Plant Circular RNA Database

Detail information of BGIOSGA006009_circ_g.3

			
						 General Information
					
						CircRNA Name
						BGIOSGA006009_circ_g.3
					
						ID in PlantcircBase
						osi_circ_004113
					
						Alias
						2:26605226|26607933
					
						Organism
						
							Oryza sativa ssp. indica						
					
						Position
						
							chr2: 26605226-26607933  JBrowse»						
					
						Reference genome
						
							Oryza_indica.ASM465v1.42						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							BGIOSGA006009						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							BGIOSGA006009_circ_igg.1 BGIOSGA006009_circ_igg.2 BGIOSGA006009_circ_igg.3 BGIOSGA006009_circ_g.1 BGIOSGA006009_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						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
						BGIOSGA006009-TA:5

General Information
CircRNA Name	BGIOSGA006009_circ_g.3
ID in PlantcircBase	osi_circ_004113
Alias	2:26605226\|26607933
Organism	Oryza sativa ssp. indica
Position	chr2: 26605226-26607933 JBrowse»
Reference genome	Oryza_indica.ASM465v1.42
Type	e-circRNA
Identification method	find_circ
Parent gene	BGIOSGA006009
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	BGIOSGA006009_circ_igg.1 BGIOSGA006009_circ_igg.2 BGIOSGA006009_circ_igg.3 BGIOSGA006009_circ_g.1 BGIOSGA006009_circ_g.2
Support reads	NA
Tissues	leaf
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	BGIOSGA006009-TA: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  
						
							TTTTCAAATGCAGCTCTGTTGCAATCCTCAAGTAAAGATCTCTTTGCAGTGAGTTATGGTGGGT
TATAAATGGTCTTGCTTCAGCACCACCTGCTGCTCCctcattgagaacatgtccaacagatgaa
caagcttgcaatgagatattctcattgctctctgttttgatccctcttgcagcatttttggcgg
attcaaga

