Plant Circular RNA Database

Detail information of 3_circ_ag.4

			
						 General Information
					
						CircRNA Name
						3_circ_ag.4
					
						ID in PlantcircBase
						ath_circ_028931
					
						Alias
						Ath_circ_FC2487
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 23390331-23396479  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							AT3G63340_circ_g.1 AT3G63340_circ_g.2 AT3G63340_circ_g.3 AT3G63340_circ_g.4 AT3G63340_circ_g.5 AT3G63340_circ_g.6 AT3G63340_circ_g.7 AT3G63340_circ_g.8 AT3G63340_circ_g.9 AT3G63340_circ_g.10 						
					
						Support reads
						25
					
						Tissues
						root, aerial
					
						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  
						
							CT-AC							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
						NA

General Information
CircRNA Name	3_circ_ag.4
ID in PlantcircBase	ath_circ_028931
Alias	Ath_circ_FC2487
Organism	Arabidpsis thaliana
Position	chr3: 23390331-23396479 JBrowse»
Reference genome	TAIR10.38
Type	ag-circRNA
Identification method	CIRI
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	AT3G63340_circ_g.1 AT3G63340_circ_g.2 AT3G63340_circ_g.3 AT3G63340_circ_g.4 AT3G63340_circ_g.5 AT3G63340_circ_g.6 AT3G63340_circ_g.7 AT3G63340_circ_g.8 AT3G63340_circ_g.9 AT3G63340_circ_g.10
Support reads	25
Tissues	root, aerial
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	CT-AC 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	NA

			
						 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  
						
							CAACTTCTCAAAGATGCCATCAGATGACACTACCAGGAAGCTGTCATTAGCCACTAGAGGCTGC
CAGTCCATCACCTCAGGTGCAGAGATGACACCATAActtctataagtaaggtcaccaatcgaac
gggagacagccagctgaccattcacccttggcacaccggcccacttggtgacataacctcctgc
agctttca

									
								

					

						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: 189
Transcript exons: 23390331-23390353,23396314-23396479
CTTCTATAAGTAAGGTCACCAATCACTCCTGCTCCAGAGCTAGTTTGATTGTTTACTTCCCACA
AAAGATCACATACTTCTTGCACCTCCAACTTCTCAAAGATGCCATCAGATGACACTACCAGGAA
GCTGTCATTAGCCACTAGAGGCTGCCAGTCCATCACCTCAGGTGCAGAGATGACACCATAA
Transcript length: 193
Transcript exons: 23390331-23390365,23396322-23396479
CTTCTATAAGTAAGGTCACCAATCGAACGGGAGACCTCCAGAGCTAGTTTGATTGTTTACTTCC
CACAAAAGATCACATACTTCTTGCACCTCCAACTTCTCAAAGATGCCATCAGATGACACTACCA
GGAAGCTGTCATTAGCCACTAGAGGCTGCCAGTCCATCACCTCAGGTGCAGAGATGACACCATA
A
Transcript length: 198
Transcript exons: 23390331-23390360,23396312-23396479
CTTCTATAAGTAAGGTCACCAATCGAACGGGGCACTCCTGCTCCAGAGCTAGTTTGATTGTTTA
CTTCCCACAAAAGATCACATACTTCTTGCACCTCCAACTTCTCAAAGATGCCATCAGATGACAC
TACCAGGAAGCTGTCATTAGCCACTAGAGGCTGCCAGTCCATCACCTCAGGTGCAGAGATGACA
CCATAA
Transcript length: 203
Transcript exons: 23390331-23390363,23396310-23396479
CTTCTATAAGTAAGGTCACCAATCGAACGGGAGAAGGCACTCCTGCTCCAGAGCTAGTTTGATT
GTTTACTTCCCACAAAAGATCACATACTTCTTGCACCTCCAACTTCTCAAAGATGCCATCAGAT
GACACTACCAGGAAGCTGTCATTAGCCACTAGAGGCTGCCAGTCCATCACCTCAGGTGCAGAGA
TGACACCATAA
Transcript length: 215
Transcript exons: 23390331-23390365,23396300-23396479
CTTCTATAAGTAAGGTCACCAATCGAACGGGAGACGAGCAGTATGAAGGCACTCCTGCTCCAGA
GCTAGTTTGATTGTTTACTTCCCACAAAAGATCACATACTTCTTGCACCTCCAACTTCTCAAAG
ATGCCATCAGATGACACTACCAGGAAGCTGTCATTAGCCACTAGAGGCTGCCAGTCCATCACCT
CAGGTGCAGAGATGACACCATAA
Transcript length: 226
Transcript exons: 23390331-23390360,23396284-23396479
CTTCTATAAGTAAGGTCACCAATCGAACGGGTCTGCCAAAGAAATTGAGCAGTATGAAGGCACT
CCTGCTCCAGAGCTAGTTTGATTGTTTACTTCCCACAAAAGATCACATACTTCTTGCACCTCCA
ACTTCTCAAAGATGCCATCAGATGACACTACCAGGAAGCTGTCATTAGCCACTAGAGGCTGCCA
GTCCATCACCTCAGGTGCAGAGATGACACCATAA
Transcript length: 273
Transcript exons: 23390331-23390367,23396244-23396479
CTTCTATAAGTAAGGTCACCAATCGAACGGGAGACAGTGTCCATGCTTCCCTTCTCAAAGGCAG
TATTAACCAAGCAGTCTGCCAAAGAAATTGAGCAGTATGAAGGCACTCCTGCTCCAGAGCTAGT
TTGATTGTTTACTTCCCACAAAAGATCACATACTTCTTGCACCTCCAACTTCTCAAAGATGCCA
TCAGATGACACTACCAGGAAGCTGTCATTAGCCACTAGAGGCTGCCAGTCCATCACCTCAGGTG
CAGAGATGACACCATAA
						
					

						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.						
					

