Plant Circular RNA Database

Detail information of AT3G56720_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G56720_circ_g.1
					
						ID in PlantcircBase
						ath_circ_027870
					
						Alias
						At_ciR1800
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 21011671-21012461  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ
					
						Parent gene
						
							AT3G56720						
					
						Parent gene annotation
						
							AT3G56720 protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G56720_circ_g.2 AT3G56720_circ_g.3 AT3G56720_circ_g.4 AT3G56720_circ_g.5 AT3G56720_circ_g.6 AT3G56720_circ_g.7 AT3G56720_circ_g.8 AT3G56720_circ_g.9 						
					
						Support reads
						5/13
					
						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  
						
							GT-AG							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
						AT3G56720.5:2
AT3G56720.6:2
AT3G56720.1:2
AT3G56720.3:2
AT3G56720.2:2
AT3G56720.7:2
AT3G56720.4:2

General Information
CircRNA Name	AT3G56720_circ_g.1
ID in PlantcircBase	ath_circ_027870
Alias	At_ciR1800
Organism	Arabidpsis thaliana
Position	chr3: 21011671-21012461 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ
Parent gene	AT3G56720
Parent gene annotation	AT3G56720 protein
Parent gene strand	+
Alternative splicing	AT3G56720_circ_g.2 AT3G56720_circ_g.3 AT3G56720_circ_g.4 AT3G56720_circ_g.5 AT3G56720_circ_g.6 AT3G56720_circ_g.7 AT3G56720_circ_g.8 AT3G56720_circ_g.9
Support reads	5/13
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	GT-AG 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	AT3G56720.5:2 AT3G56720.6:2 AT3G56720.1:2 AT3G56720.3:2 AT3G56720.2:2 AT3G56720.7:2 AT3G56720.4:2

			
						 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  
						
							ATAGATGCTGCAGCAGAAGAGAAACAGACATCAATCTTAAAGCCTTCCCCCGGTGATGTTGATG
CTGCAAAAGTTGCAGCTATGCAGGCTGCTGAATTAGgaagtcctgaacgtaatcagagccctaa
tccaaagcattctaggaaagattctgaaccagttcatgtgaggaaagaggatagatgggaatct
gatcgcag

									
								

					

						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: 708
Transcript exons: 21011671-21012294,21012378-21012461
GAAGTCCTGAACGTAATCAGAGCCCTAATCCAAAGCATTCTAGGAAAGATTCTGAACCAGTTCA
TGTGAGGAAAGAGGATAGATGGGAATCTGATCGCAGTCGTTATGGTAGAGGAGGTGTTGATTCA
CATAGACATGATAGGTACTCTAGGGATGATAATTACGGATATAAGCGTGATGAGTATAACAGAC
ATGGGAGGGATGCGCGTTCTACTAGCCGTGATTCAAGAGGTGGCAGACATTCTGACCGTAGAAG
AGTGGAGACTGAATATAGCAGGTTAAGAAATGACTCAGACAGAAGTTCCCATGATAAGTATAGC
AACTCTGGACATAGAGTCAAAAGTAACGAGAAAGGTGAAGATTTGTCATCTGGTAGGAGACACT
CAGACTCAAGAGTGGAGGATAATGAGAAAAGAGGTTCTCGCTGGGGTTTTGGTGACCGTCATTC
CCGTGTTGAAAGAAAGGAACATGAGGACCCTGAGATTAGCAAGGAGAAGGAGGTTCATGTCAAA
TCTTCAAGAGACCGTTCTGATGGGAAATGTTTGGCTACAGAGGATCGAGATACTCATTCTAAGA
AACTGAAGGGTTTCATATCAGACAAGTTTACTACTGGCAATACTAATGAAGAGAAACAGACATC
AATCTTAAAGCCTTCCCCCGGTGATGTTGATGCTGCAAAAGTTGCAGCTATGCAGGCTGCTGAA
TTAG
Transcript length: 711
Transcript exons: 21011671-21012294,21012375-21012461
GAAGTCCTGAACGTAATCAGAGCCCTAATCCAAAGCATTCTAGGAAAGATTCTGAACCAGTTCA
TGTGAGGAAAGAGGATAGATGGGAATCTGATCGCAGTCGTTATGGTAGAGGAGGTGTTGATTCA
CATAGACATGATAGGTACTCTAGGGATGATAATTACGGATATAAGCGTGATGAGTATAACAGAC
ATGGGAGGGATGCGCGTTCTACTAGCCGTGATTCAAGAGGTGGCAGACATTCTGACCGTAGAAG
AGTGGAGACTGAATATAGCAGGTTAAGAAATGACTCAGACAGAAGTTCCCATGATAAGTATAGC
AACTCTGGACATAGAGTCAAAAGTAACGAGAAAGGTGAAGATTTGTCATCTGGTAGGAGACACT
CAGACTCAAGAGTGGAGGATAATGAGAAAAGAGGTTCTCGCTGGGGTTTTGGTGACCGTCATTC
CCGTGTTGAAAGAAAGGAACATGAGGACCCTGAGATTAGCAAGGAGAAGGAGGTTCATGTCAAA
TCTTCAAGAGACCGTTCTGATGGGAAATGTTTGGCTACAGAGGATCGAGATACTCATTCTAAGA
AACTGAAGGGTTTCATATCAGACAAGTTTACTACTGGCAATACTAATGCAGAAGAGAAACAGAC
ATCAATCTTAAAGCCTTCCCCCGGTGATGTTGATGCTGCAAAAGTTGCAGCTATGCAGGCTGCT
GAATTAG
						
