Special

MmuINT0032857 @ mm9

Intron Retention

Gene
ENSMUSG00000026490 | Cdc42bpa
Description
CDC42 binding protein kinase alpha [Source:MGI Symbol;Acc:MGI:2441841]
Coordinates
chr1:181991921-181995297:+
Coord C1 exon
chr1:181991921-181992014
Coord A exon
chr1:181992015-181995096
Coord C2 exon
chr1:181995097-181995297
Length
3082 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAAT
5' ss Score
7.76
3' ss Seq
AAAAATTTGAACTTTATTAGGTC
3' ss Score
4.49
Exon sequences
Seq C1 exon
AGACATCAAACCTGACAATATATTGATGGATATGAATGGACATATTCGTTTAGCAGATTTTGGTTCTTGTCTGAAGCTGATGGAAGATGGAACG
Seq A exon
GTAAATAAACATAAATTATGAATTATTCTACTCAGATATTTCCTTTTCCATGTCTTCTATGTTCTAGAGAGCCCTGCTTGCACTGACTGTCTGCCCAGCCATGCACCTGTATGTGTTCCACCTCCTTCTACAAAGCTTTGGCTATTCCTGCACGTGATAAGGCTTGTTCATCGAGTTATTTTATCTGCTTGCAATAAGTACTTAGCTTGAGAATGGCACTTTTAAGAGTCTTGTATCTTCTTTTTTGGCTGATGCCTACTATTTTACTTGAAATGTTCCTAAGTTTTTAGAATGATAAATAAGGTAAGTTTCATATAGAAAAAGAAAACATAACTCCACCTTCATTTGTACTGTTTTTCTAATTATATACTTGTTCTGAGGGACAATTTTCAGCTTTGTTTTGGTTTTTTTTTTTTTGAGACAGGGTTTTTCTGTATAGCCCTGACAGTCCTGGAACTCACTCTGTAGAGACCAGGATGGCCTTGCACTCAGAAATCTGCCTGCCTCTGTCTCCCAAGTGCTGGGATTAAAGGCGTGTGCCACCATGCCTGGCTTACTTTATAATTTTATAACAGACAACTTTTTATGTATTCCATATTTGTTTAAAGAGATGACATTTTCTCTTAATTTTTAATACCAGGGTTCTATACAAATCCATAATATAAAACTGAGTTTGCATTTGTATTTTATATTATTAAGGGTTTTCCTTGTTATCAATTATTTAAAAATCCTTAATATGGTAGATTTGTTAATTCTTCCTTTATATGGTCAGTACTTTACACATCTCCTTTGTGCCTTACTATCTGGTGAAATACTACTTTTCCCAGTATGGTTTCTTTTCAATTAAACTGACGAATTAAAATAATTTTAATAGTTAGGCTAATATTTCTATTACTGTTTAACTTTCTTTTGCTTAATTTATGTGCAATTCATCTTTTTATCCCATCACTTTCAAATGTGTGCTTCCACTATGTCTTATCTTGTTTAAGTAAATTATTTAACTGATTTTTCTCTCATTTATTCATTTTGTTTTATTTCTTTCCCAGTGTTAAATCTTTGTCCTTTAACAGGTGATTTAATCCACTCTTGGGTCTTGTGACTCAGGCCAGCGCTGTGTGCTGTTCATATAGGTTTTGCTTGTTGTCTGCCCTTTTTCTCTCCTGCCTCCTACTGTGCAGTTCAGGTTTAGCTTTCTCACTCTCTTTATTCTTGGAAGGTAACATATTTCATTTAAAATATTTTAATGCCTCTCTTTTGTTATTTTAAAAAATATTTATAGTTTACTTAACTGTAAGTTAATAATTTTTCTCACTTCATTCCCATTCAATATAATCAACTTATTTTACTTTATGCCACATATAGAAATTAATTTAAATTGCCAAAGAACTATGTCAAAACCAAAAAAAAAAGTATGGGACAGTATTTATGATTAGATTTGGCAAATGTCTTGAGGATAACATAGAATCACAACCCTTCTACCCTGTAATGGTAAATTATATTGTCCTCAAAAACGTGTGTGTATATATGAGATGACACAGCGGGCAGAATGAGAAGATAGCGTATAGAAAACTGCAACAGTGTCTGCCCATCACTTCTCTGATTACATGCTAAGAATATGTGACGAATAGTTACAGAGTGTAGATGCATCCTGACCTGTAACACTAACCTGCCCACGGTTACCTTGGGAGGCACAGGGTGAGATATTGGTCTTTCCTGAAGCTTTCTTCCAAGCTCAGCAACAGAAAAACAGTCCCAGTGAAGAATAAGAGGAGTTTCCCACAGGCTTACAAATGGGAATGAGAACATGAAAGACACTCAGCAAAACCTCTCTTTAGAGAGATGCAAGTCCAGAACCCGTGACCCCACTGTGAGTGCATCCTCTGCCACCCAGAAACAGCAAGTGTTGTCCACAGATGATTTAGAGCCTCTGGACACTGTTAGGAGGAGTATAAGACAGGGTAGTGACTGTGGAAAATAGTGTAGCTAGTTCTTCCAGATGCTAAAAATCAGTTGATAATTTATTCATTTTCATTTTTATCTGTTAACTTGTTTAATTATATTTTCAACATTTTAAAATTAAGAATTTTGTTTTAAAGTCTATTTTTTCTGTTTGGTTTCATTTGTTTGTTTGTTTTCTGAGAAAAGGTCTTTCTTGTATAATATCCTTGGCTGGCCTGGAATTTGCCTTGTAGACCATGCTGGCCACAAAAGCATAGAAATCCATCTCAGTGCTAGTATTTAAGGTGTGCACCACCATGCCTGGTGCAACTTAGAACTTAATAGTATTTAAGGTGTGCACCACCATGCCTGGTGCAACTTAGAACTTAATAGTATTTAAGGTGTGCACCACCATGCCTGGTGCAACTTAGAACTTAATAGTATTTAAGGTGTGCACCACCATGCCTGGTGCAACTTAGCACTTAATAGTATTTAAGGTGTGCACCACCATGCCTGGTGCAACTTAGCACTTAATGTACAATAACTAATCAATCTTCAGTTTTCTTAGACTCATACTTAGAGATGTCAAATTATTACCAGTGTTCATCTGAATGAGTTGTTCATATCTAACTAAGTTTTTAGTTCTACTATAATACATACATACATACATACATACACACACACGTACATACATGTTTTGATTGATTAGTTATATAGTTAATAATTTTAAAAAACAGTAAGAAAGCTGATATAGTAGTGCTGTAATCCCAGCACTTGGGAAGCAAAGTGAGGAGGATTGTGAGTCTGAGGCTGGCCTCAGCTATAAGCAAGAACTTGACTCTGATTACCAAACCAAACCAAAATTAAATAATAATAATGTTGTAAGTGAAACATTCGTTTTATTGTTAATGACTCAGATAATATTGTTTCCCTATATGCATTCAACTATAGTAAAGGTTCTATAACATTGTGAGTAATGAAGACTATTAATATAAAGGCCATATAAAATTACTCTGTAAAATCAGGAGACTAAATACAGATGATAAAAATGTCTTATTATACGCCTACATACATACTGTATATCTCAAGTACCTCTTTCTAATTAAAATTTATTTTTTAATAATAAAAATTTGAACTTTATTAG
Seq C2 exon
GTCCAGTCCTCGGTGGCAGTTGGAACTCCAGATTATATTTCTCCGGAAATCCTTCAGGCTATGGAAGACGGAAAAGGCAGATATGGACCAGAGTGTGACTGGTGGTCCTTGGGGGTCTGTATGTATGAGATGCTTTACGGAGAAACACCATTCTATGCAGAGTCTCTGGTGGAGACATATGGAAAAATTATGAATCACAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026490-Cdc42bpa:NM_001033285:6
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:
PF0006920=Pkinase=FE(11.6=100)

							
A:
NA

							
C2:
PF0006920=Pkinase=FE(24.7=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000106746





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000075980, ENSMUSP00000095059, ENSMUSP00000095061, ENSMUSP00000095062
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:227147560-227160542 
LOW PSI
HsaINT0031666
(CDC42BPA)
Human
(hg19)
chr1:227335261-227348243 
LOW PSI
HsaINT0031666
(CDC42BPA)
Rat
(rn6)
chr13:98340989-98344335 
LOW PSI
RnoINT0032631
(Cdc42bpa)
Cow
(bosTau6)
chr16:30840427-30852566 
LOW PSI
BtaINT0035037
(CDC42BPA)
Chicken
(galGal4)
chr3:11720443-11721204 
LOW PSI
GgaINT0090258
(CDC42BPA)
Chicken
(galGal3)
chr3:13268677-13269438 
LOW PSI
GgaINT0090258
(CDC42BPA)
Zebrafish
(danRer10)
chr16:13554876-13555128 
LOW PSI
DreINT0140648
(si:ch211-89p3.3)
Zebrafish
(danRer10)
chr20:18560537-18566293 
LOW PSI
DreINT0043816
(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"