Plant Circular RNA Database

Detail information of 3_circ_ag.3

			
						 General Information
					
						CircRNA Name
						3_circ_ag.3
					
						ID in PlantcircBase
						ath_circ_024251
					
						Alias
						3:10822825-10993675
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 10822825-10993675  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							3_circ_ag.4 AT3G28830_circ_g.1 AT3G28860_circ_g.1 AT3G28860_circ_g.2 AT3G28860_circ_g.3 AT3G28860_circ_g.4 AT3G28860_circ_g.5 AT3G28860_circ_g.6 3_circ_ag.7 AT3G28900_circ_g.1 AT3G28900_circ_g.2 AT3G28900_circ_g.3 AT3G28910_circ_g.1 3_circ_ig.2 AT3G28930_circ_g.1 AT3G28930_circ_g.2 3_circ_ag.3 3_circ_ag.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 3_circ_ig.8 3_circ_ig.9 AT3G28940_circ_g.1 AT3G28940_circ_g.2 AT3G28940_circ_g.3 AT3G28940_circ_g.4 AT3G28950_circ_g.1 AT3G28970_circ_g.1 AT3G28970_circ_g.2 AT3G28970_circ_g.3 AT3G28970_circ_g.4 AT3G28980_circ_g.1 						
					
						Support reads
						3/5
					
						Tissues
						flower
					
						Exon boundary  
						
							NA-NA							"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.3
ID in PlantcircBase	ath_circ_024251
Alias	3:10822825-10993675
Organism	Arabidpsis thaliana
Position	chr3: 10822825-10993675 JBrowse»
Reference genome	TAIR10.38
Type	ag-circRNA
Identification method	find_circ; CIRI2
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	3_circ_ag.4 AT3G28830_circ_g.1 AT3G28860_circ_g.1 AT3G28860_circ_g.2 AT3G28860_circ_g.3 AT3G28860_circ_g.4 AT3G28860_circ_g.5 AT3G28860_circ_g.6 3_circ_ag.7 AT3G28900_circ_g.1 AT3G28900_circ_g.2 AT3G28900_circ_g.3 AT3G28910_circ_g.1 3_circ_ig.2 AT3G28930_circ_g.1 AT3G28930_circ_g.2 3_circ_ag.3 3_circ_ag.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 3_circ_ig.8 3_circ_ig.9 AT3G28940_circ_g.1 AT3G28940_circ_g.2 AT3G28940_circ_g.3 AT3G28940_circ_g.4 AT3G28950_circ_g.1 AT3G28970_circ_g.1 AT3G28970_circ_g.2 AT3G28970_circ_g.3 AT3G28970_circ_g.4 AT3G28980_circ_g.1
Support reads	3/5
Tissues	flower
Exon boundary	NA-NA "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  
						
							CCTTGCCTTTGTTCTGACTCACAATTTGAGCGTGGATGGTATCTAACTCTTCGAGAGTCTTCAT
CACTTGTTCTTGGTAAGCTTCCATATTCTTCTTTACctctgctgatttgcttccaattctagac
cgcataactcccatcgcacccgatagtttaccagcagcagatttaatcctagaaaataaacctt
ttctttct

									
								

					

						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: 1307
Transcript exons: 10822825-10822852,10829009-10829040,10872908-10872944,10
873574-10873731,10960604-10960735,10968253-10968617,1096
8704-10968783,10976279-10976486,10976733-10976769,109934
46-10993675
CTCTGCTGATTTGCTTCCAATTCTAGACATCAAGAATTGGAAGCAAATCAGCTGAGGTAAACCT
GAGAGCATCATTCTTCTTACTCTTGTTGTGAGGTCTGTCTAAAGCTTCCTGAACAATGCTCTCA
GAGCTAGCATCAAGAGCGCTTGTAGCTTCATCTAGTAACAGAATCTTTGGGTCTTTCAACATCG
CCCTAGCAATTGCAATTCTCTGCTTCTGTCCACCTGAGAGTTGAACACCACGTTCTCCAACCTT
AGCCGTGGAGTTGAGCGGAAACCATGACCGGAGCACATTCGAGAATTAAATTAACAACGGCTGG
TTCTTGGAAACTGCCGTAGACGAAGACGTCGTGCGATGGAGATTGATCGGAGCTTGTCATTGTT
TTTATTCGCAGTAAAAGAGAGTGATCTTTTACAAATCTTGATATAAAAGAAGAAGACATATCTT
GACAACTTCTTCAAGCCGCAGTGGGAGGATCATCGAATACAAACTTCTCAAACTCTTCCCTACT
TCTCCCATCCGGATTCTTCTTCCACTCGATGAATTTCGTCGACGCCTCGATGAATTTATCCATG
TGAAGCCGTCTCCATTCCTACCAAAATCCACACACACATTTCACTAAAACCCCATTAAAGCAAC
ACAACATTCAAGAAGTAAGGTTTCAAACCTCAAAATCCCATTCTCCATACAAATTAGGATCATC
CTTGTTTGCCCATACATAGGTCTCAACTTGCTTCTTCTCCGAAGTATCCAGTCAAAACAACTTC
AACAGTCTTCCTCACATATTCACTTCCTTCAATCATATCTAAATTCTCTAACTGAGAATCTGTT
CCAACAACACATTATTCAAAACCCACTCTTTACTTACTCACTTACTCTCTTCTGCTAAGATTAG
CCAAGCTCATCAAGAATTAATCCCCTGACGATAATAATGATCCTACAGCCTCCTCCATGCTCTT
CCCATTTGGATTCTTGTTCCATTCCAACATTTTTCTAAAAGTCTCCACGAATTTCTCCGCGTGA
ACCACTCTCCATTCCTCCTCGAAATCCCATTCTCCATACATTCTAGGATCATCGAGGAAGAAGA
CGAAGATGCAGACGACTCACTCTGAGCTGCAACCTCAACGAATTGGGTTGTGACTTGTTCCCAT
TTGGTGATTGTCTGCTTAATCTGTACTTGTTGTGTGGGTGTGCATGTCAAAGAAGCCTTGCCTT
TGTTCTGACTCACAATTTGAGCGTGGATGGTATCTAACTCTTCGAGAGTCTTCATCACTTGTTC
TTGGTAAGCTTCCATATTCTTCTTTAC
						