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							CTCATTGAGAACATGTCCAACAGATGAACAAGCTTGCAATGAGATATTCTCATTGCTCTCTGTT
TTGATCCCTCTTGCAGCATTTTTGGCGGATTCAAGATCTTCTCCAAAGCTATTAAAGTCAATTC
CAGTTGCTTCTTTGACAAGAGAATGCATGGTTTCCCTCCTCCATGGTCTTTCAAGGCAGATTTC
AGTTCCCTGTTTGGTATTAAACAACAATTGTTTATCAATGTGAAAAGACACAAGAGTAATACGT
GAGTGTGTTCCAGGAAATTAGGTAGGGAAAAGGTAAACTATAGATCAAAAATCATATGCACACA
CGATCCTCATTCTTCATTTTGCTCCAGGATTTGCTTATGCACCATTTTGGTAATTTCTGAAAAT
TCGTTGATGGCACATAATTCAATGAAAAATTGAGAACATGCTTGTAGCAAGTGGTAAGTCCTCC
AGTTGTGAGCCTACCAACCAGGGTTCAAACCCTGGTTCTCACCCAAAAAAAAAAAAAAGGCCCC
TTGCTGTGTGTTCCCAAGTACAGGTTAAGACATGGCTTGTGGCAACTGGCAATGGATTACCTGT
ACGGGCAAGAGCCGGCTTTCGGGGCCATTTCTTGACCTTAAATGCAATGCCTTTGGGATGTCTC
TCCCCTTGGGTCAGGTTTTTCAATGAAAAATACAATTGAACGGTTCCATGGACCTGGCATAACC
TTCATCCTCCCAAACCACTCTCTAACATCTACTTCTCATTTTATCCCCTTCTATCTCCTGAGAG
CAACACTACCACCTGTTTCTCTCTCCCCCTACTGCGTACTGCTATCATAGCCTCTACCATTTTT
TGCTGCTGCTACTAGATCAGACCATGCCAACCTGGCAACCTTGATGCCACCAAATTCAGCCATT
CCTGTCCTCACACCAACACGCGTGGTGATAACAGGAAACAAACAGCAACAAGCACACCAAGACA
ACTGCCAGCATGAAGACAGCGTTGTCATGGATTAGTGAGGAGGCACCATTGCCAGCCATTGGCA
CTGGCAGTGACCATAAGAAATGGCATCTGTAAGTACAAGCCAGGGCACAGGAGGTGTCTTCACC
CCCTTCTTCCTTCCAATCGCCTTTGCTGTAGCGCTCTCCATTGCCACTCCAGGTCTGGAGGCCT
CACACTGGGTTGACCTTACCGTGTACTCCTTGTCAGAGCAATTTCATTTAATATGAATAGATAC
CTCCTCGAGGATGCCACCTCTCACTTGTCAGTTGTAGTATACAAAGCACCATAAGTTGTTTGCA
AACAGTACATGTACTTTGCAACATACTTGGGCTTGCAGGGGCTAAACATTGTACTATATTTTGT
ATTATACTGTATATTGTGTAGTAAATGAGAAGTAATACATTTGTTGTTGCTTGTACAACTCACC
TCTAGAGTTGAAAACAATGAATACTTGAATAGTAGCTCAATCAAAATTCAATTAATCTAAAAGG
AGAAAATGTTTTTGATGGGGCACTTTAATTTCTTTGATCAGACCTATGATTTCTAATGTCAATG
GTTTTATTTTGGTACAAATTTCTAGAGAAATCTGCAATGCAGATGTTTTAGGACCAGAAATGTT
TTTTTTCTGGCATGCCCAAGTGCCTATCTGCATATGGCTTCCAGACCAGGAAACACCAGTACGG
AAGCAAGGTGTGGATTATTGTTATTGAGCTTGGAACAGATTCAGTACAAAAGAAAAATAATAGA
AGCAACAAAGATGGCATGATTCTGCTCTGATATGTGTCCAGATGATCCAAATTAATAAGGCAAA
AATGCATTGCAATATATATATACTATATACTATAGTTACTAACTTACTATGGTAGACTTAAAGA
CTCATACCTGATAATCAACCCTAAGTTTGCCATGAGTAGCCATTGCACATCTAGTAACAATTTC
TTCAGCCAAATTCATCATGCTTTCATAGTCTGAATAGGCTTCATACATCTAGCTTCCAAATACA
AGGCAGTGAGTCAGACCTCACTTAGAGTAGAGCACATTATGCAAGAAAATGGAATAAACAGGAA
CATGGAAGATAAAACCACTAGGCTCAACCTACATGGTAAGAACAAAGCAAACATATGATATGTG
GGTAAGAACAAAGCAAACATATGATATGCACGTATTGGTGAAAAAGACCTCAATTCTTTACCTC
AATTGTGGTAAATTCAGGATTATGGCGAGTGGAAATGCCTTCATTCCGAAATATTCTCCCAATC
TCATAAACTTTCTCAAGCCCTCCAACCTGCATTTTTTTTCAGTAGTACTAAATTTGTAAATAAA
TATAAAATAGCTAAACAGTATACAGTTCGCAAAAAATTATGTTATGGTAAGATTAACATGGCAT
AACAAGCATATGTGATACTTCCATTTCGATTAGTCAACATAGTAGTCAAATCTGATCCTTCTGT
ACTCACAGGAATCATATTCACTACTATGTTGACTAATTGGAATCATATTCACTACTATGTTGAC
TAATTGAAATGGAAGTATCACAGAAATGAATACAGATACAGAGCAGGTTAAGAAAAAAGAGATA
GCTGCCAAACTGAAGAATAAAAACTGAATAGTAACCTCACCAGCATCCTTTTCAAATGCAGCTC
TGTTGCAATCCTCAAGTAAAGATCTCTTTGCAGTGAGTTATGGTGGGTTATAAATGGTCTTGCT
TCAGCACCACCTGCTGCTCC
						
