Special

MmuINT0032897 @ mm9

Intron Retention

Gene
ENSMUSG00000024769 | Cdc42bpg
Description
CDC42 binding protein kinase gamma (DMPK-like) [Source:MGI Symbol;Acc:MGI:2652845]
Coordinates
chr19:6306457-6309217:+
Coord C1 exon
chr19:6306457-6306875
Coord A exon
chr19:6306876-6309125
Coord C2 exon
chr19:6309126-6309217
Length
2250 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
TGTCCGCTCTGTCCCCTCAGCCA
3' ss Score
9.81
Exon sequences
Seq C1 exon
CCTTCACCTTCAGCCGCGGCTCCCATTGGCCGGCGCGCACCTGCCCGTCCGTCGGGGGCGGGCTTGGAGGGCGGGGCGGGCGACCAGGTGAAGGAGCGCGGGTGGCGACCGAGGAAGGTGACAGCGGGGAGGGCGGGAGGGAGGGGGGAAGCCGCGCAGAACGAGCCACGGGACCACAGACGGACCGCCGGGCGGACGGACGGACGGGGCATGCGGGCGGCCTGGCTCTAGCCCGGGTTTCGGGGCTCCAGCGGCAGCCATGGAGCAGCGGCTGCGTGCGCTGGAGCAGCTGGTACGGGGCGAAGCTGGTGGCAGCCCAGGGCTCGACGGCCTCCTGGATCTGCTGCTGGGGGTGCACCAAGAGCTCAGCAGCGCCCCCCTGCGCCGGGAGCGTAACGTGGCGCAGTTTCTGAGCTGGG
Seq A exon
GTGAGTGGTCCGGGCAACACCCGGGAAGGGAAGCTGGAGGGACGACAACACCTGGAGCTTTGTGCCCCCAGACCTTTTCCCGGGAGTGGCATATTCCTGAAACTTCCTCATTGTGCTGTATCTAACGCTTGCCGTTGGTCTCCACAGCCCGCTCGCTCACCTGCACCTTACTTCAAACTCCCAGAGACAGGTACATAAGGTACACTTCCCACATACCCTGCTACAGACCCCAGACATGTTGCCAATACACATCTTTCACAACGGTCACCTCATGCTCTACCTAGAACATACATTTAGGCGGACACCGTTTTGTGTGACATAAACATACAGACTTTCTCTATTTCCTCCGTTCTTCAAGAGGACGGGCACTTTGTTCTAGGACCCCTCTCACCTGTCACACACTCAAAAGTCCTCGTCCTTCACCTTGCAGACAAGTCTCCTTACTTCAATCCCTAGCCGGGACCAAGAACCAACCTCAACCCCTTTGGAGGATTTGGGGTCTTGTTAGAAGTGGTTTTATTTGATTCGTCTGAATCCTTGGGAATGGCTGACTTAGGGTGATCCTAAACCCAATGTGGGCACTGGACACATCTGGCCAGGCTTTGGTGAGGAGGGCATGGGAATTGGGCCTGAAACATGGGGTGTTTACCCTGTAGGCGATCAGAGTTCTTGGTGCTCCTGAGCTATGGGCAGACACAAGGCTAGGCCAAATATGGATGGGGGTCTACCAGCCAGTCCTGCCATTTCTTTCTGGGGTGAGAGCAGTTAGACGGCCCTGCCCCCGTTGCCTGCCTGTTTCTCTGTGACTCTTCTGTGTTTTACAAGTGTCTGATTTGTCATCACTCCCACATGACACCTGTACCTGGGTGTGTGCATGTGGCACATGTGTGTGTGTTTACACATATGTGTGTTTCTCCCTGCCTGCCTCTGGCACCTCTGCTTGGGACCCCAACACAGGGCATGTCTGTTGACTTCTCCCGAGGTAACTCCAAGGCCGGGTGTGACTCACGCCTCTCCTGCCCCAACTTGTCCCTGCTCCTGCCCAGAGCCCCCACCCCTTCTGGCAAGACAAAGGTATTAGGCATCCTGTCCAGGAGGTTGGATCTGGGCACCAAGTTTGGCCAATGTGGCTGGTGGTCACCTCTGATATTTCTGCAGGCTGGCAGCTGCTCCTCCCTGGCTCCATGCATAAACCTGGGAAGAGACAATTAATTTCTGTAGTGAGGTTTGCACACCTCCCCCGCTGTGGGGGTTCTGCCTGATAAACCTGTGGAACAGCTCTCTGTCCCACCCACAGGCCCGCCCAGCTGGCAGGGAGTTTACCTTCTGGCAGGGGGAAACTGAGGCAAGGTGCCAGATCGTAGATGTCCCCCAGTCCTCACTGGTCACTCCTGTCTTCATCATTTCCCAAGACTCGGTGCCCTTCCCCCTGGCCTACAGCCACTTCAGTTATGGGGAGAGCCTGGGAGTGGTTGGACCTAGCCCTTGCGGAGGTGGTGGTAGGGCAAACAGACTGTGATGCGGGAGGAGGTTCCTGCCTGTATAAGCCCCATCCAGAGAGGGAGGTAGGGCTCTAAGTGGCAGGGCTATCAAGCCTGGAAGGAATCCTGTGTGCTCACACCCTCAGGTGCTGGCATTGGGCACCAGGTGAAGTTTTTGGCCCTGTTTGAGTGTCTTGTGAGTACCTGAGCAGGCTGGTATCTGTTCCTGACCCAGAGGCCCCACTTGGGGAACACAGAGCCTGTCTTTCTGGAGCACTGTAGAAAGTGTCCTCCCTGCCCCCAGGGGCTACCCCAGGCCTCACCTCCAGCCAGATTGCTCTGTGCTACAGGGTCCCCAGACCCAGGCCCACAGTTCCTGAGTGGCAGAGAAACTTTCTGGGGACAAAGAATGTCACCTATCCAGTTTCCCAGATAGGCCCCTGGGCTGGCCTTGAGGGGTCAAAGGCTGTGAACTAGGGGTGAGAGTGGTGTCTTTATTGTCTCTAGGGTATTAGGCCCCTGGCTAAAGAAGACCACAAGGTCCCTCTGTGCCTCATAAAGAGACTACTTGGAGTCTAGAGCCCAGGAAGGTTCTGAGGCTAGGTGGTCCACTGAGTCAGGACCCTCACCATGCTTGTATCATGACCAAATAGTCCCTGCTTCTCATCTGTCCCTCAGCTGGGTTGTCTCTGGGAGAGTCACCCCTATCCTAACCTCATGGGAGATTGTAAGGAAAAAAAAACCCTCGCTGTCCGCTCTGTCCCCTCAG
Seq C2 exon
CCAGCCCCTTTGTAACAAAAGTGAAAGAGCTGCGTCTACAGAGAGATGACTTTGAGATCTTGAAGGTGATTGGCAGAGGGGCCTTTGGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024769-Cdc42bpg:NM_001033342:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0006920=Pkinase=PU(10.5=41.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000025681f1622A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000025681, ENSMUSP00000025681f1623A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr11:64841905-64844409 
LOW PSI
HsaINT1006976
(CDC42BPG)
Human
(hg19)
chr11:64609377-64611881 
HsaINT0031707
(CDC42BPG)
Rat
(rn6)
chr1:221674005-221676370 
ALTERNATIVE
RnoINT0032671
(Cdc42bpg)
Cow
(bosTau6)
chr29:43693958-43696477 
LOW PSI
BtaINT0035076
(CDC42BPG)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr20:18594488-18635744 
LOW PSI
DreINT0043785
(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"