Plant Circular RNA Database

Detail information of AT1G03960_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G03960_circ_g.3
					
						ID in PlantcircBase
						ath_circ_000520
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 1014951-1017481  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT1G03960						
					
						Parent gene annotation
						
							Probable serine/threonine protein phosphatase 2A regulatory subu
nit B''epsilon
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G03910_circ_g.1 AT1G03910_circ_g.2 AT1G03910_circ_g.3 AT1G03910_circ_g.4 AT1G03910_circ_g.5 AT1G03910_circ_g.6 AT1G03910_circ_g.7 AT1G03910_circ_g.8 1_circ_ag.9 AT1G03910_circ_g.10 AT1G03930_circ_g.1 AT1G03930_circ_g.2 AT1G03930_circ_g.3 AT1G03960_circ_g.1 AT1G03960_circ_g.2 AT1G03970_circ_g.1 AT1G03980_circ_g.1 AT1G04010_circ_g.1 AT1G04010_circ_g.2 AT1G04010_circ_g.3 AT1G04020_circ_g.1 AT1G04020_circ_g.2 AT1G04020_circ_g.3 AT1G04020_circ_g.4 AT1G04020_circ_g.5 AT1G04020_circ_g.6 AT1G04020_circ_g.7 AT1G04040_circ_g.1 AT1G04040_circ_g.2 AT1G04050_circ_g.1 AT1G04080_circ_g.1 AT1G04080_circ_g.2 AT1G04080_circ_g.3 AT1G04080_circ_g.4 AT1G04080_circ_g.5 AT1G04080_circ_g.6 AT1G04080_circ_g.7 AT1G04080_circ_g.8 AT1G04080_circ_g.9 AT1G04080_circ_g.10 AT1G04080_circ_g.11 AT1G04080_circ_g.12 AT1G04120_circ_g.1 AT1G04120_circ_g.2 AT1G04120_circ_g.3 AT1G04120_circ_g.4 AT1G04120_circ_g.5 AT1G04120_circ_g.6 AT1G04120_circ_g.7 AT1G04130_circ_g.1 AT1G04130_circ_g.2 AT1G04140_circ_g.1 AT1G04140_circ_g.2 AT1G04140_circ_g.3 AT1G04140_circ_g.4 AT1G04140_circ_g.5 AT1G04140_circ_g.6 						
					
						Support reads
						4
					
						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  
						
							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
						AT1G03960.6:9
AT1G03960.2:9
AT1G03960.5:8
AT1G03960.7:9
AT1G03960.4:9
AT1G03960.1:9
AT1G03960.3:9

General Information
CircRNA Name	AT1G03960_circ_g.3
ID in PlantcircBase	ath_circ_000520
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 1014951-1017481 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT1G03960
Parent gene annotation	Probable serine/threonine protein phosphatase 2A regulatory subu nit B''epsilon
Parent gene strand	+
Alternative splicing	AT1G03910_circ_g.1 AT1G03910_circ_g.2 AT1G03910_circ_g.3 AT1G03910_circ_g.4 AT1G03910_circ_g.5 AT1G03910_circ_g.6 AT1G03910_circ_g.7 AT1G03910_circ_g.8 1_circ_ag.9 AT1G03910_circ_g.10 AT1G03930_circ_g.1 AT1G03930_circ_g.2 AT1G03930_circ_g.3 AT1G03960_circ_g.1 AT1G03960_circ_g.2 AT1G03970_circ_g.1 AT1G03980_circ_g.1 AT1G04010_circ_g.1 AT1G04010_circ_g.2 AT1G04010_circ_g.3 AT1G04020_circ_g.1 AT1G04020_circ_g.2 AT1G04020_circ_g.3 AT1G04020_circ_g.4 AT1G04020_circ_g.5 AT1G04020_circ_g.6 AT1G04020_circ_g.7 AT1G04040_circ_g.1 AT1G04040_circ_g.2 AT1G04050_circ_g.1 AT1G04080_circ_g.1 AT1G04080_circ_g.2 AT1G04080_circ_g.3 AT1G04080_circ_g.4 AT1G04080_circ_g.5 AT1G04080_circ_g.6 AT1G04080_circ_g.7 AT1G04080_circ_g.8 AT1G04080_circ_g.9 AT1G04080_circ_g.10 AT1G04080_circ_g.11 AT1G04080_circ_g.12 AT1G04120_circ_g.1 AT1G04120_circ_g.2 AT1G04120_circ_g.3 AT1G04120_circ_g.4 AT1G04120_circ_g.5 AT1G04120_circ_g.6 AT1G04120_circ_g.7 AT1G04130_circ_g.1 AT1G04130_circ_g.2 AT1G04140_circ_g.1 AT1G04140_circ_g.2 AT1G04140_circ_g.3 AT1G04140_circ_g.4 AT1G04140_circ_g.5 AT1G04140_circ_g.6
Support reads	4
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	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	AT1G03960.6:9 AT1G03960.2:9 AT1G03960.5:8 AT1G03960.7:9 AT1G03960.4:9 AT1G03960.1:9 AT1G03960.3:9

