Special

MmuINT0117365 @ mm9

Intron Retention

Gene
ENSMUSG00000006494 | Pdk1
Description
pyruvate dehydrogenase kinase, isoenzyme 1 [Source:MGI Symbol;Acc:MGI:1926119]
Coordinates
chr2:71718096-71721664:+
Coord C1 exon
chr2:71718096-71718167
Coord A exon
chr2:71718168-71721479
Coord C2 exon
chr2:71721480-71721664
Length
3312 bp
Sequences
Splice sites
5' ss Seq
TGAGTGAGT
5' ss Score
6.51
3' ss Seq
TGACCGAGAGGTTTGTTTAGATT
3' ss Score
-4.62
Exon sequences
Seq C1 exon
GTATATCCAAAGCCTTCAGGAGTTGCTTGATTTTAAAGACAAAAGTGCTGAAGATGCTAAAACTATTTATGA
Seq A exon
GTGAGTATCATTGTATGATCCTATTCAGAATACAATTTTATATTCTTTTTTTTTTTTGATGCAAAAGCAAGAGGAATTTATTGTTCTAGCACATTGGTGTCATTCCCTACCTGAAGGAGAGGTAGTGACCATATTCTTTTTTAAAAATAACTTACTTTATTTTGTATGCATTGGTGTGAGAAACTGGAGTTACAAATTGTTGTGAGCCACCATGTGGTTGCTGGGGATTGAACCCGGATTCTCTAGAAGAGCAGCCAGTGCTCTTAACCACTGAACCATCTCTCCTGTCCCTAATTTTATATTTTTAAAACACCATACAAATGTGTAAATGTGGTTACCTTAACTTGCTACTAGATCACTTTAAGGAAATTGATTAACACTGAGGATTCTTTAACTGTACAGTGTAGTTAAACGTAACATAGGATCCATGTATAGCAACCCACACAGGTACTAAAGACATCAAGACAGCATAAACCAGGGAGCTGGACTGGATGTAAACAACGCTACACTGCCCTCTCTACTGTAAAAAGAGAGTTCAAATGTGATGACCAGTAGACATCTAGATGTTACCTGGATGCCTCTTGGTCTGTTAACCTGGGGAGGGCACACCAGTCAGTCCCAGAGGGACAGCCACCTCTGCTCACTGCTTGTTCACGTGTGCATATGTTGCCTGGATAGTCGGAAGTTTTATAGTTTTAAACAAAAGATCGCCGAGCAGTAGTGGCGCACACCTTTAATCCCAGCACTTGGGAGGCAGAGCCAGGAGGATCTCTATAAGTTCGAGGCCAGCCTGTTTATAGAGTGAGTTCCCAGAGAGACCCTGTCTTTAAAAACCAAGAAAAAAAAATCTAGACTTTTCATGTAAGGTCTCTAATTTTGAAACATAGCAACTGCTTATGCTTCTTTTGTTATATAGAAGGGTTATAAAAAATATCTCTGGGTTTCTATGGTTTGTTACATTATGAGCTAATGTAAATCCTATGCCCAATTTCATAGCCCCAATGCCAGAGTTGATAAGCCCAATTAGTTACTTACTTAGGGAGTTATCTGCTTATAATGAATGTTGTTATGTCTTCAGAAACTGTCATATCTTTTTTTTTTTTCCTAAGAAAGAGGTGCTCTTTGTTTTTTTGTTTTTGTTTTTAACGGGACTATCAGTACTGCATTTTTCAAACATGCTTTTGGTTTGAAAGTCACTCATCAGCTGTTCACTATGAAGGTGAGTGATGTCATTTAGTGTTTAAAGCAACTCTACTGAGATAGTGCATTTATACACAAAGAGAGTTGTAGCTTGGGGTCTTATAACTAGTAAATGGTAGGCCTAGAAACACAGCAAAAGGCCAATGGTAGACTATTTTATAAATGCTACTGTAGAACCCTTTGAAAACCGTCACTGAGAGCTGAGCCTAGGGAAAAAAGTGAGCAGTCGGGCCGAATAATACTGTCATCTATATTCCTTTAAAAACCTATGCATATGCAGGCTCCTGTGTGTTTGTGTGGAGGATGGAGGACACCCTCAGGTATCAGCCTCTGGAATGTCTGCCATCTACCTACTTTGAGTTAGGCTGGCTTGGCCAGTGAACACCAGTTGTCCTATCTGTTTCTCCAGCGCTGAGCTTACAGATGTGTGCCACCACACTTGACATGATGAATGTGTGCAGACAGAATTCGGTCATTATGCTTGTGTGACAAGCACTTTAGCAACTGAGCTGTCTCCCCAAACCAGTTCCCCCCCCCCCCCCCCCCCCCCCCCGACAAGGCCTCATATGTGGCCCAGGTTTTCTTAGAAACCACTGTGTAGTCTAGTCTGGCTTCTGGTCCACAGTGAGTTGCCTGGTTCGGCCTCTGCCTGGCATTACAGGTGAGCTACTGTGCCCTGCTCAACAGTTTTTGTTCTAAAGAGTGGAACAAGAAAGTAAGGAGGGGATTGGAATTTTCAGTTGTTTTCGGGGAAAAAAAATTATATTTTGTCTTAATAGCTTGGTTTTGAAGTTTATTCCCTCTCGTGCGCACTGGCCAGGAAGAACGACGCTGCAACAGGATCCTTCTGCACACGTTTATTGGGAGAGCTTGATTGTAGAGGCGAAAAGACCTCAAGCCCAGAACTGGTGCTGCTTTTATATGCCTAGGACAGGCGTTCTCTCTCATCTGATTGGTTAACTTGTCTCTCATCTGATTGGTTAACTTGTCTCTCATCTGATTGGTTAACTTGTCTCTCATCTGATTGGTTAACTTTTGTCAATTCTCAAAACCTCACCTTGGTAAAAGAACCTTTACTGGCTATGTATGTGTGGTGGCCAGCTGTAGCCAACTGCCACTCTGCAACTGCCACTCTGTAACTGCCACTCTGTAATGGCTTCCCACAATTCCCAACTAAGAATTCCAAAAGTGTGAAAATCACTGGCGCTAATGACACTCAGGCTGGTGTCTCGGAAAGCACTCATTCAGAAGTGTGAGCCCTGGTGACTAGTTGCATCACAATTAAGACTTCTTTCTTTTATCTTATTCCTTAAATTGACGAAAGCAAGAAGGCAGTGCGACTTGAAAATCTCTTTTAATCCAACAGTTTCCTTTTTCTCATCCACTTTGGTTTTTGTGTTTAGTTTTGTGTTTTGGTTTGGTTTTGATTTTGGTTTTGGTTTTGGTTTTGGTTTTGGTTTTCAAGACAGGGTTTCTCTGCATGCGCAGCCCTGGTTATCCTGGAACTCTGTAGACCAGGCTGGCCTCAAGCTCAGAGATGCCCTGAGTGCTGAGATTAAAGGTGTGCGCCACCACTGCCCCTCTTCTCACGCATGATATAAATCCAGGGGGAATGAAACCAGAGTTGCTTTTTCGATTTTCTGTCCCACGTGGTTTCTTTTCTCTGAACTCTAGGGAGGAATCCACAGCCAGCTTTCTTGGCTTTCTCAGCTTGATTCCTTGGGGAGTGTTTCCCTAGAAACAAGGAACTTTCTTAGGCCGTGTGTCTCTGGAACGCTGTCCTCATTAGTGAGCCTCAGATGCGTAGGTAATACTGGATACAGGAAACCCTGACACTGTAGTGTGGCTCGGGTGACGATGGATAAGGGGAACCCTTATACTGTTCACAGTAGTATGTAGTGTTACAGGAATCCAAAAATTATGGAAGTCTTATTTTTGAGATTCTTGTACCTTGTGGGTTCTGTGTATCTCGCGAGTTGAAATGAAAGTGTGGGAGAGCCTTCGCCGGCTCTCCATTCTCTGAAGGAGGGCTTTTTGTAGTTGCGGCTTGTATCTTAGTATTGAAGTCACTTGTCAAAATATTTGGCTGTTCTGACCGAGAGGTTTGTTTAG
Seq C2 exon
ATTCACAGACACAGTGATAAGGATCAGAAACCGGCACAATGATGTCATTCCCACCATGGCCCAGGGTGTGACTGAATACAAGGAGAGCTTCGGGGTGGATCCTGTCACCAGCCAAAATGTTCAGTACTTTTTGGATCGATTCTACATGAGTCGCATCTCAATTAGAATGCTACTCAACCAGCACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000006494-Pdk1:NM_172665:3
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=0.043
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF104364=BCDHK_Adom3=FE(14.5=100)

							
A:
NA

							
C2:
PF104364=BCDHK_Adom3=FE(37.6=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000006669f5861A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000006669
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:172562292-172564502 
ALTERNATIVE
HsaINT0122510
(PDK1)
Human
(hg19)
chr2:173427020-173429230 
LOW PSI
HsaINT0122510
(PDK1)
Rat
(rn6)
chr3:58538325-58541591 
ALTERNATIVE
RnoINT0109212
(Pdk1)
Cow
(bosTau6)
chr2:24097510-24101958 
LOW PSI
BtaINT0109514
(PDK1)
Chicken
(galGal4)
chr7:17203939-17204541 
LOW PSI
GgaINT0045756
(PDK1)
Chicken
(galGal3)
chr7:19080567-19081173 
LOW PSI
GgaINT0045756
(PDK1)
Zebrafish
(danRer10)
chr9:3137585-3140309 
LOW PSI
DreINT0112022
(pdk1)
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"