Plant Circular RNA Database

Detail information of AT5G40890_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G40890_circ_g.3
					
						ID in PlantcircBase
						ath_circ_041793
					
						Alias
						At_ciR939
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 16383029-16383837  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ
					
						Parent gene
						
							AT5G40890						
					
						Parent gene annotation
						
							Chloride channel protein CLC-a
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G40890_circ_g.2 						
					
						Support reads
						7/23
					
						Tissues
						leaf/whole_plant
					
						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
						AT5G40890.2:2
AT5G40890.1:2

General Information
CircRNA Name	AT5G40890_circ_g.3
ID in PlantcircBase	ath_circ_041793
Alias	At_ciR939
Organism	Arabidpsis thaliana
Position	chr5: 16383029-16383837 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ
Parent gene	AT5G40890
Parent gene annotation	Chloride channel protein CLC-a
Parent gene strand	-
Alternative splicing	AT5G40890_circ_g.2
Support reads	7/23
Tissues	leaf/whole_plant
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	AT5G40890.2:2 AT5G40890.1:2

			
						 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  
						
							CGGACCAGCCGCCGTAGGAGCAAAGTAAACAACAAGTACTGTCGCCACCAAAGTCAGACCCAAA
TTCGCCCCCGTAAAGACCATCAGACCTGTCCAAAACtggttgatgagattgtaaagccggagaa
ctttatgcagaagatgattgtacaagcttccaagaatgccaccaaagactccaatcaatgtgac
tgggatta

									
								

					

						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: 711
Transcript exons: 16383029-16383561,16383660-16383837
TGGTTGATGAGATTGTAAAGCCGGAGAACTTTATGCAGAAGATGATTGTACAAGCTTCCAAGAA
TGCCACCAAAGACTCCAATCAATGTGACTGGGATTATATCTGCTGCGTGGTACCTAACCTCTAC
ATGACTCACATCGAACATAATGAGTCCTCCTGAGCCGAAAAGTCCGCATTTCCCGGAGTTACAA
ATCTCAATGAACGCTCTTAATACAACCACCACAACGGCTGTACTGAAGAATGTTCTCCACAAGA
GAGCGCTTCTCCACCACGTAGCGACTTCCTCAAGAGCGAAAAGTACTCCTCCTACTGGTGACCT
GAAAGCAGCACATACTCCAGAGGCAGATCCACATGTAATAAGATCTCTTCGATCTCTATCGTTG
TTGAAGTAACGAAGCCATCTCCATTTGATTCTGTGATTATCTGGACCACCTTGACCAAGCAAAG
AAGCTATGCAACTTCCAATATGAACCAATGGCCCTTCTTTACCAAGATCAAGTCCAGCTGCAAC
CGCTCCAATACTTCCAACAATCTTAACCATCATGGTGGTAAAACCAAACATATTGGGAGTGTCA
ATGCCATTAAGGTAAGCTTTAATCTCAGGGATCCCCGGACCAGCCGCCGTAGGAGCAAAGTAAA
CAACAAGTACTGTCGCCACCAAAGTCAGACCCAAATTCGCCCCCGTAAAGACCATCAGACCTGT
CCAAAAC
						
					

						Genomic sequence
						
							TGGTTGATGAGATTGTAAAGCCGGAGAACTTTATGCAGAAGATGATTGTACAAGCTTCCAAGAA
TGCCACCAAAGACTCCAATCAATGTGACTGGGATTATATCTGCTGCGTGGTACCTAACCTCTAC
ATGACTCACATCGAACATAATGAGTCCTCCTGAGCCGAAAAGTCCGCATTTCCCGGAGTTACAA
ATCTCAATGAACGCTCTTAATACAACCACCACAACGGCTGTACTGAAGAATGTTCTCCACAAGA
GAGCGCTTCTCCACCACGTAGCGACTTCCTCAAGAGCGAAAAGTACTCCTCCTACTGGTGACCT
GAAAGCAGCACATACTCCAGAGGCAGATCCACATGTAATAAGATCTCTTCGATCTCTATCGTTG
TTGAAGTAACGAAGCCATCTCCATTTGATTCTGTGATTATCTGGACCACCTTGACCAAGCAAAG
AAGCTATGCAACTTCCAATATGAACCAATGGCCCTTCTTTACCAAGATCAAGTCCAGCTGCAAC
CGCTCCAATACTTCCAACAATCTAATCGGAAAAAAACCGCAAAATCCATCAGTAAAACAAAAGA
TCTCACACTAACTTTGTGGGAAGCTTCAAACTTTGTGAAGGTTTAAGAAACAAACCTTAACCAT
CATGGTGGTAAAACCAAACATATTGGGAGTGTCAATGCCATTAAGGTAAGCTTTAATCTCAGGG
ATCCCCGGACCAGCCGCCGTAGGAGCAAAGTAAACAACAAGTACTGTCGCCACCAAAGTCAGAC
CCAAATTCGCCCCCGTAAAGACCATCAGACCTGTCCAAAAC
						
