Plant Circular RNA Database

Detail information of Os09g0538800_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os09g0538800_circ_g.3
					
						ID in PlantcircBase
						osa_circ_040049
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 21215364-21217392  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os09g0538800						
					
						Parent gene annotation
						
							Similar to Synaptotagmin C. (Os09t0538800-01);Similar to Synapto
tagmin C. (Os09t0538800-02);Similar to calcium lipid binding pro
tein-like. (Os09t0538800-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os09g0538901_circ_g.1 Os09g0538901_circ_g.2 Os09g0538901_circ_g.3 Os09g0538800_circ_g.1 Os09g0538901_circ_g.2 Os09g0538901_circ_g.4 Os09g0538800_circ_g.5 						
					
						Support reads
						1
					
						Tissues
						root
					
						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
						Os09t0538800-03:7
Os09t0538800-01:7
Os09t0538800-02:7

General Information
CircRNA Name	Os09g0538800_circ_g.3
ID in PlantcircBase	osa_circ_040049
Alias	NA
Organism	Oryza sativa
Position	chr9: 21215364-21217392 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	Os09g0538800
Parent gene annotation	Similar to Synaptotagmin C. (Os09t0538800-01);Similar to Synapto tagmin C. (Os09t0538800-02);Similar to calcium lipid binding pro tein-like. (Os09t0538800-03)
Parent gene strand	-
Alternative splicing	Os09g0538901_circ_g.1 Os09g0538901_circ_g.2 Os09g0538901_circ_g.3 Os09g0538800_circ_g.1 Os09g0538901_circ_g.2 Os09g0538901_circ_g.4 Os09g0538800_circ_g.5
Support reads	1
Tissues	root
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	Os09t0538800-03:7 Os09t0538800-01:7 Os09t0538800-02:7

			
						 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  
						
							AATCCAAAGCCAAACCCAGAGAAACCAAGCACCGTACTAATCACACCCATCTCAGACTCGTTTT
AGTACCTCCAAAGTTATAGCAGATTTCAGCCTAAGGctgaacaaatctgtaaagaccagggata
gccattaaatctgctccgaaaagtttcagcccgaagtcaacgtgtggctgccaaaccaacataa
ctagtaag

									
								

					

						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: 731
Transcript exons: 21215364-21215438,21215511-21215612,21215722-21215840,21
216254-21216377,21216474-21216524,21216640-21216738,2121
7232-21217392
CTGAACAAATCTGTAAAGACCAGGGATAGCCATTAAATCTGCTCCGAAAAGTTTCAGCCCGAAG
TCAACGTGTGGCTTCTCCATGAGAGAAACAAGGATTTTTGCGAAGCAAGGAAATGTAGGGACCA
ATGGCTTCAGAGTAATACGAGGTGAAGCAAAGACTTGCAGATCCACAATCTGGACAGTTGCTTT
CAACCCATAAGCCTTTACAACAACAGTGACATTGGGATTTGCAGCCCACTTAAGAGATGGTTCC
ATTATCAATTCTTGTTCTTCTGTGACATACACTTTCATTCCTTGAAAGGTGGGTGGTAAGCTAC
CCAATGTAAGTGATTCAAACTCAATAGATTCTAGTTTATACGTCTTCCTGTTCTCTTCAATGAT
TGGCTTTGCAATATCCAGTGCAGTTCTGCAGATCGCCTTGTTGAGGTAAGGCCACATCATCTCC
AAAAATCTATTCAGCCAATCAATTCTATCATAGTCAGGATTCTTGACCCACAAAGGAATTTCAG
GAAGGATACCGTCCAACGATATTGAGTCATATTCGACAAGTGGGCGAACTTTGACGTCCTTGAC
ATCAGTTGGCTGGAAGTAGATGAAGAAGTAGTATCCGATGACAATACCAGCGGAGAATCCAAAG
CCAAACCCAGAGAAACCAAGCACCGTACTAATCACACCCATCTCAGACTCGTTTTAGTACCTCC
AAAGTTATAGCAGATTTCAGCCTAAGG
						
					

