Special

MmuINT0032884 @ mm9

Intron Retention

Gene
ENSMUSG00000021279 | Cdc42bpb
Description
CDC42 binding protein kinase beta [Source:MGI Symbol;Acc:MGI:2136459]
Coordinates
chr12:112534591-112537893:-
Coord C1 exon
chr12:112537294-112537893
Coord A exon
chr12:112534689-112537293
Coord C2 exon
chr12:112534591-112534688
Length
2605 bp
Sequences
Splice sites
5' ss Seq
GTAGTATGT
5' ss Score
3.71
3' ss Seq
GTCTGCTTCGTCTGCACCAGGTT
3' ss Score
7.54
Exon sequences
Seq C1 exon
TGATCGTCCGCGCTGCTGACTGCAAGAAGGTGTACCAGATCGAGCTGGCGCCCAAGGAGAAGATCGCCATCCTCCTGTGTGGCCGGAACCACCATGTGCACCTCTACCCCTGGTCCTCCTTCGACGGAGCAGAAGCGAGCAACTTTGACATCAAGCTCCCGGAAACAAAGGGCTGCCAGCTCATAGCGACAGGGACGCTGAGGAAGAGCTCGTCCACCTGCCTGTTTGTCGCTGTGAAGCGACTAATCCTTTGCTACGAGATCCAGAGAACTAAGCCTTTCCACAGGAAGTTCAGTGAGCTGGTGGCTCCGGGACACGTGCAGTGGATGGCCGTGTTCAAGGACAGGCTCTGTGTTGGCTACCCCTCTGGGTTCTCTCTGTTGAGCATCCAGGGGGACGGGCCGCCTCTCGACCTGGTAAATCCCACTGACCCCTCGCTCGCGTTCCTCTCACAGCAGTCTTTCGATGCCCTCTGTGCTGTGGAGCTCAAAAGTGAGGAGTACCTGCTTTGCTTCAGCCACATGGGACTGTACGTGGACCCTCAAGGTCGGAGGTCACGCATGCAGGAGCTCATGTGGCCTGCGGCTCCTGTCGCCTGTA
Seq A exon
GTATGTATATGTTTTCTGTTGCCATATCACTGTTGCTGCTGCTCACACGGACAGCCGGCATGTTCTGTTTGCTTTGGTTTGTCTCTCGGTCCCTGAGCCAGGAGTTAAGGGGCAGGATGAGAGGGTGTCTGCTCAGCGAGAGGGTGCGTGCAGGCTAGCTCTGTGCTGCAGCAGAGTTGGGGCCTGTGGTGTGGGCCAGCCTCGCTCCTCAGTGCCCTGCTCGTTCCTCACATGTCTGACAGCAGGTGCCCTCCAGGGCAGACAGCAGAGTGGATGGGGAAGGGACCTTGCATCTTCTTTTTAAAAGCATTCCCCTAGTAGAATTCGCAGAGCAGAAAAAAGTCACAGGGACTTGGCTACTAGGAGACTTAACTTCAGTGTCGGGGTCCTGTCCCTTGTAGGCTGGAGCCTGTTGATCTGTAAGGTGCTTTTGTGAGAGGGTGCTGTCCAGGGACTGGGACACCTTTCTTAGCTTGAGCAGTTGAGAGGCTGGGAGAACTAGATGCCTCTGGTGTCTGGGCTCCGCAGCACTGCTGGGCCGCCCTGCCACTCCGTTACTTTTGAAGGCCTTAAGCCGTTCATTCCATCCAGCCCTCATGGAACTGGAGGGCAGTAGCAAGCAGCAAGGAGGGCAAGCCAGCAAAGCACAAACTGGTTTGACCTGGAGGCTGTGGGGTTGCTGGGATAGGAGGTGGCTTCATGCTCCCATAATGGTGGACAACTGGCAACATCTTAGGCCGCCTCCATGATGCTCTCTCTGGCCAAAGGAGATGCCCAGAGGTGACAGGGCTGACAACTCAGTCTGTGTGCTGCAGTGGTTCTCAAACCCTTCTCCCTCACCGGGGAAGCTAGGGCAGCAGGCCCGGGCATTGCCAGCGGGAAGGGCAGCCTTGGAGATAGGAGATAACCTCTCCTGGTCCTTGCAGGCAGCCAGTGCAGCGCTCTAGGCTGTACACTCCTAACTTCCAGAATCTCATTTTTCTTCCCAGTTTGGAATTGGAACGGACACGTCCCTAAGTGCGGTGTCGTTAACAATCCTTGGTACACATAGCTAGCGTGGACACCCAGTGTTCCCTCCTCCACTTCCATGGGCAGCCCCATGTGTACCCAGTCAGCTTCAGAGATGGAAGAAGTTAGGGAACTTTGAGAGTGGAGCAGCATCAGAGTCCGCAGTGCCTCCTAGTCCTGTCTCGAGAGGCAGAGGTTCAGAGGCCCCCTAGCTTGCAGGTCTAGCTGTCTCCAAAGCACATACCCTCCAGTGCATCTGTAGTGTGTTTATTCAGACGTTCCATTTGAACTTTGTCCTTTGTTGACAAATCACAAGTGGGGTCCCCCATATATTCAGCAAGTAAGAGCACTTGTCCCAGAGTTCCCATCTGGAGAGTTTTCATCTTAGAGGTAACTGAGGGCCAGCCTCTGCACATGGCATTCAAAAACAGGACACCCACCCCCACCCCGTGTCAGAAACACCACTGTTGGATAATTTGGTGGCCAGTTCCAGCATCTTGTCCTGCCTGGGCTGACTCAGGCTGGTTGGAGTCGCACAACCTCAGTCAGTGCTGGTGGTGTCATGTGTGCTGAGGTGCTGAGGTGCCCAGCCGGCTTCGCCTGGGCTCCAGCTGTCTACTCCGTACTCTGCCCTTCCATAGATGAGAACGCTCCCGGCTCCTGGTAGTGGCCCGGCCACCTGCAGCAGCGTAGCTGAGGGAAAGTAGACATGGGCTCTGCTGTGTCCTAAACTTGAGGGTGTCTCCTTCAGCCTCACGTGCTCAGGGGCAGAGGGCCATGGGTGTGTGTCTGCAGTGTGCCAGATCAGTTGTCATAACATGACAGACAGCATTTCCTAAGAGCTGGGAGAGGAGAGGGCACCATCACAAGATGCCTTTCCTCATTTGATTGTGTGTTCAGAATAGATCACTAGAGTGGGGCCCACTGTGCCCTACAGGATCATCCCAATGTCCCAAGTGTGTCATGTGCAGAGCAGAGCAGTAGGCTAGTGTGGGTCTGAAAAACAATCACCCAGAAACCGGGGTTCTCTCTATTACCTTAGATGGCTTTTGGGACTAGAGAGGTGGCTCAGTGGTTAAGGCTGCCGTCCCAGGAGCTGGGATTTAGTTCCCAGCACCCGTGTGGCAGCTCTCAGCACCTGTAACTACAGTTCTAGGGGTCCAGCCCCCTCTTACTAATCTTCTCAGGCACTGCATGCACATGATGCACAGTCACACATGCAGATCAAACATTCATACACGTAAAAGAAAGGAAAAGTGAGGAAGACATTAGGGTTTTTGCTTGGCCATGTAGAACAGGCGGTCCCTGCCTGGACTGAACAGGTGTTAGGAGAGAGCTGAGTGAGGAAATGCTTTTTAAATCGACTTCCTCTTACTGTGCTGTGGGAAATACACCCTGGCTGGCTATAAAAGCAGTGGGTGCCTCTGTACAATTAAAACACATGTGACTTTGACATAAAGATGACTTCTGGCACGGGAGCCCCCACAGGCAGTGCTATGCACCTCCACCTGCTCGCCCGTGCCGCGGTGGCCTAAGGGCGGGCGAGGATGCGGGAGGACGGGGTTCCATGCTTACTTGTCTGCTTCGTCTGCACCAG
Seq C2 exon
GTTGCAGCCCCACCCATGTCACAGTGTACAGCGAATACGGGGTGGATGTCTTCGACGTGCGCACCATGGAGTGGGTTCAGACCATCGGCCTGCGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021279-Cdc42bpb:NM_183016:30
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0078017=CNH=FE(74.9=100)

							
A:
NA

							
C2:
PF0078017=CNH=FE(12.0=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000042565f957A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000042565
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr14:102940325-102943890 
ALTERNATIVE
HsaINT0031694
(CDC42BPB)
Human
(hg19)
chr14:103406662-103410227 
ALTERNATIVE
HsaINT0031694
(CDC42BPB)
Rat
(rn6)
chr6:135752248-135754821 
ALTERNATIVE
RnoINT0032658
(Cdc42bpb)
Cow
(bosTau6)
chr21:69283558-69285898 
ALTERNATIVE
BtaINT0035062
(CDC42BPB)
Chicken
(galGal4)
chr5:49818611-49821343 
ALTERNATIVE
GgaINT0056381
(CDC42BPB)
Chicken
(galGal3)
chr5:52423228-52425960 
LOW PSI
GgaINT0056381
(CDC42BPB)
Zebrafish
(danRer10)
chr20:18510440-18514228 
LOW PSI
DreINT0043806
(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"