					

			
		

Sequences
Splice junction sequence	CGGACCAGCCGCCGTAGGAGCAAAGTAAACAACAAGTACTGTCGCCACCAAAGTCAGACCCAAA TTCGCCCCCGTAAAGACCATCAGACCTGTCCAAAACtggttgatgagattgtaaagccggagaa ctttatgcagaagatgattgtacaagcttccaagaatgccaccaaagactccaatcaatgtgac tgggatta
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: 711 Transcript exons: 16383029-16383561,16383660-16383837 TGGTTGATGAGATTGTAAAGCCGGAGAACTTTATGCAGAAGATGATTGTACAAGCTTCCAAGAA TGCCACCAAAGACTCCAATCAATGTGACTGGGATTATATCTGCTGCGTGGTACCTAACCTCTAC ATGACTCACATCGAACATAATGAGTCCTCCTGAGCCGAAAAGTCCGCATTTCCCGGAGTTACAA ATCTCAATGAACGCTCTTAATACAACCACCACAACGGCTGTACTGAAGAATGTTCTCCACAAGA GAGCGCTTCTCCACCACGTAGCGACTTCCTCAAGAGCGAAAAGTACTCCTCCTACTGGTGACCT GAAAGCAGCACATACTCCAGAGGCAGATCCACATGTAATAAGATCTCTTCGATCTCTATCGTTG TTGAAGTAACGAAGCCATCTCCATTTGATTCTGTGATTATCTGGACCACCTTGACCAAGCAAAG AAGCTATGCAACTTCCAATATGAACCAATGGCCCTTCTTTACCAAGATCAAGTCCAGCTGCAAC CGCTCCAATACTTCCAACAATCTTAACCATCATGGTGGTAAAACCAAACATATTGGGAGTGTCA ATGCCATTAAGGTAAGCTTTAATCTCAGGGATCCCCGGACCAGCCGCCGTAGGAGCAAAGTAAA CAACAAGTACTGTCGCCACCAAAGTCAGACCCAAATTCGCCCCCGTAAAGACCATCAGACCTGT CCAAAAC
Genomic sequence	TGGTTGATGAGATTGTAAAGCCGGAGAACTTTATGCAGAAGATGATTGTACAAGCTTCCAAGAA TGCCACCAAAGACTCCAATCAATGTGACTGGGATTATATCTGCTGCGTGGTACCTAACCTCTAC ATGACTCACATCGAACATAATGAGTCCTCCTGAGCCGAAAAGTCCGCATTTCCCGGAGTTACAA ATCTCAATGAACGCTCTTAATACAACCACCACAACGGCTGTACTGAAGAATGTTCTCCACAAGA GAGCGCTTCTCCACCACGTAGCGACTTCCTCAAGAGCGAAAAGTACTCCTCCTACTGGTGACCT GAAAGCAGCACATACTCCAGAGGCAGATCCACATGTAATAAGATCTCTTCGATCTCTATCGTTG TTGAAGTAACGAAGCCATCTCCATTTGATTCTGTGATTATCTGGACCACCTTGACCAAGCAAAG AAGCTATGCAACTTCCAATATGAACCAATGGCCCTTCTTTACCAAGATCAAGTCCAGCTGCAAC CGCTCCAATACTTCCAACAATCTAATCGGAAAAAAACCGCAAAATCCATCAGTAAAACAAAAGA TCTCACACTAACTTTGTGGGAAGCTTCAAACTTTGTGAAGGTTTAAGAAACAAACCTTAACCAT CATGGTGGTAAAACCAAACATATTGGGAGTGTCAATGCCATTAAGGTAAGCTTTAATCTCAGGG ATCCCCGGACCAGCCGCCGTAGGAGCAAAGTAAACAACAAGTACTGTCGCCACCAAAGTCAGAC CCAAATTCGCCCCCGTAAAGACCATCAGACCTGTCCAAAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.325395926