						Genomic sequence
						
							CTGAACAAATCTGTAAAGACCAGGGATAGCCATTAAATCTGCTCCGAAAAGTTTCAGCCCGAAG
TCAACGTGTGGCTGCCAAACCAACATAACTAGTAAGAAGGTTGCCAGCAGGGTAATAAACATAC
AAGCGATCAGATATCAGACCTTCTCCATGAGAGAAACAAGGATTTTTGCGAAGCAAGGAAATGT
AGGGACCAATGGCTTCAGAGTAATACGAGGTGAAGCAAAGACTTGCAGATCCACAATCTGAAAT
TTTGTTTCACATGAACAATGAATAACTTAATTAGCTCAATTCTATATCATATCACATAATGAGA
ACACCAATTACTACTTCAGCCCATGACAAAAAAAAAACCTGGACAGTTGCTTTCAACCCATAAG
CCTTTACAACAACAGTGACATTGGGATTTGCAGCCCACTTAAGAGATGGTTCCATTATCAATTC
TTGTTCTTCTGTGACATACACTTTCATTCCTGGAGAAGCAAATATCATACAACAGATTCAGTGT
AATGCCAGGGTACAAAGAGAGCTGAGCACATAGAACATTATTGTCCACCATACATGTTTATGGT
GATGTCCATATGACATTAACTTACAATAAGTAATAAACAAGCTGTACAGACCTATGGCTATAAT
GCATAGAGTTGGTCATAAAAACATAGTATGACAGCTTAGTGGGAACAAAGTAGTAGCAATGCAT
TCATATTCTATATCTCCAGCGATGCAAACCATAACTACTCTGATGCTGATTTGATTACAGTTGA
TCGTAAAACAAGTTGATATGAACACAACTGTTTGCACAATATACAGAAACAAGGGCCACTTCTA
AGGAAAAGACATGTGAACTACATATGTATGCATGTATATAATGAGAAAGTGCACTAACCTTGAA
AGGTGGGTGGTAAGCTACCCAATGTAAGTGATTCAAACTCAATAGATTCTAGTTTATACGTCTT
CCTGTTCTCTTCAATGATTGGCTTTGCAATATCCAGTGCAGTTCTGCAGATCGCCTACAGGATA
AATGCACAATAAAGTTTCTATTGTCAATCAGAGAGATCCATTTCATTCTTGGTGACTTGGTGTA
GTCTACAGCAAGATAAGGGTACCTTGTTGAGGTAAGGCCACATCATCTCCAAAAATCTATTCAG
CCAATCAATCTAACAAAGAATAAGAGGAAGATGAGAAATATGAGATAAGCTAGCATTGATGCTG
TTCAAGTGCATGAGTTTTCTTCAGCGAGTAGATGATAGTTTAAAGAATGGGTAAGCATACTCTA
TCATAGTCAGGATTCTTGACCCACAAAGGAATTTCAGGAAGGATACCGTCCAACGATATTGAGT
CATATTCGACAAGTGGGCGAACTTTGACGTCCTGAAAGGCAATCAGAGGAAGAAATTACCCCCA
TGCAGCACAACAATATGGTGCATTACACCAAGAAAAACTCAAATGTGTGCCGTTCCAGTACATA
TGGTATCAATGGACATGTACATGCATATATATAGTGTAATAGGTCATCATACACCAACTGAAAG
GTTGCCTTTATTTGAAAATCATGAAAGATATCGTTTAAACACCCAAATAAAATAATAGATGCTT
ATATATGGCATATTAACAGTATGTGGTTGAGACTAACTGAATTAGGACTTCACAAAAAACTAAA
TGAGTTCATCAATGCCTCCGTCGTCAAATTATTTTCTGTAACAGCAAGAGCCAAACTGTTCCCA
GGCCATTTTGGTTGTAAGGTGTAGACATCTGTTAATAAGCAGCACCACACATTCCACAACACAA
GTATTCATTATATGACAATATGATAAAATTTTATACAGTATGAAAGGAAGAGAATCATTGAAAT
ATAGATGTGCACCTTGACATCAGTTGGCTGGAAGTAGATGAAGAAGTAGTATCCGATGACAATA
CCAGCGGAGAATCCAAAGCCAAACCCAGAGAAACCAAGCACCGTACTAATCACACCCATCTCAG
ACTCGTTTTAGTACCTCCAAAGTTATAGCAGATTTCAGCCTAAGG
						