					

						Genomic sequence
						
							GAAGTCCTGAACGTAATCAGAGCCCTAATCCAAAGCATTCTAGGAAAGATTCTGAACCAGTTCA
TGTGAGGAAAGAGGATAGATGGGAATCTGATCGCAGTCGTTATGGTAGAGGAGGTGTTGATTCA
CATAGACATGATAGGTACTCTAGGGATGATAATTACGGATATAAGCGTGATGAGTATAACAGAC
ATGGGAGGGATGCGCGTTCTACTAGCCGTGATTCAAGAGGTGGCAGACATTCTGACCGTAGAAG
AGTGGAGACTGAATATAGCAGGTTAAGAAATGACTCAGACAGAAGTTCCCATGATAAGTATAGC
AACTCTGGACATAGAGTCAAAAGTAACGAGAAAGGTGAAGATTTGTCATCTGGTAGGAGACACT
CAGACTCAAGAGTGGAGGATAATGAGAAAAGAGGTTCTCGCTGGGGTTTTGGTGACCGTCATTC
CCGTGTTGAAAGAAAGGAACATGAGGACCCTGAGATTAGCAAGGAGAAGGAGGTTCATGTCAAA
TCTTCAAGAGACCGTTCTGATGGGAAATGTTTGGCTACAGAGGATCGAGATACTCATTCTAAGA
AACTGAAGGGTTTCATATCAGACAAGTTTACTACTGGCAATACTAATGGTAAGACTTTTGTTCT
GTTCTTTACAAATGTTTTCTTTCTGTGTTATGTAGATCCTTGCTCTAAGTTATAGATGCTGCAG
CAGAAGAGAAACAGACATCAATCTTAAAGCCTTCCCCCGGTGATGTTGATGCTGCAAAAGTTGC
AGCTATGCAGGCTGCTGAATTAG
						
					

			
		

