Plant Circular RNA Database

Detail information of AT3G58570_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT3G58570_circ_g.3
					
						ID in PlantcircBase
						ath_circ_028130
					
						Alias
						3:21658341-21659370
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 21658341-21659370  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G58570						
					
						Parent gene annotation
						
							DEAD-box ATP-dependent RNA helicase 52
							
						Parent gene strand
						+
					
						Alternative splicing
						
							3_circ_ag.5 AT3G58530_circ_g.1 AT3G58530_circ_g.2 AT3G58530_circ_g.3 AT3G58530_circ_g.4 AT3G58530_circ_g.5 AT3G58560_circ_g.1 AT3G58560_circ_g.2 AT3G58560_circ_g.3 AT3G58560_circ_g.4 AT3G58570_circ_g.1 AT3G58570_circ_g.2 AT3G58570_circ_g.4 AT3G58570_circ_g.5 						
					
						Support reads
						2/1
					
						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
						AT3G58570.1:2

General Information
CircRNA Name	AT3G58570_circ_g.3
ID in PlantcircBase	ath_circ_028130
Alias	3:21658341-21659370
Organism	Arabidpsis thaliana
Position	chr3: 21658341-21659370 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G58570
Parent gene annotation	DEAD-box ATP-dependent RNA helicase 52
Parent gene strand	+
Alternative splicing	3_circ_ag.5 AT3G58530_circ_g.1 AT3G58530_circ_g.2 AT3G58530_circ_g.3 AT3G58530_circ_g.4 AT3G58530_circ_g.5 AT3G58560_circ_g.1 AT3G58560_circ_g.2 AT3G58560_circ_g.3 AT3G58560_circ_g.4 AT3G58570_circ_g.1 AT3G58570_circ_g.2 AT3G58570_circ_g.4 AT3G58570_circ_g.5
Support reads	2/1
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	AT3G58570.1:2

			
						 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  
						
							TTTAATTGTCCAAAGAGTAGAGTTTGTTCATGATTCTGACAAAAGAAGCCATCTAATGGACCTT
CTTCATGCCCAGAGGGAGAATGGTAACCAAGGAAAGattagggagcttgaaagaggagttgata
ttcttgttgcaactcctgggagattaaatgatttgcttgagagaggtagagtctcattacagat
ggtaagat

						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: 411
Transcript exons: 21658341-21658583,21659203-21659370
ATTAGGGAGCTTGAAAGAGGAGTTGATATTCTTGTTGCAACTCCTGGGAGATTAAATGATTTGC
TTGAGAGAGGTAGAGTCTCATTACAGATGGTAAGATTCTTGGCACTTGATGAGGCGGACAGAAT
GCTGGACATGGGTTTTGAACCACAAATCAGGAAGATCGTTCAGCAGATGGACATGCCTCCTCCT
GGTGTCCGGCAGACAATGTTGTTCAGTGCTACATTTCCTAGGGAGATACAGAGACTTGCATCTG
ATTTTCTTTCAAATTACATATTTCTGGCTGTTGGAAGAGTGGGTTCAAGTACGGATTTAATTGT
CCAAAGAGTAGAGTTTGTTCATGATTCTGACAAAAGAAGCCATCTAATGGACCTTCTTCATGCC
CAGAGGGAGAATGGTAACCAAGGAAAG
						
						Genomic sequence
						
							ATTAGGGAGCTTGAAAGAGGAGTTGATATTCTTGTTGCAACTCCTGGGAGATTAAATGATTTGC
TTGAGAGAGGTAGAGTCTCATTACAGATGGTAAGATTCTTGGCACTTGATGAGGCGGACAGAAT
GCTGGACATGGGTTTTGAACCACAAATCAGGAAGATCGTTCAGCAGATGGACATGCCTCCTCCT
GGTGTCCGGCAGACAATGTTGTTCAGTGCTACATTTCCTAGGGAGATACAGGTTTGTGGAACTC
GTTCACATGCCATTTCTATGTTTTCTCCTTACCGGAGAAGATTCTCAGCTATCTCTATCTTCAG
TCTTTCTTGCTCTGTTAGTGTCTTCATTGTTATGGGACTACGTTATTTGGGTCTTTTGGGTCTC
CAGTACAATTGTTCTGAGAATTATTATCTTTTAAATCAACTTGGATAAATCTGACCGAGCACTT
ATCCTTAACTTGTGTAAATGATCTGATATTTGCATGGAGTGAGGAAGAATATAGCGGTTCTTAT
GTTAGTGATATGAAAGAACAAGATAGCGATTCATTTCAATGAAATTTAATATACTTGGGAGTAA
GAGGGAACTAAGGGTAGCTGCTTGTTGTAGGTCCGTGATTGTTCTATAACTGAAGAAAAGAGTG
AGATTTGGTAGGTCTGGGAAATGAGAAGGATGATCGGTACATAATCTTGTTTTCCTTTATTACT
GGAGGGTTCAATTCGTTGTCTAAATAATGTTTATTGTTTAAGTTGACACTACCAAAATTTTGGC
TCTTAAAATTACAAGATAGAAGTTGCGTACTGTGCAGCAAAGGAATCTTTTACATTCCATATGC
ACTTAATTATGATTTTGTTTTTGTGTGCAGAGACTTGCATCTGATTTTCTTTCAAATTACATAT
TTCTGGCTGTTGGAAGAGTGGGTTCAAGTACGGATTTAATTGTCCAAAGAGTAGAGTTTGTTCA
TGATTCTGACAAAAGAAGCCATCTAATGGACCTTCTTCATGCCCAGAGGGAGAATGGTAACCAA
GGAAAG

