Special

MmuINT0128484 @ mm9

Intron Retention

Gene
ENSMUSG00000015090 | Ptgds
Description
prostaglandin D2 synthase (brain) [Source:MGI Symbol;Acc:MGI:99261]
Coordinates
chr2:25322807-25323439:-
Coord C1 exon
chr2:25323338-25323439
Coord A exon
chr2:25322866-25323337
Coord C2 exon
chr2:25322807-25322865
Length
472 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGG
5' ss Score
8.48
3' ss Seq
CTGGGCTTCTTTCTTGGCAGATA
3' ss Score
9.56
Exon sequences
Seq C1 exon
GCAGAACCCAGACTCTGAAGGACGAGCTGAAGGAGAAATTCACCACCTTTAGCAAGGCCCAGGGCCTCACAGAGGAGGACATTGTTTTCCTGCCCCAACCGG
Seq A exon
GTGAGGGGGGCTAAGCTGCTGGGGAGGGAATTATAGTCAGATTAGTGCAGCCTCTGGTTGCAGCAAGTGAGGGCAACTAGGGCGAGCTTAGCCTTGCCCTACTACCTGCTAGTCCAGGGGGCTTCAAGGAAATAAATGGAGGTGTCAGTCTGTCCGACATTATTACATCTACCTACAGCCCCCTTTATTGGGAATCCTGTTCCTGGTGGACACCTAGCTCCCCTGTCTGCCAGCCCCCTAGCTAGGGGTGCAGGGGTGATACTGGAACAAACAGATGGAGAAAGACACCTTTTATGTTTTAAAGGACAGATTGGGGCAGAGGTGGGTGGAGTCTGAAGTTTGGGGGCTCAGCCAAAGCTAGTTCTCCATGGCCTTGGGGAGGCTTCTTAGAGTCCAGGAAGAAGCATGGAGTCCTGGTGAATGTGTGTCTAAGCCTGGTGCTCACTACTTCCCTGGGCTTCTTTCTTGGCAG
Seq C2 exon
ATAAGTGCATTCAAGAGTAAACGCAGGTGAGAGAAGTCAGTCAGAGGGCTGGTCACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015090-Ptgds:NM_008963:5
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:
PF0006118=Lipocalin=FE(23.4=100),PF0144313=Viral_helicase1=FE(44.7=100)

							
A:
NA

							
C2:
PF0006118=Lipocalin=PD(0.1=0.0),PF0144313=Viral_helicase1=PD(6.6=71.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000015234





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000109889, ENSMUSP00000109897
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:136980285-136980832 
ALTERNATIVE
HsaINT0133982
(PTGDS)
Human
(hg19)
chr9:139874737-139875284 
ALTERNATIVE
HsaINT0133982
(PTGDS)
Rat
(rn6)
chr3:2686754-2687163 
LOW PSI
RnoINT0119680
(Ptgds)
Cow
(bosTau6)
chr11:106248105-106248711 
LOW PSI
BtaINT0119602
(PTGDS)
Chicken
(galGal4)
chr17:509422-509574 
LOW PSI
GgaINT1022876
(PTGDS)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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






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