Plant Circular RNA Database

Detail information of Os09g0249700_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os09g0249700_circ_g.4
					
						ID in PlantcircBase
						osa_circ_038557
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 3760679-3761756  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							Os09g0249700						
					
						Parent gene annotation
						
							Protein phosphatase 2A A subunit (Phosphatase 2A regulatory A su
bunit). (Os09t0249700-01);Similar to Phosphatase 2A regulatory A
 subunit. (Os09t0249700-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os09g0249000_circ_ag.1 Os09g0249600_circ_ig.1 Os09g0249700_circ_g.1 Os09g0249700_circ_g.2 Os09g0249700_circ_g.3 Os09g0249700_circ_g.5 Os09g0249700_circ_g.6 Os09g0249700_circ_g.7 Os09g0249700_circ_g.8 Os09g0249700_circ_g.9 Os09g0249700_circ_g.10 Os09g0249700_circ_g.11 Os09g0249700_circ_g.12 Os09g0249700_circ_g.13 Os09g0249700_circ_g.14 Os09g0249700_circ_g.15 Os09g0249700_circ_g.16 						
					
						Support reads
						47
					
						Tissues
						shoot, root, seed
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							CT-AC							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						Os09t0249700-01:5
Os09t0249700-02:5

General Information
CircRNA Name	Os09g0249700_circ_g.4
ID in PlantcircBase	osa_circ_038557
Alias	NA
Organism	Oryza sativa
Position	chr9: 3760679-3761756 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	Os09g0249700
Parent gene annotation	Protein phosphatase 2A A subunit (Phosphatase 2A regulatory A su bunit). (Os09t0249700-01);Similar to Phosphatase 2A regulatory A subunit. (Os09t0249700-02)
Parent gene strand	-
Alternative splicing	Os09g0249000_circ_ag.1 Os09g0249600_circ_ig.1 Os09g0249700_circ_g.1 Os09g0249700_circ_g.2 Os09g0249700_circ_g.3 Os09g0249700_circ_g.5 Os09g0249700_circ_g.6 Os09g0249700_circ_g.7 Os09g0249700_circ_g.8 Os09g0249700_circ_g.9 Os09g0249700_circ_g.10 Os09g0249700_circ_g.11 Os09g0249700_circ_g.12 Os09g0249700_circ_g.13 Os09g0249700_circ_g.14 Os09g0249700_circ_g.15 Os09g0249700_circ_g.16
Support reads	47
Tissues	shoot, root, seed
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	CT-AC The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	Os09t0249700-01:5 Os09t0249700-02:5

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							ACAATAACTGGAAGGATATGTGCTACACAATCTTGTGGTTCCAACAATTTCCCAAGAGCAGCAC
AGCCTTCAACTGCCAACAAGCGTACGGAATCTTGATctgattaacttgatcgagcttgctgatt
atattgagccgaacatcaggaaattcatccttgagcaaagaaaggaaaataggaagaagttgtt
cgattgta

									
								

					

						Assembled circRNA sequence  
						
							Yes
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							Transcript length: 521
Transcript exons: 3760679-3760783,3760926-3761006,3761093-3761234,3761395-
3761474,3761644-3761756
CTGATTAACTTGATCGAGCTTGCTGATTATATTGAGCCGAACATCAGGAAATTCATCCTTGAGC
AAAGAAAGGAAAATAGGAAGAAGTTGTTCGATTGTAGCCTCCTTTCCCAAGACCGGGGCCATTC
CCATAATAACTGAAGCCAAAGCTGAACGAACATGCTGAGATGAATCTGATGACAATTCCTTGAC
ACAAGGAAGAATATGCTGAATTGCAAGCTGAGGACTTAAAATCCTACAGAACTTAGTAACTTTC
CCTGCAGCCGCTATCCGCACTTCCGCCTCATTGTCACGAAGGAGACGAACATATGCCGGCACCA
ACTGCTCCCTAGAATGTTCAGGACCAACTGCCTCGCAGAGCTCATACAATTGATTGGCAACCAT
ATAACGAACTCGCCATGATTTGTCCTGGGAGAAATTGACAATAACTGGAAGGATATGTGCTACA
CAATCTTGTGGTTCCAACAATTTCCCAAGAGCAGCACAGCCTTCAACTGCCAACAAGCGTACGG
AATCTTGAT
						