Sequences
Splice junction sequence	ATAGATGCTGCAGCAGAAGAGAAACAGACATCAATCTTAAAGCCTTCCCCCGGTGATGTTGATG CTGCAAAAGTTGCAGCTATGCAGGCTGCTGAATTAGgaagtcctgaacgtaatcagagccctaa tccaaagcattctaggaaagattctgaaccagttcatgtgaggaaagaggatagatgggaatct gatcgcag
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: 708 Transcript exons: 21011671-21012294,21012378-21012461 GAAGTCCTGAACGTAATCAGAGCCCTAATCCAAAGCATTCTAGGAAAGATTCTGAACCAGTTCA TGTGAGGAAAGAGGATAGATGGGAATCTGATCGCAGTCGTTATGGTAGAGGAGGTGTTGATTCA CATAGACATGATAGGTACTCTAGGGATGATAATTACGGATATAAGCGTGATGAGTATAACAGAC ATGGGAGGGATGCGCGTTCTACTAGCCGTGATTCAAGAGGTGGCAGACATTCTGACCGTAGAAG AGTGGAGACTGAATATAGCAGGTTAAGAAATGACTCAGACAGAAGTTCCCATGATAAGTATAGC AACTCTGGACATAGAGTCAAAAGTAACGAGAAAGGTGAAGATTTGTCATCTGGTAGGAGACACT CAGACTCAAGAGTGGAGGATAATGAGAAAAGAGGTTCTCGCTGGGGTTTTGGTGACCGTCATTC CCGTGTTGAAAGAAAGGAACATGAGGACCCTGAGATTAGCAAGGAGAAGGAGGTTCATGTCAAA TCTTCAAGAGACCGTTCTGATGGGAAATGTTTGGCTACAGAGGATCGAGATACTCATTCTAAGA AACTGAAGGGTTTCATATCAGACAAGTTTACTACTGGCAATACTAATGAAGAGAAACAGACATC AATCTTAAAGCCTTCCCCCGGTGATGTTGATGCTGCAAAAGTTGCAGCTATGCAGGCTGCTGAA TTAG Transcript length: 711 Transcript exons: 21011671-21012294,21012375-21012461 GAAGTCCTGAACGTAATCAGAGCCCTAATCCAAAGCATTCTAGGAAAGATTCTGAACCAGTTCA TGTGAGGAAAGAGGATAGATGGGAATCTGATCGCAGTCGTTATGGTAGAGGAGGTGTTGATTCA CATAGACATGATAGGTACTCTAGGGATGATAATTACGGATATAAGCGTGATGAGTATAACAGAC ATGGGAGGGATGCGCGTTCTACTAGCCGTGATTCAAGAGGTGGCAGACATTCTGACCGTAGAAG AGTGGAGACTGAATATAGCAGGTTAAGAAATGACTCAGACAGAAGTTCCCATGATAAGTATAGC AACTCTGGACATAGAGTCAAAAGTAACGAGAAAGGTGAAGATTTGTCATCTGGTAGGAGACACT CAGACTCAAGAGTGGAGGATAATGAGAAAAGAGGTTCTCGCTGGGGTTTTGGTGACCGTCATTC CCGTGTTGAAAGAAAGGAACATGAGGACCCTGAGATTAGCAAGGAGAAGGAGGTTCATGTCAAA TCTTCAAGAGACCGTTCTGATGGGAAATGTTTGGCTACAGAGGATCGAGATACTCATTCTAAGA AACTGAAGGGTTTCATATCAGACAAGTTTACTACTGGCAATACTAATGCAGAAGAGAAACAGAC ATCAATCTTAAAGCCTTCCCCCGGTGATGTTGATGCTGCAAAAGTTGCAGCTATGCAGGCTGCT GAATTAG
Genomic sequence	GAAGTCCTGAACGTAATCAGAGCCCTAATCCAAAGCATTCTAGGAAAGATTCTGAACCAGTTCA TGTGAGGAAAGAGGATAGATGGGAATCTGATCGCAGTCGTTATGGTAGAGGAGGTGTTGATTCA CATAGACATGATAGGTACTCTAGGGATGATAATTACGGATATAAGCGTGATGAGTATAACAGAC ATGGGAGGGATGCGCGTTCTACTAGCCGTGATTCAAGAGGTGGCAGACATTCTGACCGTAGAAG AGTGGAGACTGAATATAGCAGGTTAAGAAATGACTCAGACAGAAGTTCCCATGATAAGTATAGC AACTCTGGACATAGAGTCAAAAGTAACGAGAAAGGTGAAGATTTGTCATCTGGTAGGAGACACT CAGACTCAAGAGTGGAGGATAATGAGAAAAGAGGTTCTCGCTGGGGTTTTGGTGACCGTCATTC CCGTGTTGAAAGAAAGGAACATGAGGACCCTGAGATTAGCAAGGAGAAGGAGGTTCATGTCAAA TCTTCAAGAGACCGTTCTGATGGGAAATGTTTGGCTACAGAGGATCGAGATACTCATTCTAAGA AACTGAAGGGTTTCATATCAGACAAGTTTACTACTGGCAATACTAATGGTAAGACTTTTGTTCT GTTCTTTACAAATGTTTTCTTTCTGTGTTATGTAGATCCTTGCTCTAAGTTATAGATGCTGCAG CAGAAGAGAAACAGACATCAATCTTAAAGCCTTCCCCCGGTGATGTTGATGCTGCAAAAGTTGC AGCTATGCAGGCTGCTGAATTAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.180265132

