Special

MmuINT0117564 @ mm9

Intron Retention

Gene
ENSMUSG00000026784 | Pdss1
Description
prenyl (solanesyl) diphosphate synthase, subunit 1 [Source:MGI Symbol;Acc:MGI:1889278]
Coordinates
chr2:22768120-22770833:+
Coord C1 exon
chr2:22768120-22768261
Coord A exon
chr2:22768262-22770721
Coord C2 exon
chr2:22770722-22770833
Length
2460 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
TTTATTCTCTTTTTTTCCAGGCT
3' ss Score
10.27
Exon sequences
Seq C1 exon
AGAGATGCAAGCCAGCCAGCGCTCCATAGCCTTAGTTGCAGAAATGATCCACACTGCTACTCTGGTTCATGATGACGTTATTGATGATGCAAGTTCTCGAAGAGGAAAACATACAGTTAATAAAATCTGGGGTGAGAAAAAG
Seq A exon
GTATGATGGTTTTTAATGTTACTTTGAAAAATCTTTCTTACCAAACCACATGCTGATGGGATTGCGTTTGCTTTTTAGACTTGTAAAATAGACTTGTTTGAATGTGGTCTCTGAAAGGAGTGTTTCTGTTGCCTCTGTAAAGGTCTGACAGCAAAAACGAACTCAGTGATTCTCCTTAATCTCTGTTGTTCTTACGTGAATTTTTCTAGTTATAAGAGAAAGCATTTTCATGCGTATTTCTTGCGGATTCCTACATTTTTCTGTTCAACTCAGATTGCCTACATTGATTTGAAACCATAAGCATTTGTTAACTTGCTGCATGTTCAAGAGTGTCAAAGCAAATAGAAACTATAAAACAAGAGAAATCACAGAAATAGTATTCTACTACCAAAACTTACTGTAAAGAGATCCTAATAAGATTTGCTATACATACAGGCGTATGCACACACACACAAATGCTGGTATGTATGTATATATATATATATGTATGTATATATATATTTGTTTGTTTGTTTGTTTTAAACTTTATCTGCATTTATTTTATGCTGAATTTATTCCCGGGCCATGAGTTTTTGTTTCTTCAGTTCCTTCTGGGATATCTTTTTCTTCTGTGCAGCCTCCTCTTCTGGCTTTGGAACGATCTGTTCCTTCCCAGTGAGGATCATCTCAATGTGGCAGGGGGAACTCATGTGTGGGTTAATCCGGCCATGAGCTCTGTAGGTTCGTCGGAGCATCTTAGGTGCCTTGTTCACCTGGATGAGTTTAATGACTAGAGAATCTATGTCTAAACCCTCAGTTCAGCATTACTCTCTGCATTTTTAAGCATGTGCAGCAAAAATTCGCCACCGACCCTGTGTCCAGCCCCACTGTTTGTCCTGGGTGCACCTACTGACTCCACCATTATACCGCCGGAATGGCACACCTTGCTTCTTTAAAGTGTCATCCTTCAGATACTTGGTGGCTTTGCATATATGCACACCCTTGATGGCCTGGGTGGTTTCCCTGGTGTTTTTAAAGTGAACACGAAGGTTTGAACCTCTTGATTTGCATGATTTTGTGGGGTTTTCTGGGTCAAGAGAGTAGCGAACGATTTTGGCACGTGACCTGTGAACACAGCAGCTCTGGTCGCTTCCAGGAAGAGGTTATATTTGATATATAGAGAAAGAGATTATTATTTTATGGGTATGGGTATTTTGCCTTCATGCATACACGTATAGCAGAAGAGGGCATTGGATCCCCCTAGTAGTGGGTTGACAGGAGGTTAGAAGCTATGATGTGGGTGCTGGGAATCAACCTGGGGTCCTTTGGAAGATCATCCAGTACTCTTCTACTGAGCCATTTCTCTGGCCCCTGTATATTTATTTTAAATTGTATTTCCTGTTTTATTAGCATTGCTTGAAGAGAATATGTAAAATAGGTACTTTGGATTGAGGATTTATAAGTTATGGGTTGAAGAATGAAGATGAACAAATGAAAAAGAGGATGTGTAAGCCTTCCTTCTGTGAGCAAGCGTTCTCCCACACATGTGCCTCCATTGGCAGTCTTACATAGTTGAGAACCAACCAAAGCACATAAAGCCAGTCTACCCTCTTACATTGTTCTTCAGATGAAGCATATGGTTCCCTCCTGTTTGTCAGTACTCTCATGTACTTTAATTGGAATGAATTTTTGCAAAATGGTGAGTAATTAGTAAGCATATGCTAAGTAGCAGTATTCTAGATAATAGAGAACAGAAAAATACTAAGATGGTTATTTTGAAAATTCTATTACCTTGGGCAGGGATGTAGCTCTGTTGCGAGAACTCATGCTCAGCATATAAAAGGCCTAGATTCAACTGCTGGCTTCTCATGCATGAATGACGTCTCTAATCCTGGGACTCAGGAGGTGGAGCAGAAAGATCAAGAGTTTAAAGTCCGCTTTGCCTACATACCTAGTGGAAGACAGCTCAGCTAGCTTGCTTACTTGCTCCTTCCTTCCTTCTTTCTTTTCTCTCTCTCTCTCTCTCTCTCTCCCTCTCTCTCTTTCTCTCTCTCTTTCTTTTCTCTTTTTGAGACAGGGTTTCTCTGTGTAACCCTGGCTGTCCTAGAACTTGCCATGCAGACCAAACAGACCGTAAACTCAAAGCAATCTCCTGCCTCCATCTTCAGAGTACTGGAATTAAAGGCATGCTCCACCACTTCTCTGTGACAGCCTAGCTTTTTAAAACATGAAATCCTATGAGTAAAACATTCTGTGAACTCTAGCATTTCTGTGTAACAGAGTAGTACTGATGTATATCTTTAGTGTGCATGTAAAGTGTACGATATAATTTGACTGTATAATTTTTAACTGATAATTTGTTCTGGTAACATTAATATCCTGGGTATCAAACCTAGGCTTTGTGTATGCTAGGCAAGTGCCTAACTGCTGAGCTAGCTGTGAACTTTTTTATCTGTGATGTTTTATTCTCTTTTTTTCCAG
Seq C2 exon
GCTGTTCTTGCTGGAGATTTAATTCTTTCTGCAGCGTCTGTAGCTCTGGCACGGATTGGAAACACAGCTGTTGTATCTATGTTAGCCCAAGTTATTGAAGATTTGGTGCGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026784-Pdss1:NM_019501:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.005 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0034812=polyprenyl_synt=FE(17.9=100),PF073076=HEPPP_synt_1=FE(34.8=100)

							
A:
NA

							
C2:
PF0034812=polyprenyl_synt=FE(14.1=100),PF073076=HEPPP_synt_1=FE(27.4=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000055689





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000121873
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr10:26720360-26723805 
ALTERNATIVE
HsaINT0122725
(PDSS1)
Human
(hg19)
chr10:27009289-27012734 
ALTERNATIVE
HsaINT0122725
(PDSS1)
Rat
(rn6)
chr17:90051995-90053665 
ALTERNATIVE
RnoINT0109413
(Pdss1)
Cow
(bosTau6)
chr13:18200454-18201960 
LOW PSI
BtaINT0109712
(PDSS1)
Chicken
(galGal4)
chr2:15988667-15989432 
ALTERNATIVE
GgaINT0098075
(PDSS1)
Chicken
(galGal3)
chr2:16016231-16016996 
LOW PSI
GgaINT0098075
(E1BZW8_CHICK)
Zebrafish
(danRer10)
chr24:5989627-5991605 
LOW PSI
DreINT0112205
(pdss1)
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"