					

			
		

Sequences
Splice junction sequence	TTTTCAAATGCAGCTCTGTTGCAATCCTCAAGTAAAGATCTCTTTGCAGTGAGTTATGGTGGGT TATAAATGGTCTTGCTTCAGCACCACCTGCTGCTCCctcattgagaacatgtccaacagatgaa caagcttgcaatgagatattctcattgctctctgttttgatccctcttgcagcatttttggcgg attcaaga
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CTCATTGAGAACATGTCCAACAGATGAACAAGCTTGCAATGAGATATTCTCATTGCTCTCTGTT TTGATCCCTCTTGCAGCATTTTTGGCGGATTCAAGATCTTCTCCAAAGCTATTAAAGTCAATTC CAGTTGCTTCTTTGACAAGAGAATGCATGGTTTCCCTCCTCCATGGTCTTTCAAGGCAGATTTC AGTTCCCTGTTTGGTATTAAACAACAATTGTTTATCAATGTGAAAAGACACAAGAGTAATACGT GAGTGTGTTCCAGGAAATTAGGTAGGGAAAAGGTAAACTATAGATCAAAAATCATATGCACACA CGATCCTCATTCTTCATTTTGCTCCAGGATTTGCTTATGCACCATTTTGGTAATTTCTGAAAAT TCGTTGATGGCACATAATTCAATGAAAAATTGAGAACATGCTTGTAGCAAGTGGTAAGTCCTCC AGTTGTGAGCCTACCAACCAGGGTTCAAACCCTGGTTCTCACCCAAAAAAAAAAAAAAGGCCCC TTGCTGTGTGTTCCCAAGTACAGGTTAAGACATGGCTTGTGGCAACTGGCAATGGATTACCTGT ACGGGCAAGAGCCGGCTTTCGGGGCCATTTCTTGACCTTAAATGCAATGCCTTTGGGATGTCTC TCCCCTTGGGTCAGGTTTTTCAATGAAAAATACAATTGAACGGTTCCATGGACCTGGCATAACC TTCATCCTCCCAAACCACTCTCTAACATCTACTTCTCATTTTATCCCCTTCTATCTCCTGAGAG CAACACTACCACCTGTTTCTCTCTCCCCCTACTGCGTACTGCTATCATAGCCTCTACCATTTTT TGCTGCTGCTACTAGATCAGACCATGCCAACCTGGCAACCTTGATGCCACCAAATTCAGCCATT CCTGTCCTCACACCAACACGCGTGGTGATAACAGGAAACAAACAGCAACAAGCACACCAAGACA ACTGCCAGCATGAAGACAGCGTTGTCATGGATTAGTGAGGAGGCACCATTGCCAGCCATTGGCA CTGGCAGTGACCATAAGAAATGGCATCTGTAAGTACAAGCCAGGGCACAGGAGGTGTCTTCACC CCCTTCTTCCTTCCAATCGCCTTTGCTGTAGCGCTCTCCATTGCCACTCCAGGTCTGGAGGCCT CACACTGGGTTGACCTTACCGTGTACTCCTTGTCAGAGCAATTTCATTTAATATGAATAGATAC