Plant Circular RNA Database

Detail information of AT5G42660_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT5G42660_circ_g.2
					
						ID in PlantcircBase
						ath_circ_042087
					
						Alias
						Ath_circ_FC3649
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 17103385-17104764  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT5G42660						
					
						Parent gene annotation
						
							AT5g42660/MJB21_3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G42660_circ_g.1 AT5G42660_circ_g.3 AT5G42660_circ_g.4 						
					
						Support reads
						2
					
						Tissues
						inflorescences
					
						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
						AT5G42660.1:4

General Information
CircRNA Name	AT5G42660_circ_g.2
ID in PlantcircBase	ath_circ_042087
Alias	Ath_circ_FC3649
Organism	Arabidpsis thaliana
Position	chr5: 17103385-17104764 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	AT5G42660
Parent gene annotation	AT5g42660/MJB21_3
Parent gene strand	-
Alternative splicing	AT5G42660_circ_g.1 AT5G42660_circ_g.3 AT5G42660_circ_g.4
Support reads	2
Tissues	inflorescences
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	AT5G42660.1:4

			
						 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  
						
							TCAGTTAGATACACAACTCTCTTAACCGGAGAGCCTGAATCTTTACGCTCTAAGATATCAAGAT
GCTCAAGCTCCTCAGGTGGTAAAAGCTTCAAACAACcttttttcccgttgaatcttttatcttc
gggtaatttgtcatgtcggtattgatttatctgcacttcaacttcttcgggtgtagctttgtgt
ttcttgat

									
								

					

						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: 816
Transcript exons: 17103385-17103661,17104005-17104160,17104279-17104455,17
104559-17104764
CTTTTTTCCCGTTGAATCTTTTATCTTCGGGTAATTTGTCATGTCGGTATTGATTTATCTGCAC
TTCAACTTCTTCGGGTGTAGCTTTGTGTTTCTTGATGACAGCGTTTGCCTCGTCGTATACACTG
CTTCGAGCTCCATGTTCTGAAATTGCAAGCACCGAGTTTGTTCGCCAAAGAAGAGCATCTAGTA
CACCAAGTGGGTCTCTTCTAAACTGGGATTTTGAGTCTACCCAAATCGAGTACTTGGCATCTGG
GAAAAGGCGATGGGCCAACATCTTTGGGATCTTCCCATTAAGCCTTTGGTCTGTAAAAGGAAGA
TCCTTTACAATCACAATACGCCACTTTCCAATGTGATCATTCTCATCGATCTTATGACCCTCTG
CTTCTTGTGTTGTAAGAGTAACTTCATCCCAAAACGCAACATAGCAAACCTTTTGACTTGATGT
CTTAGACATTCCAATAGGTTCATAAAGGTTATCTCCACCACCAAACGCACACGTCGAGACCACT
ACTTCACATGATGTCATAAACTTCTTATCCTTATCCGAAATCCTAAATCCCCCATTTTCATTGA
AAAACCCACAATGCAAAGAAACTGTTTCCCTTACCTGAAAACTATTTTCTCTCTCAGCAAAAGT
CTGGTTCCCCGTGAATAAATTAAACCGCGTCCCATTACCACGAACACCTCTCATTTCTCCCACC
GACACATCCGTATCAGTTAGATACACAACTCTCTTAACCGGAGAGCCTGAATCTTTACGCTCTA
AGATATCAAGATGCTCAAGCTCCTCAGGTGGTAAAAGCTTCAAACAAC
						
					