Conservation Information
Conserved circRNAs	NA
PMCS	0.180265132

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21012443-21012458(+)
						
						Potential amino acid sequence
						
							MQAAELGSPERNQSPNPKHSRKDSEPVHVRKEDRWESDRSRYGRGGVDSHRHDRYSRDDNYGYK
RDEYNRHGRDARSTSRDSRGGRHSDRRRVETEYSRLRNDSDRSSHDKYSNSGHRVKSNEKGEDL
SSGRRHSDSRVEDNEKRGSRWGFGDRHSRVERKEHEDPEISKEKEVHVKSSRDRSDGKCLATED
RDTHSKKLKGFISDKFTTGNTNEEKQTSILKPSPGDVDAAKVAAMQAAELGSPERNQSPNPKHS
RKDSEPVHVRKEDRWESDRSRYGRGGVDSHRHDRYSRDDNYGYKRDEYNRHGRDARSTSRDSRG
GRHSDRRRVETEYSRLRNDSDRSSHDKYSNSGHRVKSNEKGEDLSSGRRHSDSRVEDNEKRGSR
WGFGDRHSRVERKEHEDPEISKEKEVHVKSSRDRSDGKCLATEDRDTHSKKLKGFISDKFTTGN
TNEEKQTSILKPSPGDVDAAKVAAMQAAELGSPERNQSPNPKHSRKDSEPVHVRKEDRWESDRS
RYGRGGVDSHRHDRYSRDDNYGYKRDEYNRHGRDARSTSRDSRGGRHSDRRRVETEYSRLRNDS
DRSSHDKYSNSGHRVKSNEKGEDLSSGRRHSDSRVEDNEKRGSRWGFGDRHSRVERKEHEDPEI
SKEKEVHVKSSRDRSDGKCLATEDRDTHSKKLKGFISDKFTTGNTNEEKQTSILKPSPGDVDAA
KVAAMQAAEL(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21012443-21012458(+)
Potential amino acid sequence	MQAAELGSPERNQSPNPKHSRKDSEPVHVRKEDRWESDRSRYGRGGVDSHRHDRYSRDDNYGYK RDEYNRHGRDARSTSRDSRGGRHSDRRRVETEYSRLRNDSDRSSHDKYSNSGHRVKSNEKGEDL SSGRRHSDSRVEDNEKRGSRWGFGDRHSRVERKEHEDPEISKEKEVHVKSSRDRSDGKCLATED RDTHSKKLKGFISDKFTTGNTNEEKQTSILKPSPGDVDAAKVAAMQAAELGSPERNQSPNPKHS RKDSEPVHVRKEDRWESDRSRYGRGGVDSHRHDRYSRDDNYGYKRDEYNRHGRDARSTSRDSRG GRHSDRRRVETEYSRLRNDSDRSSHDKYSNSGHRVKSNEKGEDLSSGRRHSDSRVEDNEKRGSR WGFGDRHSRVERKEHEDPEISKEKEVHVKSSRDRSDGKCLATEDRDTHSKKLKGFISDKFTTGN TNEEKQTSILKPSPGDVDAAKVAAMQAAELGSPERNQSPNPKHSRKDSEPVHVRKEDRWESDRS RYGRGGVDSHRHDRYSRDDNYGYKRDEYNRHGRDARSTSRDSRGGRHSDRRRVETEYSRLRNDS DRSSHDKYSNSGHRVKSNEKGEDLSSGRRHSDSRVEDNEKRGSRWGFGDRHSRVERKEHEDPEI SKEKEVHVKSSRDRSDGKCLATEDRDTHSKKLKGFISDKFTTGNTNEEKQTSILKPSPGDVDAA KVAAMQAAEL(+)
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 AT3G56720_circ_g.1

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