CTCCTCGAGGATGCCACCTCTCACTTGTCAGTTGTAGTATACAAAGCACCATAAGTTGTTTGCA AACAGTACATGTACTTTGCAACATACTTGGGCTTGCAGGGGCTAAACATTGTACTATATTTTGT ATTATACTGTATATTGTGTAGTAAATGAGAAGTAATACATTTGTTGTTGCTTGTACAACTCACC TCTAGAGTTGAAAACAATGAATACTTGAATAGTAGCTCAATCAAAATTCAATTAATCTAAAAGG AGAAAATGTTTTTGATGGGGCACTTTAATTTCTTTGATCAGACCTATGATTTCTAATGTCAATG GTTTTATTTTGGTACAAATTTCTAGAGAAATCTGCAATGCAGATGTTTTAGGACCAGAAATGTT TTTTTTCTGGCATGCCCAAGTGCCTATCTGCATATGGCTTCCAGACCAGGAAACACCAGTACGG AAGCAAGGTGTGGATTATTGTTATTGAGCTTGGAACAGATTCAGTACAAAAGAAAAATAATAGA AGCAACAAAGATGGCATGATTCTGCTCTGATATGTGTCCAGATGATCCAAATTAATAAGGCAAA AATGCATTGCAATATATATATACTATATACTATAGTTACTAACTTACTATGGTAGACTTAAAGA CTCATACCTGATAATCAACCCTAAGTTTGCCATGAGTAGCCATTGCACATCTAGTAACAATTTC TTCAGCCAAATTCATCATGCTTTCATAGTCTGAATAGGCTTCATACATCTAGCTTCCAAATACA AGGCAGTGAGTCAGACCTCACTTAGAGTAGAGCACATTATGCAAGAAAATGGAATAAACAGGAA CATGGAAGATAAAACCACTAGGCTCAACCTACATGGTAAGAACAAAGCAAACATATGATATGTG GGTAAGAACAAAGCAAACATATGATATGCACGTATTGGTGAAAAAGACCTCAATTCTTTACCTC AATTGTGGTAAATTCAGGATTATGGCGAGTGGAAATGCCTTCATTCCGAAATATTCTCCCAATC TCATAAACTTTCTCAAGCCCTCCAACCTGCATTTTTTTTCAGTAGTACTAAATTTGTAAATAAA TATAAAATAGCTAAACAGTATACAGTTCGCAAAAAATTATGTTATGGTAAGATTAACATGGCAT AACAAGCATATGTGATACTTCCATTTCGATTAGTCAACATAGTAGTCAAATCTGATCCTTCTGT ACTCACAGGAATCATATTCACTACTATGTTGACTAATTGGAATCATATTCACTACTATGTTGAC TAATTGAAATGGAAGTATCACAGAAATGAATACAGATACAGAGCAGGTTAAGAAAAAAGAGATA GCTGCCAAACTGAAGAATAAAAACTGAATAGTAACCTCACCAGCATCCTTTTCAAATGCAGCTC TGTTGCAATCCTCAAGTAAAGATCTCTTTGCAGTGAGTTATGGTGGGTTATAAATGGTCTTGCT TCAGCACCACCTGCTGCTCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_015559* zma_circ_000924 						
					
