Plant Circular RNA Database

Detail information of AT3G50530_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT3G50530_circ_g.3
					
						ID in PlantcircBase
						ath_circ_026841
					
						Alias
						3:18754836-18755675
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 18754836-18755675  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G50530						
					
						Parent gene annotation
						
							CDPK-related kinase
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G50530_circ_g.1 AT3G50530_circ_g.2 AT3G50530_circ_g.4 AT3G50530_circ_g.5 AT3G50530_circ_g.6 AT3G50530_circ_g.7 AT3G50530_circ_g.8 						
					
						Support reads
						1/1
					
						Tissues
						seedling;root
					
						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
						AT3G50530.1:4
AT3G50530.2:3

General Information
CircRNA Name	AT3G50530_circ_g.3
ID in PlantcircBase	ath_circ_026841
Alias	3:18754836-18755675
Organism	Arabidpsis thaliana
Position	chr3: 18754836-18755675 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G50530
Parent gene annotation	CDPK-related kinase
Parent gene strand	+
Alternative splicing	AT3G50530_circ_g.1 AT3G50530_circ_g.2 AT3G50530_circ_g.4 AT3G50530_circ_g.5 AT3G50530_circ_g.6 AT3G50530_circ_g.7 AT3G50530_circ_g.8
Support reads	1/1
Tissues	seedling;root
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	AT3G50530.1:4 AT3G50530.2:3

			
						 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  
						
							AAAGGACTCAAACGACGCAAAGGTTCCAATGGATATTCTGGTTTTCAAACTTATGAGAGCTTAT
TTACGATCATCATCTCTCCGTAAAGCTGCATTAAGAaggtgggaagtacacagaggaggatgca
aagaccgttatgatacaaatattgaatgtggttgctttttgtcatctgcaaggcgttgtacaca
gagatctt

									
								

					

						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: 598
Transcript exons: 18754836-18754944,18755027-18755105,18755199-18755495,18
755563-18755675
AGGTGGGAAGTACACAGAGGAGGATGCAAAGACCGTTATGATACAAATATTGAATGTGGTTGCT
TTTTGTCATCTGCAAGGCGTTGTACACAGAGATCTTAAACCAGAGAATTTTCTTTTTACCTCAA
AAGAAGACACCTCTCAATTGAAGGCAATAGATTTCGGTTTGTCAGATTACGTGAGACCAGATGA
GAGGCTCAATGACATTGTTGGTAGTGCATACTATGTAGCACCTGAAGTTCTGCATAGATCTTAC
AGTACAGAAGCTGATATTTGGAGTGTTGGTGTGATTGTATATATTCTATTGTGTGGAAGCCGAC
CGTTTTGGGCTAGGACAGAATCAGGAATCTTTCGTGCTGTTCTAAAAGCTGATCCAAGTTTTGA
TGACCCTCCTTGGCCTTTGTTATCTTCAGAGGCAAGAGATTTTGTAAAGCGGTTGCTAAACAAA
GATCCGCGTAAAAGATTAACAGCTGCTCAAGCCTTAAGTCATCCATGGATAAAGGACTCAAACG
ACGCAAAGGTTCCAATGGATATTCTGGTTTTCAAACTTATGAGAGCTTATTTACGATCATCATC
TCTCCGTAAAGCTGCATTAAGA
						
					

						Genomic sequence
						
							AGGTGGGAAGTACACAGAGGAGGATGCAAAGACCGTTATGATACAAATATTGAATGTGGTTGCT
TTTTGTCATCTGCAAGGCGTTGTACACAGAGATCTTAAACCAGAGGTACTAAAAGCTCTTTATT
GGTACTTATACATTTGATGTTCATTGCAATCTTTATGAAGTTCACTTAAACTGTTTGGATCAGA
ATTTTCTTTTTACCTCAAAAGAAGACACCTCTCAATTGAAGGCAATAGATTTCGGTTTGTCAGA
TTACGTGAGACCAGGTAAAGCCCTTAGATTATATGCTATATGTAAACTTAGATTCCAGAACCTA
GAGACCAGCATTTGCTTATATGCGTTGACAATTGCATTTGCAGATGAGAGGCTCAATGACATTG
TTGGTAGTGCATACTATGTAGCACCTGAAGTTCTGCATAGATCTTACAGTACAGAAGCTGATAT
TTGGAGTGTTGGTGTGATTGTATATATTCTATTGTGTGGAAGCCGACCGTTTTGGGCTAGGACA
GAATCAGGAATCTTTCGTGCTGTTCTAAAAGCTGATCCAAGTTTTGATGACCCTCCTTGGCCTT
TGTTATCTTCAGAGGCAAGAGATTTTGTAAAGCGGTTGCTAAACAAAGATCCGCGTAAAAGATT
AACAGCTGCTCAAGCCTTAAGTAAGTGTAGAATGCATACAAAATTGTTTCAATGTGAAAAGATT
TGTAATCTTGTTTATTGTTTCAGGTCATCCATGGATAAAGGACTCAAACGACGCAAAGGTTCCA
ATGGATATTCTGGTTTTCAAACTTATGAGAGCTTATTTACGATCATCATCTCTCCGTAAAGCTG
CATTAAGA
						