					

			
		

Sequences
Splice junction sequence	AATCCAAAGCCAAACCCAGAGAAACCAAGCACCGTACTAATCACACCCATCTCAGACTCGTTTT AGTACCTCCAAAGTTATAGCAGATTTCAGCCTAAGGctgaacaaatctgtaaagaccagggata gccattaaatctgctccgaaaagtttcagcccgaagtcaacgtgtggctgccaaaccaacataa ctagtaag
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: 731 Transcript exons: 21215364-21215438,21215511-21215612,21215722-21215840,21 216254-21216377,21216474-21216524,21216640-21216738,2121 7232-21217392 CTGAACAAATCTGTAAAGACCAGGGATAGCCATTAAATCTGCTCCGAAAAGTTTCAGCCCGAAG TCAACGTGTGGCTTCTCCATGAGAGAAACAAGGATTTTTGCGAAGCAAGGAAATGTAGGGACCA ATGGCTTCAGAGTAATACGAGGTGAAGCAAAGACTTGCAGATCCACAATCTGGACAGTTGCTTT CAACCCATAAGCCTTTACAACAACAGTGACATTGGGATTTGCAGCCCACTTAAGAGATGGTTCC ATTATCAATTCTTGTTCTTCTGTGACATACACTTTCATTCCTTGAAAGGTGGGTGGTAAGCTAC CCAATGTAAGTGATTCAAACTCAATAGATTCTAGTTTATACGTCTTCCTGTTCTCTTCAATGAT TGGCTTTGCAATATCCAGTGCAGTTCTGCAGATCGCCTTGTTGAGGTAAGGCCACATCATCTCC AAAAATCTATTCAGCCAATCAATTCTATCATAGTCAGGATTCTTGACCCACAAAGGAATTTCAG GAAGGATACCGTCCAACGATATTGAGTCATATTCGACAAGTGGGCGAACTTTGACGTCCTTGAC ATCAGTTGGCTGGAAGTAGATGAAGAAGTAGTATCCGATGACAATACCAGCGGAGAATCCAAAG CCAAACCCAGAGAAACCAAGCACCGTACTAATCACACCCATCTCAGACTCGTTTTAGTACCTCC AAAGTTATAGCAGATTTCAGCCTAAGG
Genomic sequence	CTGAACAAATCTGTAAAGACCAGGGATAGCCATTAAATCTGCTCCGAAAAGTTTCAGCCCGAAG TCAACGTGTGGCTGCCAAACCAACATAACTAGTAAGAAGGTTGCCAGCAGGGTAATAAACATAC AAGCGATCAGATATCAGACCTTCTCCATGAGAGAAACAAGGATTTTTGCGAAGCAAGGAAATGT AGGGACCAATGGCTTCAGAGTAATACGAGGTGAAGCAAAGACTTGCAGATCCACAATCTGAAAT TTTGTTTCACATGAACAATGAATAACTTAATTAGCTCAATTCTATATCATATCACATAATGAGA ACACCAATTACTACTTCAGCCCATGACAAAAAAAAAACCTGGACAGTTGCTTTCAACCCATAAG CCTTTACAACAACAGTGACATTGGGATTTGCAGCCCACTTAAGAGATGGTTCCATTATCAATTC TTGTTCTTCTGTGACATACACTTTCATTCCTGGAGAAGCAAATATCATACAACAGATTCAGTGT AATGCCAGGGTACAAAGAGAGCTGAGCACATAGAACATTATTGTCCACCATACATGTTTATGGT GATGTCCATATGACATTAACTTACAATAAGTAATAAACAAGCTGTACAGACCTATGGCTATAAT GCATAGAGTTGGTCATAAAAACATAGTATGACAGCTTAGTGGGAACAAAGTAGTAGCAATGCAT TCATATTCTATATCTCCAGCGATGCAAACCATAACTACTCTGATGCTGATTTGATTACAGTTGA TCGTAAAACAAGTTGATATGAACACAACTGTTTGCACAATATACAGAAACAAGGGCCACTTCTA AGGAAAAGACATGTGAACTACATATGTATGCATGTATATAATGAGAAAGTGCACTAACCTTGAA AGGTGGGTGGTAAGCTACCCAATGTAAGTGATTCAAACTCAATAGATTCTAGTTTATACGTCTT CCTGTTCTCTTCAATGATTGGCTTTGCAATATCCAGTGCAGTTCTGCAGATCGCCTACAGGATA AATGCACAATAAAGTTTCTATTGTCAATCAGAGAGATCCATTTCATTCTTGGTGACTTGGTGTA GTCTACAGCAAGATAAGGGTACCTTGTTGAGGTAAGGCCACATCATCTCCAAAAATCTATTCAG CCAATCAATCTAACAAAGAATAAGAGGAAGATGAGAAATATGAGATAAGCTAGCATTGATGCTG TTCAAGTGCATGAGTTTTCTTCAGCGAGTAGATGATAGTTTAAAGAATGGGTAAGCATACTCTA TCATAGTCAGGATTCTTGACCCACAAAGGAATTTCAGGAAGGATACCGTCCAACGATATTGAGT CATATTCGACAAGTGGGCGAACTTTGACGTCCTGAAAGGCAATCAGAGGAAGAAATTACCCCCA TGCAGCACAACAATATGGTGCATTACACCAAGAAAAACTCAAATGTGTGCCGTTCCAGTACATA TGGTATCAATGGACATGTACATGCATATATATAGTGTAATAGGTCATCATACACCAACTGAAAG GTTGCCTTTATTTGAAAATCATGAAAGATATCGTTTAAACACCCAAATAAAATAATAGATGCTT ATATATGGCATATTAACAGTATGTGGTTGAGACTAACTGAATTAGGACTTCACAAAAAACTAAA TGAGTTCATCAATGCCTCCGTCGTCAAATTATTTTCTGTAACAGCAAGAGCCAAACTGTTCCCA GGCCATTTTGGTTGTAAGGTGTAGACATCTGTTAATAAGCAGCACCACACATTCCACAACACAA GTATTCATTATATGACAATATGATAAAATTTTATACAGTATGAAAGGAAGAGAATCATTGAAAT ATAGATGTGCACCTTGACATCAGTTGGCTGGAAGTAGATGAAGAAGTAGTATCCGATGACAATA CCAGCGGAGAATCCAAAGCCAAACCCAGAGAAACCAAGCACCGTACTAATCACACCCATCTCAG ACTCGTTTTAGTACCTCCAAAGTTATAGCAGATTTCAGCCTAAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.375860506

