
Chicken
(galGal4)
chr5:49832624-49835246 
ALTERNATIVE
GgaINT0056372
(CDC42BPB)
Chicken
(galGal3)
chr5:52437243-52439865 
LOW PSI
GgaINT0056372
(CDC42BPB)
Zebrafish
(danRer10)
chr20:18525784-18531927 
LOW PSI
DreINT0043797
(cdc42bpb)
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"