					

			
		

Sequences
Splice junction sequence	AAAGGACTCAAACGACGCAAAGGTTCCAATGGATATTCTGGTTTTCAAACTTATGAGAGCTTAT TTACGATCATCATCTCTCCGTAAAGCTGCATTAAGAaggtgggaagtacacagaggaggatgca aagaccgttatgatacaaatattgaatgtggttgctttttgtcatctgcaaggcgttgtacaca gagatctt
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: 598 Transcript exons: 18754836-18754944,18755027-18755105,18755199-18755495,18 755563-18755675 AGGTGGGAAGTACACAGAGGAGGATGCAAAGACCGTTATGATACAAATATTGAATGTGGTTGCT TTTTGTCATCTGCAAGGCGTTGTACACAGAGATCTTAAACCAGAGAATTTTCTTTTTACCTCAA AAGAAGACACCTCTCAATTGAAGGCAATAGATTTCGGTTTGTCAGATTACGTGAGACCAGATGA GAGGCTCAATGACATTGTTGGTAGTGCATACTATGTAGCACCTGAAGTTCTGCATAGATCTTAC AGTACAGAAGCTGATATTTGGAGTGTTGGTGTGATTGTATATATTCTATTGTGTGGAAGCCGAC CGTTTTGGGCTAGGACAGAATCAGGAATCTTTCGTGCTGTTCTAAAAGCTGATCCAAGTTTTGA TGACCCTCCTTGGCCTTTGTTATCTTCAGAGGCAAGAGATTTTGTAAAGCGGTTGCTAAACAAA GATCCGCGTAAAAGATTAACAGCTGCTCAAGCCTTAAGTCATCCATGGATAAAGGACTCAAACG ACGCAAAGGTTCCAATGGATATTCTGGTTTTCAAACTTATGAGAGCTTATTTACGATCATCATC TCTCCGTAAAGCTGCATTAAGA
Genomic sequence	AGGTGGGAAGTACACAGAGGAGGATGCAAAGACCGTTATGATACAAATATTGAATGTGGTTGCT TTTTGTCATCTGCAAGGCGTTGTACACAGAGATCTTAAACCAGAGGTACTAAAAGCTCTTTATT GGTACTTATACATTTGATGTTCATTGCAATCTTTATGAAGTTCACTTAAACTGTTTGGATCAGA ATTTTCTTTTTACCTCAAAAGAAGACACCTCTCAATTGAAGGCAATAGATTTCGGTTTGTCAGA TTACGTGAGACCAGGTAAAGCCCTTAGATTATATGCTATATGTAAACTTAGATTCCAGAACCTA GAGACCAGCATTTGCTTATATGCGTTGACAATTGCATTTGCAGATGAGAGGCTCAATGACATTG TTGGTAGTGCATACTATGTAGCACCTGAAGTTCTGCATAGATCTTACAGTACAGAAGCTGATAT TTGGAGTGTTGGTGTGATTGTATATATTCTATTGTGTGGAAGCCGACCGTTTTGGGCTAGGACA GAATCAGGAATCTTTCGTGCTGTTCTAAAAGCTGATCCAAGTTTTGATGACCCTCCTTGGCCTT TGTTATCTTCAGAGGCAAGAGATTTTGTAAAGCGGTTGCTAAACAAAGATCCGCGTAAAAGATT AACAGCTGCTCAAGCCTTAAGTAAGTGTAGAATGCATACAAAATTGTTTCAATGTGAAAAGATT TGTAATCTTGTTTATTGTTTCAGGTCATCCATGGATAAAGGACTCAAACGACGCAAAGGTTCCA ATGGATATTCTGGTTTTCAAACTTATGAGAGCTTATTTACGATCATCATCTCTCCGTAAAGCTG CATTAAGA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.439842327

Conservation Information
Conserved circRNAs	NA
PMCS	0.439842327

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR866-3p 						
					
						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	ath-miR866-3p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT3G50530_circ_g.3

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