			
						 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  
						
							GTATGCGAGATTGTCAATGGAGGAAGATGTAGATGAAGTCTCAAATGGGAGTGCAGATGTCTGG
GATGAACCACTCGAACCTCCATTTTAGTCCATAGTGaattcaaatccattacgaaacaagtctg
caagctgccttcttttctttctcctgcacttttcagaaagatcgatcccaattgcactgatata
gttacaag

									
								

					

						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
						
							AATTCAAATCCATTACGAAACAAGTCTGCAAGCTGCCTTCTTTTCTTTCTCCTGCACTTTTCAG
AAAGATCGATCCCAATTGCACTGATATAGTTACAAGGTAGCTCCATATATGACTCATTTATTCT
TTTATAAAATGTTTTTTAAAAGTAGTATGAGAACTTTGGGTGCTTGCTCTATTTTCTTATAAAG
CTTTGTTGGGTAATTGGTGCGGTACTAATGTTTGCTGATTGACCAATTGTCCTCAGGGATGCAT
TTATCAAGTATTGGATTGATGGCAATATGTTAACTATGGACACAGCCTCCCAGATATATAATAT
ACTAAGGCAGCAGGGCTGCAGCTATCTCAGACAGGTCTTTTTGTGATTCTTCTCCCGCTTTTCT
CCAACCGCGTTCTGATTTATTTTCCAACAATTGTCTTCCTTTTCTTAACCCATTGTGCCATACA
TTTTGATCATTTCTTGGATTTGGCTACAGGCAGACTTCAAACCAGTTCTTGATGAGCTTCTGGC
AACACATCCTGGATTAGAATTTTTGAGGACGATAAGCGAGTTTCAAGAAAGATATGGTAGGAAC
CATTGATTTGTGACTTACTGATTGTCATGGTGTTAAAAATGATGAAACCTACTCAATAAGACGT
TCTTTCTGTGCATACATCTTTATATCTCTACTAGATATGTACTTATGTTAGATTCATACTTGTA
CTAATTTTAATCCTTTGTTGATTACCCAGCTGAAACGGTCATCTACAGAATATTTTACTACATT
AACAGATCCGGAACTGGCTGCCTTACTCTTAGAGAGCTGAGACGTGGAAATTTAATTGCTGCTA
TGCAACAACTTGATGAAGAGGACGACATTAATAAAATTATTAGGTGAGTTTATTTTTTCTTTTC
ATAATTTCCTAACAATAAGTATTTGAAATTCAAACATATTCTGTTGTTATATAAGGAGTAAACA
AGCTTACGAAAATATATTAAAGTTCGAGGGTTTATCACATATGTAACATTAAACAGTTCAAAAT
GGAAGAGCTATATGAGTATTGGCTTATACCTTCATATTGCTTCTGTAACAGAACTTATGCCTGA
TTTTACCATTTGCAATCATGTCGTTTCTTTTAATTTTCAGGTACTTCTCCTATGAGCACTTCTA
CGTGATATACTGCAAATTTTGGGAACTTGATGGTGACCATGATTGTTTTATTGATAAGGACAAT
CTCATCAAATATGGTAATAATGCCCTTACCTACAGGATTGTTGATAGAATATTTTCACAGGTTG
GTTCCCAAAATTGTTCCTGCCTAGACCTTCTTAAAAGCTAAGTTATATAGTATGATGTGATCCT
TTTTATTTGATCTCCATGCGTCTTGTGGCTATGTTTCTCTTTTAGATTCCAAGGAAGTTTACGA
GTAAAGTTGAAGGGAAGATGAGTTATGAAGATTTTGTGTACTTCATTCTCGCTGAGGAAGACAA
GTCTTCCGAGCCTAGTCTTGAGTATTGGTACACATCTCCCCCTCCGTGTTGATATTGGTTTTCC
TTAATGAATGTTGCCCCTTGGTTTAGATCACAAGATCTTGATATATATACTACAACGGAGTCAA
AACCAGTGACTTGAGGACTTGTTACTTGTAACAAGTCCTCTTCCTCAGATATATTTAGTAATCA
TTGTATGGTACCATTTTTTCATGAACATAGGATCCTTGTTTATACTCGGGCACTAACAATCTAA
CAATCTGATACTAGTTTATAGCCTAGTATGCTCATCTATCTATTATGGATGTCAAAACTCAATA
TTTTTGCAAGTCCGTGTATTTTACTTGACACTGATTGAAATTTTCCGTGCAGGTTCAAATGCGT
AGACTTGGATGGAAATGGGGTAATCACTTCAAACGAAATGCAGTTTTTCTTCGAAGAGCAGCTG
CATCGCATGGAATGCATAACCCAGGAAGCTGTTCTTTTCAGTGATATCCTATGTCAAATAATTG
ACATGATTGGACCCGAGGTTAGTTACTTTACAAACCAGAACATGGTTGTTTGATTTTTCCGAGC
TTTTTTGTTATTTATCATTTATTTGACTGGAATCATCTATATGGTGGATGTCCTTGCAGAAGGA
GAACTGTATCACCCTCCAGGATCTGAAAGGATCGAAACTTTCAGCAAACGTTTTCAATATACTC
TTCAACCTTAATAAGTTCATGGCATTTGAAACACGTGACCCATTTCTCATTCGCCAGGTAAGTT
TGGCTTACCAGTGGAGTTTTTATAGCACTCAAGAGGGAAAAAAATAACAAAGAATATGACTTCT
TTTAACTGCTAAAGGCAGTTTGTAGTAGTTCGGATTGAGGCAATTAGAACAAGTATAATTCTCT
TTCATTGCTGTAGGAACGGGAAGATCCAAATTTGACAGAGTGGGATCGATTTGCTCAGAGAGAG
TATGCGAGATTGTCAATGGAGGAAGATGTAGATGAAGTCTCAAATGGGAGTGCAGATGTCTGGG
ATGAACCACTCGAACCTCCATTTTAGTCCATAGTG
						