						Genomic sequence
						
							CTTTTTTCCCGTTGAATCTTTTATCTTCGGGTAATTTGTCATGTCGGTATTGATTTATCTGCAC
TTCAACTTCTTCGGGTGTAGCTTTGTGTTTCTTGATGACAGCGTTTGCCTCGTCGTATACACTG
CTTCGAGCTCCATGTTCTGAAATTGCAAGCACCGAGTTTGTTCGCCAAAGAAGAGCATCTAGTA
CACCAAGTGGGTCTCTTCTAAACTGGGATTTTGAGTCTACCCAAATCGAGTACTTGGCATCTGG
GAAAAGGCGATGGGCCAACATCTGACAGCATGTAGATTCATTAGTATCATTATGAAGCATCTTA
TATCAGACATACATGTGCTTGAAAGCAAAACGGAAACTCAAATATTGTGACTCCAACCATATTT
AAACAAGATTAAAAGATGTAAGGAAAAAAAAAAGACAACAGTGAGCTAATTCAAATCGAGCACA
TACCATTTTACACAGCACAAAATGAAAACCAAAGAAGGTTAAATTTGGTTGTAATGGAAACATT
TTACACAGTACCATGAACGCATAATCAGAAACGTTTAACACCCAGCGAATAAGATTGCTACGTG
CAGTACAAATCATCACATGTGCCTCTGAAGTAGATGAGTAGTACCTTTGGGATCTTCCCATTAA
GCCTTTGGTCTGTAAAAGGAAGATCCTTTACAATCACAATACGCCACTTTCCAATGTGATCATT
CTCATCGATCTTATGACCCTCTGCTTCTTGTGTTGTAAGAGTAACTTCATCCCAAAACGCAACA
TAGCAAACCTGCATCCAAAAAACTCATTCAGGATTGGATGCAGCAGAGAGAGAATCACGATTTG
TTCAAACTCCGTACTCGATATGCAAGAGAAACAGTGGACAGGAGAAAATCAGAGTGACCAACCT
TTTGACTTGATGTCTTAGACATTCCAATAGGTTCATAAAGGTTATCTCCACCACCAAACGCACA
CGTCGAGACCACTACTTCACATGATGTCATAAACTTCTTATCCTTATCCGAAATCCTAAATCCC
CCATTTTCATTGAAAAACCCACAATGCAAAGAAACTGTTTCCCTTACCTGATGCAATAAAGCCA
ATACTCAGTTCAAGATCCATATAAAAAATTCCTAAAATTATAGGAAACTCAAGTTCTTAAGCCT
TGTAGAGTTACCAAATCATGACCTGAAAACTATTTTCTCTCTCAGCAAAAGTCTGGTTCCCCGT
GAATAAATTAAACCGCGTCCCATTACCACGAACACCTCTCATTTCTCCCACCGACACATCCGTA
TCAGTTAGATACACAACTCTCTTAACCGGAGAGCCTGAATCTTTACGCTCTAAGATATCAAGAT
GCTCAAGCTCCTCAGGTGGTAAAAGCTTCAAACAAC
						
					

			
		

