Special

MmuINT0119672 @ mm9

Intron Retention

Gene
ENSMUSG00000030660 | Pik3c2a
Description
phosphatidylinositol 3-kinase, C2 domain containing, alpha polypeptide [Source:MGI Symbol;Acc:MGI:1203729]
Coordinates
chr7:123517242-123519947:-
Coord C1 exon
chr7:123519737-123519947
Coord A exon
chr7:123517365-123519736
Coord C2 exon
chr7:123517242-123517364
Length
2372 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
ATTAAGCTTTCTTTTCTCAGTTA
3' ss Score
5.28
Exon sequences
Seq C1 exon
GGTCACTGAATCCTGAAAATCCTGTTCAAGTAAGCATGGATCACCTAACAACAGCGATTTATGATCTTCTCAGGCTCCATGCAAATTCTAGTAGGTGTTCTACAGGCTGTCCCCGAGGGAGCAGGAACATCAAGGAAGCATGGACTGCAACGGAGCAGCTCCAGTTCACTGTCTATGCCGCACACGGAATTTCCAGTAACTGGGTATCAAA
Seq A exon
GTAAGTAGCTGCTTAAAGGACATCCACAGCTTTACCCACAAGTTACACTTAGTGTTAGTAACTACTTTTATCTTTTTTGTTTAAATGAACAATTTAAAGATCACTGGGAACCCTTGTACCTTTGTGGTTTTAATAAAATTACAGAGCTGTCTGAAGTAATTGTAGTGAAAAATGTCATTTTTATGACATAAAAAAAGAGCAAGAGAGCCAGGTATGATGGTGCACACCTTTAATCTCAGCCCTCTGAAGGTGGAGGCAGAGGCAGGCAGATCTTTGAGTTCAAACCTAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCTGGGCTACACAGAGAAACCCTGTCTCAAAAAAACAAAATAAAACAAGAAAACAACAGCAAAAAACAAAAAACAGAAAAAGACAAAAAACAACAACAACAACAAAAAACACAGGAAAATATATAGTGAAATTGAGAAACAAAAATGTTATTTAAAAGAATTACCTTAAGATTGCTGAGCTTTTCTGCCTGCCTTTTAGAATCAACATAATTTGAAACAAAATGTAATGGGACTAGAATTCAGGCCCTATATCCCTTTAATAGCTCACAGTCTACCAACTGCTAATATTTGAATTCTGTAAGAGCATATTCCTTCTTATGATGTCTTTTATAAGGGTTTTCCTCTTGACTTCTTTTGTTAAAATCTTTAAGGCATAGCATTTTGGGGCCAATTTTAATTTACTTTAAAATAACTAATATAAACTGAAAAGTGTAAAATTAATATTTTACTGAAATATGTTCATGGTGGCTTAAAACGTTCAATAAAAAAGTCTAGTGGAGAGTTAAAAAATTCCACTTGAATTGAGCTTCAATTAAATTCAATTGAATTGAAATGATAGAGTGTTTGTTGTTGTTTTGTTTTCAAATAGGGTCTCTCTGTAGTCCTGGCAGTTCTGGAATTTGCTATGTAGCCTTGAACTCTGTAGCTGAAAGTGGTGTTGTTAAGTCATGAAAAATAAGTGTTTACTGAGCCCCATCTACAAGTAGAGTTTTCAGTACTGGAAATCCAGTAACAAATGAGAACAATGCCTTTCTAGAGCGTTTGTTTAAATGGCTATTCCTGCCTGTTTCTTTTTGTCTGTCTCGCTATACTGCTCAGGCTGCTCTCATCTTCAGAGACTGAGTGATCCTTTCACTGCAGCCTTTTAAGTAGTAGGGTTACAGGTGCGTTCCAAAATGCCCAGCTGAAAACATGGCAAACAAATTGTGTTGCTTTTTTTAAACTTGTATTTTCCTTTGTTCATTGGAGTTCCATATAGGAGGACCCACATAGTAGGAGAGAACCAACTCCCACAGGTTGTCTGTCCTTTATCCTCCATACACACCCTTTCATGGACTTAGATACACTCTAAATAAATGAAATGAAAAAAAAATGTTTTTTTCATTTGACACAGGGTAGCCCCAGCTGTCCAAAAACTCTCTCTATAGACCAGGCTGGCCTCAAACTCAGAGATCCACATGCCTCTGCCTCCCAAGGTCTGGGATTAAAGGCGGGGGCAACCACTGCCCTGTATAACTTTAAGTTATAGATATAGGTGGGCATGGCATGCAGCCCTTTGGTCCTAGTACTTGGAAGGTGGAGACAGAGGAATGCAAAGTCTCCAAGACCAACCACCACCCTACCTATTCACACCCAGAAAAAGCTGTGGATAGGAGTAGAATGATTAGCATGTAAACCTAGAAGTAAGTTAGAGTAGAAGAATGCCGTTTTATTGAGTCCAAGGTTCTTAGAAGATTGTCTTATTGTGTCAGTATGAACAGCAGTTTGGAACTAAGTTATTGGTGTTTAGTGAAAAGAATGCAGCAATACCTGTGAAGATTGGCTGAATTCCTGGGTCTGTATATTGTTAAATAAAGCTTAGCTGAATATTACTGTGGTGTAGCAAAGGAAAGTAGCATCAGCATCTCCACTACTGCTAAGGAAGAGACCAAAGAAACTGAGCAAACCTCAACAAAAGACAGGGATGTGATAGAAGTGACACCAAGGGAAGAGAATGTTGGTACTTCGTGAGTTTTAACTAGAAATGGATAAGCACATAGTCTGTTATCATTTGCCTGCCCTCTTAGCACAATACCTGAAACAGCTTATATTCTATGGGGATCATTATAGTCCCAGCATTCCCAGCCCCAGGCTGACACTTGGGGTATATGCTTCCCACGCTACTTTTTTTGTTACACCATTCCTCTGTTTCTGTAGAATCTTCAAAGGTTAAATTTCACGTGGATTTCAAAAAACAAAAGGTGACCATTTTGTCACTTGGGAAAAATTGCTAATGTACTTGTGTTAGATAGTTATTACCAACCTAGAAATCAAATTAAGCTTTCTTTTCTCAG
Seq C2 exon
TTATGAAAAATACTACTTGATATGTTCCCTGTCTCACAATGGGAAGGATCTTTTTAAGCCTATTCAGTCAAAGAAGGTTGGCACGTACAAGAATTTCTTCTATCTTATTAAATGGGATGAACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030660-Pik3c2a:NM_011083:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.127 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0079219=PI3K_C2=PU(0.1=0.0)

							
A:
NA

							
C2:
PF0079219=PI3K_C2=PU(29.1=97.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000126092





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000081710
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr11:17132039-17134818 
ALTERNATIVE
HsaINT0124914
(PIK3C2A)
Human
(hg19)
chr11:17153586-17156365 
ALTERNATIVE
HsaINT0124914
(PIK3C2A)
Rat
(rn6)
chr1:185291714-185294488 
ALTERNATIVE
RnoINT0111232
(Pik3c2a)
Cow
(bosTau6)
chr15:35900519-35902996 
LOW PSI
BtaINT0111658
(PIK3C2A)
Chicken
(galGal4)
chr5:11160063-11160138 
ALTERNATIVE
GgaINT1021571
(PIK3C2A)
Chicken
(galGal3)
chr5:12865736-12865811 
GgaINT0059918
(PIK3C2A)
Zebrafish
(danRer10)
chr18:27058361-27060154 
LOW PSI
DreINT0114186
(pik3c2a)
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"