						PMCS

Conservation Information
Conserved circRNAs	osa_circ_015559* zma_circ_000924
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							26607833-26605228(-)
26606277-26607899(-)
26607890-26605249(+)
						
						Potential amino acid sequence
						
							MLVGGLEKVYEIGRIFRNEGISTRHNPEFTTIEMYEAYSDYESMMNLAEEIVTRCAMATHGKLR
VDYQEYTVRSTQCEASRPGVAMESATAKAIGRKKGVKTPPVPWLVLTDAISYGHCQCQWLAMGT
EICLERPWRRETMHSLVKEATGIDFNSFGEDLESAKNAARGIKTESNENISLQACSSVGHVLNE
GAAGGAEARPFITHHNSLQRDLYLRIATELHLKRMLVGGLEKVYEIGRIFRNEGISTRHNPEFT
TIEMYEAYSDYESMMNLAEEIVTRCAMATHGKLRVDYQEYTVRSTQCEASRPGVAMESATAKAI
GRKKGVKTPPVPWLVLTDAISYGHCQCQWLAMGTEICLERPWRRETMHSLVKEATGIDFNSFGE
DLESAKNAARGIKTESNENISLQACSSVGHVLNEGAAGGAEARPFITHHNSLQRDLYLRIATEL
HLKRMLVGGLEKVYEIGRIFRNEGISTRHNPEFTTIEMYEAYSDYESMMNLAEEIVTRCAMATH
GKLRVDYQEYTVRSTQCEASRPGVAMESATAKAIGRKKGVKTPPVPWLVLTDAISYGHCQCQWL
AMGTEICLERPWRRETMHSLVKEATGIDFNSFGEDLESAKNAARGIKTESNENISLQACSSVGH
VLNEGAAGGAEARPFITHHNSLQRDLYLRIATELHLKRMLVGGLEKVYEIGRIFRNEGISTRHN
PEFTTIEMYEAYSDYESMMNLAEEIVTRCAMATHGKLRVDYQEYTVRSTQCEASRPGVAMESAT
AKAIGRKKGVKTPPVPWLVLTDAISYGHCQCQWLAMGTEICLERPWRRETMHSLVKEATGIDFN
SFGEDLESAKNAARGIKTESNENISLQACSSVGHVLNE(-)
MPFLMVTASANGWQWELKSALKDHGGGKPCILLSKKQLELTLIALEKILNPPKMLQEGSKQRAM
RISHCKLVHLLDMFSMREQQVVLKQDHL*(-)
MVGYKWSCFSTTCCSLIENMSNR*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						leaf senescence

Functional Information
Coding potential	Y
Potential coding position	26607833-26605228(-) 26606277-26607899(-) 26607890-26605249(+)
Potential amino acid sequence	MLVGGLEKVYEIGRIFRNEGISTRHNPEFTTIEMYEAYSDYESMMNLAEEIVTRCAMATHGKLR VDYQEYTVRSTQCEASRPGVAMESATAKAIGRKKGVKTPPVPWLVLTDAISYGHCQCQWLAMGT EICLERPWRRETMHSLVKEATGIDFNSFGEDLESAKNAARGIKTESNENISLQACSSVGHVLNE GAAGGAEARPFITHHNSLQRDLYLRIATELHLKRMLVGGLEKVYEIGRIFRNEGISTRHNPEFT TIEMYEAYSDYESMMNLAEEIVTRCAMATHGKLRVDYQEYTVRSTQCEASRPGVAMESATAKAI GRKKGVKTPPVPWLVLTDAISYGHCQCQWLAMGTEICLERPWRRETMHSLVKEATGIDFNSFGE DLESAKNAARGIKTESNENISLQACSSVGHVLNEGAAGGAEARPFITHHNSLQRDLYLRIATEL HLKRMLVGGLEKVYEIGRIFRNEGISTRHNPEFTTIEMYEAYSDYESMMNLAEEIVTRCAMATH GKLRVDYQEYTVRSTQCEASRPGVAMESATAKAIGRKKGVKTPPVPWLVLTDAISYGHCQCQWL AMGTEICLERPWRRETMHSLVKEATGIDFNSFGEDLESAKNAARGIKTESNENISLQACSSVGH VLNEGAAGGAEARPFITHHNSLQRDLYLRIATELHLKRMLVGGLEKVYEIGRIFRNEGISTRHN PEFTTIEMYEAYSDYESMMNLAEEIVTRCAMATHGKLRVDYQEYTVRSTQCEASRPGVAMESAT AKAIGRKKGVKTPPVPWLVLTDAISYGHCQCQWLAMGTEICLERPWRRETMHSLVKEATGIDFN SFGEDLESAKNAARGIKTESNENISLQACSSVGHVLNE(-) MPFLMVTASANGWQWELKSALKDHGGGKPCILLSKKQLELTLIALEKILNPPKMLQEGSKQRAM RISHCKLVHLLDMFSMREQQVVLKQDHL(-) MVGYKWSCFSTTCCSLIENMSNR(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	leaf senescence

			
						 Other Information
					
						References
						Huang et al., 2021

circRNA

Detail information of BGIOSGA006009_circ_g.3

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