Conservation Information
Conserved circRNAs	NA
PMCS	0.375860506

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21217344-21217389(-)
						
						Potential amino acid sequence
						
							MGVISTVLGFSGFGFGFSAGIVIGYYFFIYFQPTDVKDVKVRPLVEYDSISLDGILPEIPLWVK
NPDYDRIDWLNRFLEMMWPYLNKAICRTALDIAKPIIEENRKTYKLESIEFESLTLGSLPPTFQ
GMKVYVTEEQELIMEPSLKWAANPNVTVVVKAYGLKATVQIVDLQVFASPRITLKPLVPTFPCF
AKILVSLMEKPHVDFGLKLFGADLMAIPGLYRFVQP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21217344-21217389(-)
Potential amino acid sequence	MGVISTVLGFSGFGFGFSAGIVIGYYFFIYFQPTDVKDVKVRPLVEYDSISLDGILPEIPLWVK NPDYDRIDWLNRFLEMMWPYLNKAICRTALDIAKPIIEENRKTYKLESIEFESLTLGSLPPTFQ GMKVYVTEEQELIMEPSLKWAANPNVTVVVKAYGLKATVQIVDLQVFASPRITLKPLVPTFPCF AKILVSLMEKPHVDFGLKLFGADLMAIPGLYRFVQP*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os09g0538800_circ_g.3

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