Plant Circular RNA Database

Detail information of AT5G09660_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G09660_circ_g.3
					
						ID in PlantcircBase
						ath_circ_037272
					
						Alias
						5:2993810-2995584
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 2993810-2995584  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G09660						
					
						Parent gene annotation
						
							Malate dehydrogenase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							5_circ_ag.29 AT5G09570_circ_g.1 AT5G09570_circ_g.2 AT5G09570_circ_g.3 AT5G09580_circ_g.1 AT5G09590_circ_g.1 AT5G09590_circ_g.2 AT5G09590_circ_g.3 AT5G09590_circ_g.4 AT5G09590_circ_g.5 AT5G09590_circ_g.6 AT5G09620_circ_g.1 AT5G09650_circ_g.1 AT5G09650_circ_g.2 AT5G09660_circ_g.1 AT5G09660_circ_g.2 AT5G09660_circ_g.4 AT5G09660_circ_g.5 AT5G09660_circ_g.6 AT5G09660_circ_g.7 AT5G09660_circ_g.8 AT5G09660_circ_g.9 AT5G09660_circ_g.10 AT5G09660_circ_g.11 AT5G09660_circ_g.12 AT5G09660_circ_g.13 AT5G09660_circ_g.14 AT5G09690_circ_g.1 AT5G09690_circ_g.2 AT5G09690_circ_g.3 5_circ_ag.4 5_circ_ag.5 5_circ_ag.6 5_circ_ag.7 5_circ_ag.8 5_circ_ag.9 5_circ_ag.10 5_circ_ag.11 ENSRNA049493670_circ_g.1 ENSRNA049493670_circ_g.2 ENSRNA049493670_circ_g.3 ENSRNA049493670_circ_g.4 ENSRNA049493670_circ_g.5 ENSRNA049493670_circ_g.6 						
					
						Support reads
						2
					
						Tissues
						flower
					
						Exon boundary  
						
							Yes-No							"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
						AT5G09660.3:5
AT5G09660.5:7
AT5G09660.1:7
AT5G09660.2:6
AT5G09660.4:6

General Information
CircRNA Name	AT5G09660_circ_g.3
ID in PlantcircBase	ath_circ_037272
Alias	5:2993810-2995584
Organism	Arabidpsis thaliana
Position	chr5: 2993810-2995584 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G09660
Parent gene annotation	Malate dehydrogenase
Parent gene strand	-
Alternative splicing	5_circ_ag.29 AT5G09570_circ_g.1 AT5G09570_circ_g.2 AT5G09570_circ_g.3 AT5G09580_circ_g.1 AT5G09590_circ_g.1 AT5G09590_circ_g.2 AT5G09590_circ_g.3 AT5G09590_circ_g.4 AT5G09590_circ_g.5 AT5G09590_circ_g.6 AT5G09620_circ_g.1 AT5G09650_circ_g.1 AT5G09650_circ_g.2 AT5G09660_circ_g.1 AT5G09660_circ_g.2 AT5G09660_circ_g.4 AT5G09660_circ_g.5 AT5G09660_circ_g.6 AT5G09660_circ_g.7 AT5G09660_circ_g.8 AT5G09660_circ_g.9 AT5G09660_circ_g.10 AT5G09660_circ_g.11 AT5G09660_circ_g.12 AT5G09660_circ_g.13 AT5G09660_circ_g.14 AT5G09690_circ_g.1 AT5G09690_circ_g.2 AT5G09690_circ_g.3 5_circ_ag.4 5_circ_ag.5 5_circ_ag.6 5_circ_ag.7 5_circ_ag.8 5_circ_ag.9 5_circ_ag.10 5_circ_ag.11 ENSRNA049493670_circ_g.1 ENSRNA049493670_circ_g.2 ENSRNA049493670_circ_g.3 ENSRNA049493670_circ_g.4 ENSRNA049493670_circ_g.5 ENSRNA049493670_circ_g.6
Support reads	2
Tissues	flower
Exon boundary	Yes-No "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	AT5G09660.3:5 AT5G09660.5:7 AT5G09660.1:7 AT5G09660.2:6 AT5G09660.4:6

			
						 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  
						
							AAACCTGAGGAGTGAGATGAGCTGAAATCCTAGCAATCCTCTGGTTGGCATCTCCACGAAACTC
CATTGTTGTGTTCCTCAGTTTCCTCTCGTTAGGAAGctttcgtattcgtttaagggtccaagct
gatacacttcctctgctcctgtacggccaaggcgcacttttgttgcaaagaaagctaattctgt
cacctgtg