					

						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	CCTTGCCTTTGTTCTGACTCACAATTTGAGCGTGGATGGTATCTAACTCTTCGAGAGTCTTCAT CACTTGTTCTTGGTAAGCTTCCATATTCTTCTTTACctctgctgatttgcttccaattctagac cgcataactcccatcgcacccgatagtttaccagcagcagatttaatcctagaaaataaacctt ttctttct
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: 1307 Transcript exons: 10822825-10822852,10829009-10829040,10872908-10872944,10 873574-10873731,10960604-10960735,10968253-10968617,1096 8704-10968783,10976279-10976486,10976733-10976769,109934 46-10993675 CTCTGCTGATTTGCTTCCAATTCTAGACATCAAGAATTGGAAGCAAATCAGCTGAGGTAAACCT GAGAGCATCATTCTTCTTACTCTTGTTGTGAGGTCTGTCTAAAGCTTCCTGAACAATGCTCTCA GAGCTAGCATCAAGAGCGCTTGTAGCTTCATCTAGTAACAGAATCTTTGGGTCTTTCAACATCG CCCTAGCAATTGCAATTCTCTGCTTCTGTCCACCTGAGAGTTGAACACCACGTTCTCCAACCTT AGCCGTGGAGTTGAGCGGAAACCATGACCGGAGCACATTCGAGAATTAAATTAACAACGGCTGG TTCTTGGAAACTGCCGTAGACGAAGACGTCGTGCGATGGAGATTGATCGGAGCTTGTCATTGTT TTTATTCGCAGTAAAAGAGAGTGATCTTTTACAAATCTTGATATAAAAGAAGAAGACATATCTT GACAACTTCTTCAAGCCGCAGTGGGAGGATCATCGAATACAAACTTCTCAAACTCTTCCCTACT TCTCCCATCCGGATTCTTCTTCCACTCGATGAATTTCGTCGACGCCTCGATGAATTTATCCATG TGAAGCCGTCTCCATTCCTACCAAAATCCACACACACATTTCACTAAAACCCCATTAAAGCAAC ACAACATTCAAGAAGTAAGGTTTCAAACCTCAAAATCCCATTCTCCATACAAATTAGGATCATC CTTGTTTGCCCATACATAGGTCTCAACTTGCTTCTTCTCCGAAGTATCCAGTCAAAACAACTTC AACAGTCTTCCTCACATATTCACTTCCTTCAATCATATCTAAATTCTCTAACTGAGAATCTGTT CCAACAACACATTATTCAAAACCCACTCTTTACTTACTCACTTACTCTCTTCTGCTAAGATTAG CCAAGCTCATCAAGAATTAATCCCCTGACGATAATAATGATCCTACAGCCTCCTCCATGCTCTT CCCATTTGGATTCTTGTTCCATTCCAACATTTTTCTAAAAGTCTCCACGAATTTCTCCGCGTGA ACCACTCTCCATTCCTCCTCGAAATCCCATTCTCCATACATTCTAGGATCATCGAGGAAGAAGA CGAAGATGCAGACGACTCACTCTGAGCTGCAACCTCAACGAATTGGGTTGTGACTTGTTCCCAT TTGGTGATTGTCTGCTTAATCTGTACTTGTTGTGTGGGTGTGCATGTCAAAGAAGCCTTGCCTT TGTTCTGACTCACAATTTGAGCGTGGATGGTATCTAACTCTTCGAGAGTCTTCATCACTTGTTC TTGGTAAGCTTCCATATTCTTCTTTAC
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
						0.368677176

Conservation Information
Conserved circRNAs	NA
PMCS	0.368677176

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR854a ath-miR414 ath-miR5650 ath-miR854d ath-miR5658 ath-miR5021 						
					
						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-miR854a ath-miR414 ath-miR5650 ath-miR854d ath-miR5658 ath-miR5021
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of 3_circ_ag.3

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