Conservation Information
Conserved circRNAs	NA
PMCS	0.325395926

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							16383822-16383031(-)
						
						Potential amino acid sequence
						
							MVFTGANLGLTLVATVLVVYFAPTAAGPGIPEIKAYLNGIDTPNMFGFTTMMVKIVGSIGAVAA
GLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWRWLRYFNNDRDRRDLITCGSASGVCAAFRSP
VGGVLFALEEVATWWRSALLWRTFFSTAVVVVVLRAFIEICNSGKCGLFGSGGLIMFDVSHVEV
RYHAADIIPVTLIGVFGGILGSLYNHLLHKVLRLYNLINQFWTGLMVFTGANLGLTLVATVLVV
YFAPTAAGPGIPEIKAYLNGIDTPNMFGFTTMMVKIVGSIGAVAAGLDLGKEGPLVHIGSCIAS
LLGQGGPDNHRIKWRWLRYFNNDRDRRDLITCGSASGVCAAFRSPVGGVLFALEEVATWWRSAL
LWRTFFSTAVVVVVLRAFIEICNSGKCGLFGSGGLIMFDVSHVEVRYHAADIIPVTLIGVFGGI
LGSLYNHLLHKVLRLYNLINQFWTGLMVFTGANLGLTLVATVLVVYFAPTAAGPGIPEIKAYLN
GIDTPNMFGFTTMMVKIVGSIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWRWLRY
FNNDRDRRDLITCGSASGVCAAFRSPVGGVLFALEEVATWWRSALLWRTFFSTAVVVVVLRAFI
EICNSGKCGLFGSGGLIMFDVSHVEVRYHAADIIPVTLIGVFGGILGSLYNHLLHKVLRLYNLI
NQFWTGLMVFTGANLGLTLVATVLVVYFAPTAAGPGIPEIKAYLNGIDTPNMFGFTTMMVKIVG
SIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWRWLRYFNNDRDRRDLITCGSASGV
CAAFRSPVGGVLFALEEVATWWRSALLWRTFFSTAVVVVVLRAFIEICNSGKCGLFGSGGLIMF
DVSHVEVRYHAADIIPVTLIGVFGGILGSLYNHLLHKVLRLYNLIN(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	16383822-16383031(-)
Potential amino acid sequence	MVFTGANLGLTLVATVLVVYFAPTAAGPGIPEIKAYLNGIDTPNMFGFTTMMVKIVGSIGAVAA GLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWRWLRYFNNDRDRRDLITCGSASGVCAAFRSP VGGVLFALEEVATWWRSALLWRTFFSTAVVVVVLRAFIEICNSGKCGLFGSGGLIMFDVSHVEV RYHAADIIPVTLIGVFGGILGSLYNHLLHKVLRLYNLINQFWTGLMVFTGANLGLTLVATVLVV YFAPTAAGPGIPEIKAYLNGIDTPNMFGFTTMMVKIVGSIGAVAAGLDLGKEGPLVHIGSCIAS LLGQGGPDNHRIKWRWLRYFNNDRDRRDLITCGSASGVCAAFRSPVGGVLFALEEVATWWRSAL LWRTFFSTAVVVVVLRAFIEICNSGKCGLFGSGGLIMFDVSHVEVRYHAADIIPVTLIGVFGGI LGSLYNHLLHKVLRLYNLINQFWTGLMVFTGANLGLTLVATVLVVYFAPTAAGPGIPEIKAYLN GIDTPNMFGFTTMMVKIVGSIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWRWLRY FNNDRDRRDLITCGSASGVCAAFRSPVGGVLFALEEVATWWRSALLWRTFFSTAVVVVVLRAFI EICNSGKCGLFGSGGLIMFDVSHVEVRYHAADIIPVTLIGVFGGILGSLYNHLLHKVLRLYNLI NQFWTGLMVFTGANLGLTLVATVLVVYFAPTAAGPGIPEIKAYLNGIDTPNMFGFTTMMVKIVG SIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWRWLRYFNNDRDRRDLITCGSASGV CAAFRSPVGGVLFALEEVATWWRSALLWRTFFSTAVVVVVLRAFIEICNSGKCGLFGSGGLIMF DVSHVEVRYHAADIIPVTLIGVFGGILGSLYNHLLHKVLRLYNLIN(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of AT5G40890_circ_g.3

Address

Any questions?

Supported by