					

						Genomic sequence
						
							CTGATTAACTTGATCGAGCTTGCTGATTATATTGAGCCGAACATCAGGAAATTCATCCTTGAGC
AAAGAAAGGAAAATAGGAAGAAGTTGTTCGATTGTAGCCTCCTACAGAATGCCAGAAACAAAGC
AAGTCAGGTTTCCAACAATCGTGAAGCAATGGTAGTAAACAACTGAACAGTAAAGCTGTTGCAA
ACAAATAATTTGAATTATTTCAAGTAAAATTTTATGAAGATATTTTGCTTGTGACCTTTCCCAA
GACCGGGGCCATTCCCATAATAACTGAAGCCAAAGCTGAACGAACATGCTGAGATGAATCTGAT
GACAATTCCTGCAGATGCAGTTGGCAAGTTAGTTTGCTGGGAATAAACAGCAGCAGAAAACCAG
TTAATAATATTTGGTTAAGCGTTGGCCCACCTTGACACAAGGAAGAATATGCTGAATTGCAAGC
TGAGGACTTAAAATCCTACAGAACTTAGTAACTTTCCCTGCAGCCGCTATCCGCACTTCCGCCT
CATTGTCACGAAGGAGACGAACATATGCCGGCACCAACTGCTCCCTATTACCAAACACATGAAC
ATACCATAGATGAATATTGGAATCAGATTACAAAATTATGTATTTAGATAAGAAATAAATAATA
ACTTGCACCATTTAAGGACCAAAGTATTTATGATTGGTTTTGACAGAAAAGATTTAGGACATAA
GGCGCATAATACCTAGAATGTTCAGGACCAACTGCCTCGCAGAGCTCATACAATTGATTGGCAA
CCATATAACGAACTCGCCATGATTTGTCCTATTTAATGAGTTACAGAGAGTAAAAGATGTCATA
ATTATGGTAACACATACAACAGAAGCAACTCGGAGCATCAGGAACCTCTAGCAACTAATGAATG
TCTGCAAATAAATATTATATGTGATATCAAGTAGATGACACTGAGGTACCAAGTAGGGGTGTAA
TTTACCTGGGAGAAATTGACAATAACTGGAAGGATATGTGCTACACAATCTTGTGGTTCCAACA
ATTTCCCAAGAGCAGCACAGCCTTCAACTGCCAACAAGCGTACGGAATCTTGAT
						
					

			
		

