Plant Circular RNA Database

Detail information of AT1G65260_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT1G65260_circ_g.4
					
						ID in PlantcircBase
						ath_circ_008766
					
						Alias
						1:24236840-24238354
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 24236840-24238354  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G65260						
					
						Parent gene annotation
						
							Membrane-associated protein VIPP1, chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							1_circ_ag.3 AT1G65080_circ_g.1 AT1G65130_circ_g.1 AT1G65220_circ_g.1 AT1G65220_circ_g.2 AT1G65220_circ_g.3 AT1G65220_circ_g.4 AT1G65220_circ_g.5 AT1G65220_circ_g.6 AT1G65230_circ_g.1 AT1G65230_circ_g.2 AT1G65230_circ_g.3 AT1G65230_circ_g.4 AT1G65230_circ_g.5 AT1G65260_circ_g.1 AT1G65260_circ_g.2 AT1G65260_circ_g.3 AT1G65260_circ_g.5 AT1G65260_circ_g.6 AT1G65260_circ_g.7 AT1G65260_circ_g.8 AT1G65260_circ_g.9 AT1G65260_circ_g.10 AT1G65260_circ_g.11 AT1G65260_circ_g.12 AT1G65260_circ_g.13 AT1G65260_circ_g.14 AT1G65260_circ_g.15 AT1G65270_circ_g.1 AT1G65270_circ_g.2 AT1G65270_circ_g.3 AT1G65270_circ_g.4 AT1G65270_circ_g.5 AT1G65270_circ_g.6 AT1G65280_circ_g.1 AT1G65280_circ_g.2 AT1G65280_circ_g.3 AT1G65290_circ_g.1 AT1G65290_circ_g.2 AT1G65295_circ_g.1 AT1G65320_circ_g.1 AT1G65350_circ_g.1 AT1G65370_circ_g.1 AT1G65370_circ_g.2 						
					
						Support reads
						1/2
					
						Tissues
						root;flower
					
						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
						AT1G65260.2:5
AT1G65260.1:5

General Information
CircRNA Name	AT1G65260_circ_g.4
ID in PlantcircBase	ath_circ_008766
Alias	1:24236840-24238354
Organism	Arabidpsis thaliana
Position	chr1: 24236840-24238354 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G65260
Parent gene annotation	Membrane-associated protein VIPP1, chloroplastic
Parent gene strand	+
Alternative splicing	1_circ_ag.3 AT1G65080_circ_g.1 AT1G65130_circ_g.1 AT1G65220_circ_g.1 AT1G65220_circ_g.2 AT1G65220_circ_g.3 AT1G65220_circ_g.4 AT1G65220_circ_g.5 AT1G65220_circ_g.6 AT1G65230_circ_g.1 AT1G65230_circ_g.2 AT1G65230_circ_g.3 AT1G65230_circ_g.4 AT1G65230_circ_g.5 AT1G65260_circ_g.1 AT1G65260_circ_g.2 AT1G65260_circ_g.3 AT1G65260_circ_g.5 AT1G65260_circ_g.6 AT1G65260_circ_g.7 AT1G65260_circ_g.8 AT1G65260_circ_g.9 AT1G65260_circ_g.10 AT1G65260_circ_g.11 AT1G65260_circ_g.12 AT1G65260_circ_g.13 AT1G65260_circ_g.14 AT1G65260_circ_g.15 AT1G65270_circ_g.1 AT1G65270_circ_g.2 AT1G65270_circ_g.3 AT1G65270_circ_g.4 AT1G65270_circ_g.5 AT1G65270_circ_g.6 AT1G65280_circ_g.1 AT1G65280_circ_g.2 AT1G65280_circ_g.3 AT1G65290_circ_g.1 AT1G65290_circ_g.2 AT1G65295_circ_g.1 AT1G65320_circ_g.1 AT1G65350_circ_g.1 AT1G65370_circ_g.1 AT1G65370_circ_g.2
Support reads	1/2
Tissues	root;flower
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	AT1G65260.2:5 AT1G65260.1:5

			
						 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  
						
							AAGTTATTACCTTTTTTCTTAACAGGACAACGCTACTGCTTTGAAAACTCAACTAGATCAGCAA
AAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGGgtggagcgctgagagtgaatgtgttgag
attagcttgtgataatagactcaggtgcaatggtcatggtgctactatgaatctttttgaacga
ttttctag