									
								

					

						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
						
							CTTTCGTATTCGTTTAAGGGTCCAAGCTGATACACTTCCTCTGCTCCTGTACGGCCAAGGCGCA
CTTTTGTTGCAAAGAAAGCTAATTCTGTCACCTGTGGTCAATTGCCATTTCAAGTTAAAACCGT
TGAAACAATGAAAGAGAGTGAAAGAGTTTTCAAGATTCACCTGTGAAGCAACAAAAGAGCATTC
TACGACATTCGCATCTCCTCTTAACCCGCGAAGGCAAGCATCTGCAAACTTGGCTGCAGCATAT
GCCTATAGTAGTAGTACATTTCACATGGATTCAGTACACTGTTCCAGAGAAATAAACAGGTGTA
ATGATGATGTATTAAAGTGATTTGGTTTGGTTTTACCATTGAAAGTGTTGCAGAACCAGCTCCA
GCTTTTGCCTCCACAACTTCAGTTCCACCATTTTGAATCCGGTTTGTCAGGTACTCAATTTCTT
GAGGTGTGAAGCTGCTAGGAGGTTTAACCTGAGGAAAAAGGATTATGCAAAAACAATCAGTTAG
CAGAGAAGCTAATGTAATGGAAATGAACCTTTCGTCCTATTCATATGATACCTGTGACAGTAGT
GGCAAGATTGTGACTCCGGCGTGTCCCCCAACTACTGGCACATCGACTTCTCTTGGATCAAGGC
CAAGAACTTCTGCCTGCACAAGAATTTAAAAAGATAAATTCTTAGTGTTTAAAACTCAACAAAA
CCAAATGGAGTGAGGAATCATTAGGCATTATTACCACAAATGTGTTGGCACGAGCAACATCGAG
TGTAGTAACTCCAAGGAGCTTCTTAGGATCATAAGTTCCAGCTTTCTTGAAAACCTCAGCGGCA
ATGGGGACAGTAGAGTTCACAGGGTTGCTGATCAAGTTGACAATAGCATTAGGACAACATTTTG
CTACACCTTCACATAGTGTTTTAACAATCCCAGCATTGATTTTAAACAGATCATCGCGGGTCAT
CCCTGGTTTCCTCGGTATACCGGCTGGTATGATCACAAGATCCATACCCGTTAGCGCGTCCTCA
AGCTGCTTCGCTCCCAAGAACCCGCGGACCTAATCAATCAAGAGTGGTCATTACTCATTCATTA
GCAAGAAGAAGTAATCTTATGTGAAGTTTTCAAAGTTTAAGAGAGATACTTACAACAGCTCCAG
TGTCCATATGACTGACGTCAGCAGTGACGCCAGGAGCATTGACAACATCGTAGAGATGAAGTAA
AGAGACAAGAGGGTTCATCTTCATCAGCAAAGATAAAGATTGTCCAATTCCACCTGCAGCTCCA
AGAATTGCTACTTTGAATCCTGGATTACCACCTTTAGCTCTGCAGTTTTCCCGTCCGATTACAG
AGTTCTTGGCCTCCATCTAATGGTTGATCAATCATGAATAAGAAGAAGAAATTTCACTATCAGT
CCTAGATGACTTCAACGGAGTCATAAACAGATTGGTCTCTCTAATGGCATCAGAAATCTTCAGT
TACTAATTTCAAGAAATGGAAATATACACTTGTAGAAGCGAATGTCAAGTTCATGGTTGAACTA
TAAATATTCAGAACGTTGATGAGTCTAGACAAATCAGTTTTGTTTGAGAGTGAATACAAACTAT
TCTGGTTTTAGTAGAACAACCATCGAATTTAAGAATATAAAAAAAGATAACTTGAGTTAACAGC
AAAGGTAAAGAAAACCTGAGGAGTGAGATGAGCTGAAATCCTAGCAATCCTCTGGTTGGCATCT
CCACGAAACTCCATTGTTGTGTTCCTCAGTTTCCTCTCGTTAGGAAG
						
					

			
		