Sequences
Splice junction sequence	ACAATAACTGGAAGGATATGTGCTACACAATCTTGTGGTTCCAACAATTTCCCAAGAGCAGCAC AGCCTTCAACTGCCAACAAGCGTACGGAATCTTGATctgattaacttgatcgagcttgctgatt atattgagccgaacatcaggaaattcatccttgagcaaagaaaggaaaataggaagaagttgtt cgattgta
Assembled circRNA sequence	Yes The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	Transcript length: 521 Transcript exons: 3760679-3760783,3760926-3761006,3761093-3761234,3761395- 3761474,3761644-3761756 CTGATTAACTTGATCGAGCTTGCTGATTATATTGAGCCGAACATCAGGAAATTCATCCTTGAGC AAAGAAAGGAAAATAGGAAGAAGTTGTTCGATTGTAGCCTCCTTTCCCAAGACCGGGGCCATTC CCATAATAACTGAAGCCAAAGCTGAACGAACATGCTGAGATGAATCTGATGACAATTCCTTGAC ACAAGGAAGAATATGCTGAATTGCAAGCTGAGGACTTAAAATCCTACAGAACTTAGTAACTTTC CCTGCAGCCGCTATCCGCACTTCCGCCTCATTGTCACGAAGGAGACGAACATATGCCGGCACCA ACTGCTCCCTAGAATGTTCAGGACCAACTGCCTCGCAGAGCTCATACAATTGATTGGCAACCAT ATAACGAACTCGCCATGATTTGTCCTGGGAGAAATTGACAATAACTGGAAGGATATGTGCTACA CAATCTTGTGGTTCCAACAATTTCCCAAGAGCAGCACAGCCTTCAACTGCCAACAAGCGTACGG AATCTTGAT
Genomic sequence	CTGATTAACTTGATCGAGCTTGCTGATTATATTGAGCCGAACATCAGGAAATTCATCCTTGAGC AAAGAAAGGAAAATAGGAAGAAGTTGTTCGATTGTAGCCTCCTACAGAATGCCAGAAACAAAGC AAGTCAGGTTTCCAACAATCGTGAAGCAATGGTAGTAAACAACTGAACAGTAAAGCTGTTGCAA ACAAATAATTTGAATTATTTCAAGTAAAATTTTATGAAGATATTTTGCTTGTGACCTTTCCCAA GACCGGGGCCATTCCCATAATAACTGAAGCCAAAGCTGAACGAACATGCTGAGATGAATCTGAT GACAATTCCTGCAGATGCAGTTGGCAAGTTAGTTTGCTGGGAATAAACAGCAGCAGAAAACCAG TTAATAATATTTGGTTAAGCGTTGGCCCACCTTGACACAAGGAAGAATATGCTGAATTGCAAGC TGAGGACTTAAAATCCTACAGAACTTAGTAACTTTCCCTGCAGCCGCTATCCGCACTTCCGCCT CATTGTCACGAAGGAGACGAACATATGCCGGCACCAACTGCTCCCTATTACCAAACACATGAAC ATACCATAGATGAATATTGGAATCAGATTACAAAATTATGTATTTAGATAAGAAATAAATAATA ACTTGCACCATTTAAGGACCAAAGTATTTATGATTGGTTTTGACAGAAAAGATTTAGGACATAA GGCGCATAATACCTAGAATGTTCAGGACCAACTGCCTCGCAGAGCTCATACAATTGATTGGCAA CCATATAACGAACTCGCCATGATTTGTCCTATTTAATGAGTTACAGAGAGTAAAAGATGTCATA ATTATGGTAACACATACAACAGAAGCAACTCGGAGCATCAGGAACCTCTAGCAACTAATGAATG TCTGCAAATAAATATTATATGTGATATCAAGTAGATGACACTGAGGTACCAAGTAGGGGTGTAA TTTACCTGGGAGAAATTGACAATAACTGGAAGGATATGTGCTACACAATCTTGTGGTTCCAACA ATTTCCCAAGAGCAGCACAGCCTTCAACTGCCAACAAGCGTACGGAATCTTGAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_018821 						
					
						PMCS
						0.185385652

Conservation Information
Conserved circRNAs	osi_circ_018821
PMCS	0.185385652

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3761675-3760679(+)
3761452-3761681(-)
						
						Potential amino acid sequence
						
							MCYTILWFQQFPKSSTAFNCQQAYGILI*(+)
MVANQLYELCEAVGPEHSREQLVPAYVRLLRDNEAEVRIAAAGKVTKFCRILSPQLAIQHILPC
VKELSSDSSQHVRSALASVIMGMAPVLGKEATIEQLLPIFLSLLKDEFPDVRLNIISKLDQVNQ
IKIPYACWQLKAVLLLGNCWNHKIV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3761675-3760679(+) 3761452-3761681(-)
Potential amino acid sequence	MCYTILWFQQFPKSSTAFNCQQAYGILI(+) MVANQLYELCEAVGPEHSREQLVPAYVRLLRDNEAEVRIAAAGKVTKFCRILSPQLAIQHILPC VKELSSDSSQHVRSALASVIMGMAPVLGKEATIEQLLPIFLSLLKDEFPDVRLNIISKLDQVNQ IKIPYACWQLKAVLLLGNCWNHKIV(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os09g0249700_circ_g.4

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