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							GTGGAGCGCTGAGAGTGAATGTGTTGAGATTAGCTTGTGATAATAGACTCAGGTGCAATGGTCA
TGGTGCTACTATGAATCTTTTTGAACGATTTTCTAGAGTGGTCAAGGTACTTATACCCTTTCTC
ATTCTGTATTTGACTGTCATTATGCATTGGAGTTCATTAATCAGTTCTCTTGTTTATTTTTCAT
TTTAATAAGCGAAGTCATATGCAAATGCGCTCATAAGCTCTTTTGAAGACCCGGAGAAAATCCT
GGAGCAAACTGTCATTGAAATGAATAGTGATTTGACAAAGATGCGTCAAGCCACTGCACAGGTG
CACTTCTTACTCTTGAACAAACTTTATACATTTTCCTGTACGATATTTTTCTTCTTCATTTTTT
TACTACAGCATGGTTGGCCCCTATTTATGAGATTAGCTAACTTGTGTATTATCAACGTGTCTGA
AGGTTTTAGCATCACAAAAGCAGTTACAGAACAAATATAAAGCTGCACAGCAGTCTTCTGATGA
TTGGTATGTGTGCTTTTGCGTGGACCTTGCTTCCATACCTAAATTCTTCTCTGAGCTGATTATT
CTTACATGTTACACGTTTAAATAGGTACAAAAGAGCACAACTTGCTCTTGCAAAAGGAGATGAG
GATCTTGCACGTGAGGCCCTTAAACGACGAAAGTCTTTTGCTGTAGGTTATATCTATCCATTCT
TTTGTCCACCAGTTTTCTGTTTCTTAAGTTTGCTTACTCCAACAAATGAAAGACCCTAATCGTT
TAGCGCATCGAGCGATTTGAGGCTGATCTCTTGGTTTTCTGCAAGGTTTAGTTAGGTGGTGGTG
AAAGTAAAATGGAAAAATTTAGATATCTAAGTATTCTGTAATTCTCCTCAGGACTTGCCCCCTT
TTCCAATCATTTTTTGATGCAATAGAGCTTGGCAGTGTTTATAGTACTCTTTTGAAATATATTG
TTTGTTGAGTTTGTTAAGGTGATTGCAGTGACAAAAGATATTTTGGATATATATAACACTACAG
ATGCAGCCAAAAACGACCCTTCTGTGTTTCTACATATTAGGATGTTGACTATTGTCTTTCAGTA
TCAGAAAAAAAAATCAAAATCAAATTTTGGTTCTATGTAGAATTTCGGAAACAGCCAAACACGA
TTCTTCAGTGTTTTTTACATATCAGTATCTTGGCTATCATCTTTGATGTGCTTTTGTTTGAGCA
ACAGACCGTATGGCTCTTTTTCAGTTTTGTTGATTTATGTATTTGTGTAACCTTTGCAAATGGC
TAACGAATAATAGGCAGGTAAATTTTCACTATCTTTTACCTGCTGATACCTTATCGACTACTGA
AGTCTCTTGAATACATCCATTCTCTAACTTTATAAAGTTACCTTAAAAAAAAACTAGAACTTTA
GGTTTTGAAGTTATTACCTTTTTTCTTAACAGGACAACGCTACTGCTTTGAAAACTCAACTAGA
TCAGCAAAAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGG
						
					

			
		

Sequences
Splice junction sequence	AAGTTATTACCTTTTTTCTTAACAGGACAACGCTACTGCTTTGAAAACTCAACTAGATCAGCAA AAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGGgtggagcgctgagagtgaatgtgttgag attagcttgtgataatagactcaggtgcaatggtcatggtgctactatgaatctttttgaacga ttttctag
Assembled circRNA sequence	NA 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	NA
Genomic sequence	GTGGAGCGCTGAGAGTGAATGTGTTGAGATTAGCTTGTGATAATAGACTCAGGTGCAATGGTCA TGGTGCTACTATGAATCTTTTTGAACGATTTTCTAGAGTGGTCAAGGTACTTATACCCTTTCTC ATTCTGTATTTGACTGTCATTATGCATTGGAGTTCATTAATCAGTTCTCTTGTTTATTTTTCAT TTTAATAAGCGAAGTCATATGCAAATGCGCTCATAAGCTCTTTTGAAGACCCGGAGAAAATCCT GGAGCAAACTGTCATTGAAATGAATAGTGATTTGACAAAGATGCGTCAAGCCACTGCACAGGTG CACTTCTTACTCTTGAACAAACTTTATACATTTTCCTGTACGATATTTTTCTTCTTCATTTTTT TACTACAGCATGGTTGGCCCCTATTTATGAGATTAGCTAACTTGTGTATTATCAACGTGTCTGA AGGTTTTAGCATCACAAAAGCAGTTACAGAACAAATATAAAGCTGCACAGCAGTCTTCTGATGA TTGGTATGTGTGCTTTTGCGTGGACCTTGCTTCCATACCTAAATTCTTCTCTGAGCTGATTATT CTTACATGTTACACGTTTAAATAGGTACAAAAGAGCACAACTTGCTCTTGCAAAAGGAGATGAG GATCTTGCACGTGAGGCCCTTAAACGACGAAAGTCTTTTGCTGTAGGTTATATCTATCCATTCT TTTGTCCACCAGTTTTCTGTTTCTTAAGTTTGCTTACTCCAACAAATGAAAGACCCTAATCGTT TAGCGCATCGAGCGATTTGAGGCTGATCTCTTGGTTTTCTGCAAGGTTTAGTTAGGTGGTGGTG AAAGTAAAATGGAAAAATTTAGATATCTAAGTATTCTGTAATTCTCCTCAGGACTTGCCCCCTT TTCCAATCATTTTTTGATGCAATAGAGCTTGGCAGTGTTTATAGTACTCTTTTGAAATATATTG TTTGTTGAGTTTGTTAAGGTGATTGCAGTGACAAAAGATATTTTGGATATATATAACACTACAG ATGCAGCCAAAAACGACCCTTCTGTGTTTCTACATATTAGGATGTTGACTATTGTCTTTCAGTA TCAGAAAAAAAAATCAAAATCAAATTTTGGTTCTATGTAGAATTTCGGAAACAGCCAAACACGA TTCTTCAGTGTTTTTTACATATCAGTATCTTGGCTATCATCTTTGATGTGCTTTTGTTTGAGCA ACAGACCGTATGGCTCTTTTTCAGTTTTGTTGATTTATGTATTTGTGTAACCTTTGCAAATGGC TAACGAATAATAGGCAGGTAAATTTTCACTATCTTTTACCTGCTGATACCTTATCGACTACTGA AGTCTCTTGAATACATCCATTCTCTAACTTTATAAAGTTACCTTAAAAAAAAACTAGAACTTTA GGTTTTGAAGTTATTACCTTTTTTCTTAACAGGACAACGCTACTGCTTTGAAAACTCAACTAGA TCAGCAAAAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.117442294

Conservation Information
Conserved circRNAs	NA
PMCS	0.117442294

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

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT1G65260_circ_g.4

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