Sequences
Splice junction sequence	TCAGTTAGATACACAACTCTCTTAACCGGAGAGCCTGAATCTTTACGCTCTAAGATATCAAGAT GCTCAAGCTCCTCAGGTGGTAAAAGCTTCAAACAACcttttttcccgttgaatcttttatcttc gggtaatttgtcatgtcggtattgatttatctgcacttcaacttcttcgggtgtagctttgtgt ttcttgat
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: 816 Transcript exons: 17103385-17103661,17104005-17104160,17104279-17104455,17 104559-17104764 CTTTTTTCCCGTTGAATCTTTTATCTTCGGGTAATTTGTCATGTCGGTATTGATTTATCTGCAC TTCAACTTCTTCGGGTGTAGCTTTGTGTTTCTTGATGACAGCGTTTGCCTCGTCGTATACACTG CTTCGAGCTCCATGTTCTGAAATTGCAAGCACCGAGTTTGTTCGCCAAAGAAGAGCATCTAGTA CACCAAGTGGGTCTCTTCTAAACTGGGATTTTGAGTCTACCCAAATCGAGTACTTGGCATCTGG GAAAAGGCGATGGGCCAACATCTTTGGGATCTTCCCATTAAGCCTTTGGTCTGTAAAAGGAAGA TCCTTTACAATCACAATACGCCACTTTCCAATGTGATCATTCTCATCGATCTTATGACCCTCTG CTTCTTGTGTTGTAAGAGTAACTTCATCCCAAAACGCAACATAGCAAACCTTTTGACTTGATGT CTTAGACATTCCAATAGGTTCATAAAGGTTATCTCCACCACCAAACGCACACGTCGAGACCACT ACTTCACATGATGTCATAAACTTCTTATCCTTATCCGAAATCCTAAATCCCCCATTTTCATTGA AAAACCCACAATGCAAAGAAACTGTTTCCCTTACCTGAAAACTATTTTCTCTCTCAGCAAAAGT CTGGTTCCCCGTGAATAAATTAAACCGCGTCCCATTACCACGAACACCTCTCATTTCTCCCACC GACACATCCGTATCAGTTAGATACACAACTCTCTTAACCGGAGAGCCTGAATCTTTACGCTCTA AGATATCAAGATGCTCAAGCTCCTCAGGTGGTAAAAGCTTCAAACAAC
Genomic sequence	CTTTTTTCCCGTTGAATCTTTTATCTTCGGGTAATTTGTCATGTCGGTATTGATTTATCTGCAC TTCAACTTCTTCGGGTGTAGCTTTGTGTTTCTTGATGACAGCGTTTGCCTCGTCGTATACACTG CTTCGAGCTCCATGTTCTGAAATTGCAAGCACCGAGTTTGTTCGCCAAAGAAGAGCATCTAGTA CACCAAGTGGGTCTCTTCTAAACTGGGATTTTGAGTCTACCCAAATCGAGTACTTGGCATCTGG GAAAAGGCGATGGGCCAACATCTGACAGCATGTAGATTCATTAGTATCATTATGAAGCATCTTA TATCAGACATACATGTGCTTGAAAGCAAAACGGAAACTCAAATATTGTGACTCCAACCATATTT AAACAAGATTAAAAGATGTAAGGAAAAAAAAAAGACAACAGTGAGCTAATTCAAATCGAGCACA TACCATTTTACACAGCACAAAATGAAAACCAAAGAAGGTTAAATTTGGTTGTAATGGAAACATT TTACACAGTACCATGAACGCATAATCAGAAACGTTTAACACCCAGCGAATAAGATTGCTACGTG CAGTACAAATCATCACATGTGCCTCTGAAGTAGATGAGTAGTACCTTTGGGATCTTCCCATTAA GCCTTTGGTCTGTAAAAGGAAGATCCTTTACAATCACAATACGCCACTTTCCAATGTGATCATT CTCATCGATCTTATGACCCTCTGCTTCTTGTGTTGTAAGAGTAACTTCATCCCAAAACGCAACA TAGCAAACCTGCATCCAAAAAACTCATTCAGGATTGGATGCAGCAGAGAGAGAATCACGATTTG TTCAAACTCCGTACTCGATATGCAAGAGAAACAGTGGACAGGAGAAAATCAGAGTGACCAACCT TTTGACTTGATGTCTTAGACATTCCAATAGGTTCATAAAGGTTATCTCCACCACCAAACGCACA CGTCGAGACCACTACTTCACATGATGTCATAAACTTCTTATCCTTATCCGAAATCCTAAATCCC CCATTTTCATTGAAAAACCCACAATGCAAAGAAACTGTTTCCCTTACCTGATGCAATAAAGCCA ATACTCAGTTCAAGATCCATATAAAAAATTCCTAAAATTATAGGAAACTCAAGTTCTTAAGCCT TGTAGAGTTACCAAATCATGACCTGAAAACTATTTTCTCTCTCAGCAAAAGTCTGGTTCCCCGT GAATAAATTAAACCGCGTCCCATTACCACGAACACCTCTCATTTCTCCCACCGACACATCCGTA TCAGTTAGATACACAACTCTCTTAACCGGAGAGCCTGAATCTTTACGCTCTAAGATATCAAGAT GCTCAAGCTCCTCAGGTGGTAAAAGCTTCAAACAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.149190472

Conservation Information
Conserved circRNAs	NA
PMCS	0.149190472

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							17104643-17103387(-)
						