					

			
		

Sequences
Splice junction sequence	GTATGCGAGATTGTCAATGGAGGAAGATGTAGATGAAGTCTCAAATGGGAGTGCAGATGTCTGG GATGAACCACTCGAACCTCCATTTTAGTCCATAGTGaattcaaatccattacgaaacaagtctg caagctgccttcttttctttctcctgcacttttcagaaagatcgatcccaattgcactgatata gttacaag
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	AATTCAAATCCATTACGAAACAAGTCTGCAAGCTGCCTTCTTTTCTTTCTCCTGCACTTTTCAG AAAGATCGATCCCAATTGCACTGATATAGTTACAAGGTAGCTCCATATATGACTCATTTATTCT TTTATAAAATGTTTTTTAAAAGTAGTATGAGAACTTTGGGTGCTTGCTCTATTTTCTTATAAAG CTTTGTTGGGTAATTGGTGCGGTACTAATGTTTGCTGATTGACCAATTGTCCTCAGGGATGCAT TTATCAAGTATTGGATTGATGGCAATATGTTAACTATGGACACAGCCTCCCAGATATATAATAT ACTAAGGCAGCAGGGCTGCAGCTATCTCAGACAGGTCTTTTTGTGATTCTTCTCCCGCTTTTCT CCAACCGCGTTCTGATTTATTTTCCAACAATTGTCTTCCTTTTCTTAACCCATTGTGCCATACA TTTTGATCATTTCTTGGATTTGGCTACAGGCAGACTTCAAACCAGTTCTTGATGAGCTTCTGGC AACACATCCTGGATTAGAATTTTTGAGGACGATAAGCGAGTTTCAAGAAAGATATGGTAGGAAC CATTGATTTGTGACTTACTGATTGTCATGGTGTTAAAAATGATGAAACCTACTCAATAAGACGT TCTTTCTGTGCATACATCTTTATATCTCTACTAGATATGTACTTATGTTAGATTCATACTTGTA CTAATTTTAATCCTTTGTTGATTACCCAGCTGAAACGGTCATCTACAGAATATTTTACTACATT AACAGATCCGGAACTGGCTGCCTTACTCTTAGAGAGCTGAGACGTGGAAATTTAATTGCTGCTA TGCAACAACTTGATGAAGAGGACGACATTAATAAAATTATTAGGTGAGTTTATTTTTTCTTTTC ATAATTTCCTAACAATAAGTATTTGAAATTCAAACATATTCTGTTGTTATATAAGGAGTAAACA AGCTTACGAAAATATATTAAAGTTCGAGGGTTTATCACATATGTAACATTAAACAGTTCAAAAT GGAAGAGCTATATGAGTATTGGCTTATACCTTCATATTGCTTCTGTAACAGAACTTATGCCTGA TTTTACCATTTGCAATCATGTCGTTTCTTTTAATTTTCAGGTACTTCTCCTATGAGCACTTCTA CGTGATATACTGCAAATTTTGGGAACTTGATGGTGACCATGATTGTTTTATTGATAAGGACAAT CTCATCAAATATGGTAATAATGCCCTTACCTACAGGATTGTTGATAGAATATTTTCACAGGTTG