Sequences
Splice junction sequence	TTTAATTGTCCAAAGAGTAGAGTTTGTTCATGATTCTGACAAAAGAAGCCATCTAATGGACCTT CTTCATGCCCAGAGGGAGAATGGTAACCAAGGAAAGattagggagcttgaaagaggagttgata ttcttgttgcaactcctgggagattaaatgatttgcttgagagaggtagagtctcattacagat ggtaagat
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: 411 Transcript exons: 21658341-21658583,21659203-21659370 ATTAGGGAGCTTGAAAGAGGAGTTGATATTCTTGTTGCAACTCCTGGGAGATTAAATGATTTGC TTGAGAGAGGTAGAGTCTCATTACAGATGGTAAGATTCTTGGCACTTGATGAGGCGGACAGAAT GCTGGACATGGGTTTTGAACCACAAATCAGGAAGATCGTTCAGCAGATGGACATGCCTCCTCCT GGTGTCCGGCAGACAATGTTGTTCAGTGCTACATTTCCTAGGGAGATACAGAGACTTGCATCTG ATTTTCTTTCAAATTACATATTTCTGGCTGTTGGAAGAGTGGGTTCAAGTACGGATTTAATTGT CCAAAGAGTAGAGTTTGTTCATGATTCTGACAAAAGAAGCCATCTAATGGACCTTCTTCATGCC CAGAGGGAGAATGGTAACCAAGGAAAG
Genomic sequence	ATTAGGGAGCTTGAAAGAGGAGTTGATATTCTTGTTGCAACTCCTGGGAGATTAAATGATTTGC TTGAGAGAGGTAGAGTCTCATTACAGATGGTAAGATTCTTGGCACTTGATGAGGCGGACAGAAT GCTGGACATGGGTTTTGAACCACAAATCAGGAAGATCGTTCAGCAGATGGACATGCCTCCTCCT GGTGTCCGGCAGACAATGTTGTTCAGTGCTACATTTCCTAGGGAGATACAGGTTTGTGGAACTC GTTCACATGCCATTTCTATGTTTTCTCCTTACCGGAGAAGATTCTCAGCTATCTCTATCTTCAG TCTTTCTTGCTCTGTTAGTGTCTTCATTGTTATGGGACTACGTTATTTGGGTCTTTTGGGTCTC CAGTACAATTGTTCTGAGAATTATTATCTTTTAAATCAACTTGGATAAATCTGACCGAGCACTT ATCCTTAACTTGTGTAAATGATCTGATATTTGCATGGAGTGAGGAAGAATATAGCGGTTCTTAT GTTAGTGATATGAAAGAACAAGATAGCGATTCATTTCAATGAAATTTAATATACTTGGGAGTAA GAGGGAACTAAGGGTAGCTGCTTGTTGTAGGTCCGTGATTGTTCTATAACTGAAGAAAAGAGTG AGATTTGGTAGGTCTGGGAAATGAGAAGGATGATCGGTACATAATCTTGTTTTCCTTTATTACT GGAGGGTTCAATTCGTTGTCTAAATAATGTTTATTGTTTAAGTTGACACTACCAAAATTTTGGC TCTTAAAATTACAAGATAGAAGTTGCGTACTGTGCAGCAAAGGAATCTTTTACATTCCATATGC ACTTAATTATGATTTTGTTTTTGTGTGCAGAGACTTGCATCTGATTTTCTTTCAAATTACATAT TTCTGGCTGTTGGAAGAGTGGGTTCAAGTACGGATTTAATTGTCCAAAGAGTAGAGTTTGTTCA TGATTCTGACAAAAGAAGCCATCTAATGGACCTTCTTCATGCCCAGAGGGAGAATGGTAACCAA GGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.378139361

Conservation Information
Conserved circRNAs	NA
PMCS	0.378139361

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR415 						
					
						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-miR415
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT3G58570_circ_g.3

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