						Potential amino acid sequence
						
							MRGVRGNGTRFNLFTGNQTFAERENSFQVRETVSLHCGFFNENGGFRISDKDKKFMTSCEVVVS
TCAFGGGDNLYEPIGMSKTSSQKVCYVAFWDEVTLTTQEAEGHKIDENDHIGKWRIVIVKDLPF
TDQRLNGKIPKMLAHRLFPDAKYSIWVDSKSQFRRDPLGVLDALLWRTNSVLAISEHGARSSVY
DEANAVIKKHKATPEEVEVQINQYRHDKLPEDKRFNGKKGCLKLLPPEELEHLDILERKDSGSP
VKRVVYLTDTDVSVGEMRGVRGNGTRFNLFTGNQTFAERENSFQVRETVSLHCGFFNENGGFRI
SDKDKKFMTSCEVVVSTCAFGGGDNLYEPIGMSKTSSQKVCYVAFWDEVTLTTQEAEGHKIDEN
DHIGKWRIVIVKDLPFTDQRLNGKIPKMLAHRLFPDAKYSIWVDSKSQFRRDPLGVLDALLWRT
NSVLAISEHGARSSVYDEANAVIKKHKATPEEVEVQINQYRHDKLPEDKRFNGKKGCLKLLPPE
ELEHLDILERKDSGSPVKRVVYLTDTDVSVGEMRGVRGNGTRFNLFTGNQTFAERENSFQVRET
VSLHCGFFNENGGFRISDKDKKFMTSCEVVVSTCAFGGGDNLYEPIGMSKTSSQKVCYVAFWDE
VTLTTQEAEGHKIDENDHIGKWRIVIVKDLPFTDQRLNGKIPKMLAHRLFPDAKYSIWVDSKSQ
FRRDPLGVLDALLWRTNSVLAISEHGARSSVYDEANAVIKKHKATPEEVEVQINQYRHDKLPED
KRFNGKKGCLKLLPPEELEHLDILERKDSGSPVKRVVYLTDTDVSVGEMRGVRGNGTRFNLFTG
NQTFAERENSFQVRETVSLHCGFFNENGGFRISDKDKKFMTSCEVVVSTCAFGGGDNLYEPIGM
SKTSSQKVCYVAFWDEVTLTTQEAEGHKIDENDHIGKWRIVIVKDLPFTDQRLNGKIPKMLAHR
LFPDAKYSIWVDSKSQFRRDPLGVLDALLWRTNSVLAISEHGARSSVYDEANAVIKKHKATPEE
VEVQINQYRHDKLPEDKRFNGKK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	17104643-17103387(-)
Potential amino acid sequence	MRGVRGNGTRFNLFTGNQTFAERENSFQVRETVSLHCGFFNENGGFRISDKDKKFMTSCEVVVS TCAFGGGDNLYEPIGMSKTSSQKVCYVAFWDEVTLTTQEAEGHKIDENDHIGKWRIVIVKDLPF TDQRLNGKIPKMLAHRLFPDAKYSIWVDSKSQFRRDPLGVLDALLWRTNSVLAISEHGARSSVY DEANAVIKKHKATPEEVEVQINQYRHDKLPEDKRFNGKKGCLKLLPPEELEHLDILERKDSGSP VKRVVYLTDTDVSVGEMRGVRGNGTRFNLFTGNQTFAERENSFQVRETVSLHCGFFNENGGFRI SDKDKKFMTSCEVVVSTCAFGGGDNLYEPIGMSKTSSQKVCYVAFWDEVTLTTQEAEGHKIDEN DHIGKWRIVIVKDLPFTDQRLNGKIPKMLAHRLFPDAKYSIWVDSKSQFRRDPLGVLDALLWRT NSVLAISEHGARSSVYDEANAVIKKHKATPEEVEVQINQYRHDKLPEDKRFNGKKGCLKLLPPE ELEHLDILERKDSGSPVKRVVYLTDTDVSVGEMRGVRGNGTRFNLFTGNQTFAERENSFQVRET VSLHCGFFNENGGFRISDKDKKFMTSCEVVVSTCAFGGGDNLYEPIGMSKTSSQKVCYVAFWDE VTLTTQEAEGHKIDENDHIGKWRIVIVKDLPFTDQRLNGKIPKMLAHRLFPDAKYSIWVDSKSQ FRRDPLGVLDALLWRTNSVLAISEHGARSSVYDEANAVIKKHKATPEEVEVQINQYRHDKLPED KRFNGKKGCLKLLPPEELEHLDILERKDSGSPVKRVVYLTDTDVSVGEMRGVRGNGTRFNLFTG NQTFAERENSFQVRETVSLHCGFFNENGGFRISDKDKKFMTSCEVVVSTCAFGGGDNLYEPIGM SKTSSQKVCYVAFWDEVTLTTQEAEGHKIDENDHIGKWRIVIVKDLPFTDQRLNGKIPKMLAHR LFPDAKYSIWVDSKSQFRRDPLGVLDALLWRTNSVLAISEHGARSSVYDEANAVIKKHKATPEE VEVQINQYRHDKLPEDKRFNGKK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT5G42660_circ_g.2

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