Sequences
Splice junction sequence	AAACCTGAGGAGTGAGATGAGCTGAAATCCTAGCAATCCTCTGGTTGGCATCTCCACGAAACTC CATTGTTGTGTTCCTCAGTTTCCTCTCGTTAGGAAGctttcgtattcgtttaagggtccaagct gatacacttcctctgctcctgtacggccaaggcgcacttttgttgcaaagaaagctaattctgt cacctgtg
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	CTTTCGTATTCGTTTAAGGGTCCAAGCTGATACACTTCCTCTGCTCCTGTACGGCCAAGGCGCA CTTTTGTTGCAAAGAAAGCTAATTCTGTCACCTGTGGTCAATTGCCATTTCAAGTTAAAACCGT TGAAACAATGAAAGAGAGTGAAAGAGTTTTCAAGATTCACCTGTGAAGCAACAAAAGAGCATTC TACGACATTCGCATCTCCTCTTAACCCGCGAAGGCAAGCATCTGCAAACTTGGCTGCAGCATAT GCCTATAGTAGTAGTACATTTCACATGGATTCAGTACACTGTTCCAGAGAAATAAACAGGTGTA ATGATGATGTATTAAAGTGATTTGGTTTGGTTTTACCATTGAAAGTGTTGCAGAACCAGCTCCA GCTTTTGCCTCCACAACTTCAGTTCCACCATTTTGAATCCGGTTTGTCAGGTACTCAATTTCTT GAGGTGTGAAGCTGCTAGGAGGTTTAACCTGAGGAAAAAGGATTATGCAAAAACAATCAGTTAG CAGAGAAGCTAATGTAATGGAAATGAACCTTTCGTCCTATTCATATGATACCTGTGACAGTAGT GGCAAGATTGTGACTCCGGCGTGTCCCCCAACTACTGGCACATCGACTTCTCTTGGATCAAGGC CAAGAACTTCTGCCTGCACAAGAATTTAAAAAGATAAATTCTTAGTGTTTAAAACTCAACAAAA CCAAATGGAGTGAGGAATCATTAGGCATTATTACCACAAATGTGTTGGCACGAGCAACATCGAG TGTAGTAACTCCAAGGAGCTTCTTAGGATCATAAGTTCCAGCTTTCTTGAAAACCTCAGCGGCA ATGGGGACAGTAGAGTTCACAGGGTTGCTGATCAAGTTGACAATAGCATTAGGACAACATTTTG CTACACCTTCACATAGTGTTTTAACAATCCCAGCATTGATTTTAAACAGATCATCGCGGGTCAT CCCTGGTTTCCTCGGTATACCGGCTGGTATGATCACAAGATCCATACCCGTTAGCGCGTCCTCA AGCTGCTTCGCTCCCAAGAACCCGCGGACCTAATCAATCAAGAGTGGTCATTACTCATTCATTA GCAAGAAGAAGTAATCTTATGTGAAGTTTTCAAAGTTTAAGAGAGATACTTACAACAGCTCCAG TGTCCATATGACTGACGTCAGCAGTGACGCCAGGAGCATTGACAACATCGTAGAGATGAAGTAA AGAGACAAGAGGGTTCATCTTCATCAGCAAAGATAAAGATTGTCCAATTCCACCTGCAGCTCCA AGAATTGCTACTTTGAATCCTGGATTACCACCTTTAGCTCTGCAGTTTTCCCGTCCGATTACAG AGTTCTTGGCCTCCATCTAATGGTTGATCAATCATGAATAAGAAGAAGAAATTTCACTATCAGT CCTAGATGACTTCAACGGAGTCATAAACAGATTGGTCTCTCTAATGGCATCAGAAATCTTCAGT TACTAATTTCAAGAAATGGAAATATACACTTGTAGAAGCGAATGTCAAGTTCATGGTTGAACTA TAAATATTCAGAACGTTGATGAGTCTAGACAAATCAGTTTTGTTTGAGAGTGAATACAAACTAT TCTGGTTTTAGTAGAACAACCATCGAATTTAAGAATATAAAAAAAGATAACTTGAGTTAACAGC AAAGGTAAAGAAAACCTGAGGAGTGAGATGAGCTGAAATCCTAGCAATCCTCTGGTTGGCATCT CCACGAAACTCCATTGTTGTGTTCCTCAGTTTCCTCTCGTTAGGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.215157521

Conservation Information
Conserved circRNAs	NA
PMCS	0.215157521

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	NA
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT5G09660_circ_g.3

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