GTTCCCAAAATTGTTCCTGCCTAGACCTTCTTAAAAGCTAAGTTATATAGTATGATGTGATCCT TTTTATTTGATCTCCATGCGTCTTGTGGCTATGTTTCTCTTTTAGATTCCAAGGAAGTTTACGA GTAAAGTTGAAGGGAAGATGAGTTATGAAGATTTTGTGTACTTCATTCTCGCTGAGGAAGACAA GTCTTCCGAGCCTAGTCTTGAGTATTGGTACACATCTCCCCCTCCGTGTTGATATTGGTTTTCC TTAATGAATGTTGCCCCTTGGTTTAGATCACAAGATCTTGATATATATACTACAACGGAGTCAA AACCAGTGACTTGAGGACTTGTTACTTGTAACAAGTCCTCTTCCTCAGATATATTTAGTAATCA TTGTATGGTACCATTTTTTCATGAACATAGGATCCTTGTTTATACTCGGGCACTAACAATCTAA CAATCTGATACTAGTTTATAGCCTAGTATGCTCATCTATCTATTATGGATGTCAAAACTCAATA TTTTTGCAAGTCCGTGTATTTTACTTGACACTGATTGAAATTTTCCGTGCAGGTTCAAATGCGT AGACTTGGATGGAAATGGGGTAATCACTTCAAACGAAATGCAGTTTTTCTTCGAAGAGCAGCTG CATCGCATGGAATGCATAACCCAGGAAGCTGTTCTTTTCAGTGATATCCTATGTCAAATAATTG ACATGATTGGACCCGAGGTTAGTTACTTTACAAACCAGAACATGGTTGTTTGATTTTTCCGAGC TTTTTTGTTATTTATCATTTATTTGACTGGAATCATCTATATGGTGGATGTCCTTGCAGAAGGA GAACTGTATCACCCTCCAGGATCTGAAAGGATCGAAACTTTCAGCAAACGTTTTCAATATACTC TTCAACCTTAATAAGTTCATGGCATTTGAAACACGTGACCCATTTCTCATTCGCCAGGTAAGTT TGGCTTACCAGTGGAGTTTTTATAGCACTCAAGAGGGAAAAAAATAACAAAGAATATGACTTCT TTTAACTGCTAAAGGCAGTTTGTAGTAGTTCGGATTGAGGCAATTAGAACAAGTATAATTCTCT TTCATTGCTGTAGGAACGGGAAGATCCAAATTTGACAGAGTGGGATCGATTTGCTCAGAGAGAG TATGCGAGATTGTCAATGGAGGAAGATGTAGATGAAGTCTCAAATGGGAGTGCAGATGTCTGGG ATGAACCACTCGAACCTCCATTTTAGTCCATAGTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.136273315

Conservation Information
Conserved circRNAs	NA
PMCS	0.136273315

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

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT1G03960_circ_g.3

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