			
		

Sequences
Splice junction sequence	CAACTTCTCAAAGATGCCATCAGATGACACTACCAGGAAGCTGTCATTAGCCACTAGAGGCTGC CAGTCCATCACCTCAGGTGCAGAGATGACACCATAActtctataagtaaggtcaccaatcgaac gggagacagccagctgaccattcacccttggcacaccggcccacttggtgacataacctcctgc agctttca
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: 189 Transcript exons: 23390331-23390353,23396314-23396479 CTTCTATAAGTAAGGTCACCAATCACTCCTGCTCCAGAGCTAGTTTGATTGTTTACTTCCCACA AAAGATCACATACTTCTTGCACCTCCAACTTCTCAAAGATGCCATCAGATGACACTACCAGGAA GCTGTCATTAGCCACTAGAGGCTGCCAGTCCATCACCTCAGGTGCAGAGATGACACCATAA Transcript length: 193 Transcript exons: 23390331-23390365,23396322-23396479 CTTCTATAAGTAAGGTCACCAATCGAACGGGAGACCTCCAGAGCTAGTTTGATTGTTTACTTCC CACAAAAGATCACATACTTCTTGCACCTCCAACTTCTCAAAGATGCCATCAGATGACACTACCA GGAAGCTGTCATTAGCCACTAGAGGCTGCCAGTCCATCACCTCAGGTGCAGAGATGACACCATA A Transcript length: 198 Transcript exons: 23390331-23390360,23396312-23396479 CTTCTATAAGTAAGGTCACCAATCGAACGGGGCACTCCTGCTCCAGAGCTAGTTTGATTGTTTA CTTCCCACAAAAGATCACATACTTCTTGCACCTCCAACTTCTCAAAGATGCCATCAGATGACAC TACCAGGAAGCTGTCATTAGCCACTAGAGGCTGCCAGTCCATCACCTCAGGTGCAGAGATGACA CCATAA Transcript length: 203 Transcript exons: 23390331-23390363,23396310-23396479 CTTCTATAAGTAAGGTCACCAATCGAACGGGAGAAGGCACTCCTGCTCCAGAGCTAGTTTGATT GTTTACTTCCCACAAAAGATCACATACTTCTTGCACCTCCAACTTCTCAAAGATGCCATCAGAT GACACTACCAGGAAGCTGTCATTAGCCACTAGAGGCTGCCAGTCCATCACCTCAGGTGCAGAGA TGACACCATAA Transcript length: 215 Transcript exons: 23390331-23390365,23396300-23396479 CTTCTATAAGTAAGGTCACCAATCGAACGGGAGACGAGCAGTATGAAGGCACTCCTGCTCCAGA GCTAGTTTGATTGTTTACTTCCCACAAAAGATCACATACTTCTTGCACCTCCAACTTCTCAAAG ATGCCATCAGATGACACTACCAGGAAGCTGTCATTAGCCACTAGAGGCTGCCAGTCCATCACCT CAGGTGCAGAGATGACACCATAA Transcript length: 226 Transcript exons: 23390331-23390360,23396284-23396479 CTTCTATAAGTAAGGTCACCAATCGAACGGGTCTGCCAAAGAAATTGAGCAGTATGAAGGCACT CCTGCTCCAGAGCTAGTTTGATTGTTTACTTCCCACAAAAGATCACATACTTCTTGCACCTCCA ACTTCTCAAAGATGCCATCAGATGACACTACCAGGAAGCTGTCATTAGCCACTAGAGGCTGCCA GTCCATCACCTCAGGTGCAGAGATGACACCATAA Transcript length: 273 Transcript exons: 23390331-23390367,23396244-23396479 CTTCTATAAGTAAGGTCACCAATCGAACGGGAGACAGTGTCCATGCTTCCCTTCTCAAAGGCAG TATTAACCAAGCAGTCTGCCAAAGAAATTGAGCAGTATGAAGGCACTCCTGCTCCAGAGCTAGT TTGATTGTTTACTTCCCACAAAAGATCACATACTTCTTGCACCTCCAACTTCTCAAAGATGCCA TCAGATGACACTACCAGGAAGCTGTCATTAGCCACTAGAGGCTGCCAGTCCATCACCTCAGGTG CAGAGATGACACCATAA
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.711863349

Conservation Information
Conserved circRNAs	NA
PMCS	0.711863349

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR5021 						
					
						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	ath-miR5021
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of 3_circ_ag.4

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