Plant Circular RNA Database

Detail information of 3_circ_ag.15

			
						 General Information
					
						CircRNA Name
						3_circ_ag.15
					
						ID in PlantcircBase
						ath_circ_022197
					
						Alias
						At_ciR54
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 5580423-5582569  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						CIRI, find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							AT3G16420_circ_g.1 AT3G16420_circ_g.2 AT3G16420_circ_g.3 3_circ_ag.4 3_circ_ag.5 AT3G16420_circ_g.6 3_circ_ag.7 AT3G16420_circ_g.8 AT3G16420_circ_g.9 AT3G16420_circ_g.10 AT3G16420_circ_g.11 AT3G16420_circ_g.12 AT3G16420_circ_g.13 3_circ_ag.14 3_circ_ag.16 AT3G16430_circ_g.1 AT3G16430_circ_g.2 3_circ_ag.3 AT3G16450_circ_g.1 AT3G16450_circ_g.2 AT3G16450_circ_g.3 AT3G16450_circ_g.4 3_circ_ag.5 AT3G16460_circ_g.1 AT3G16460_circ_g.2 AT3G16460_circ_g.3 AT3G16460_circ_g.4 AT3G16460_circ_g.5 AT3G16460_circ_g.6 						
					
						Support reads
						152/4831
					
						Tissues
						leaf/root, aerial, seed, whole_plant
					
						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
						NA

General Information
CircRNA Name	3_circ_ag.15
ID in PlantcircBase	ath_circ_022197
Alias	At_ciR54
Organism	Arabidpsis thaliana
Position	chr3: 5580423-5582569 JBrowse»
Reference genome	TAIR10.38
Type	ag-circRNA
Identification method	CIRI, find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	AT3G16420_circ_g.1 AT3G16420_circ_g.2 AT3G16420_circ_g.3 3_circ_ag.4 3_circ_ag.5 AT3G16420_circ_g.6 3_circ_ag.7 AT3G16420_circ_g.8 AT3G16420_circ_g.9 AT3G16420_circ_g.10 AT3G16420_circ_g.11 AT3G16420_circ_g.12 AT3G16420_circ_g.13 3_circ_ag.14 3_circ_ag.16 AT3G16430_circ_g.1 AT3G16430_circ_g.2 3_circ_ag.3 AT3G16450_circ_g.1 AT3G16450_circ_g.2 AT3G16450_circ_g.3 AT3G16450_circ_g.4 3_circ_ag.5 AT3G16460_circ_g.1 AT3G16460_circ_g.2 AT3G16460_circ_g.3 AT3G16460_circ_g.4 AT3G16460_circ_g.5 AT3G16460_circ_g.6
Support reads	152/4831
Tissues	leaf/root, aerial, seed, whole_plant
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	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  
						
							CCAAGATGGTATATCGGCTGTTAAGTTTGTATACGACAAAAGCCCTGAGGAGGTCACAGGAGAA
GAACATGGAAAGAGTACTCTACTCGGATTCGAAGAGttcgtacttgactatccaagtgaataca
tcaccgcagtcgatggcacttatgataaaatctttgggagtgatggctcagtcataactatgct
caggttca

									
								

					

						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: 433
Transcript exons: 5580423-5580653,5582368-5582569
TTCGTACTTGACTATCCAAGTGAATACATCACCGCAGTCGATGGCACTTATGATAAAATCTTTG
GGAGTGATGGCTCAGTCATAACTATGCTCAGGTTCAAGACTAATAAGCAAACGTCTCCTCCCTT
TGGACTTGAAGCTGGCACAGTCTTCGAACTCAAAGAGGAAGGCCACAAGATCGTTGGTTTCCAT
GGAAGAGCCGATGTTCTGCTCCACAAAATTGGAGTCCATATTGACTCCTGCCAAGCCGCTACCG
GCACTTGGTAGTGATGATGGAACAGCATGGGATGATGGTGCTTACGTTGGGGTTAAGAAGGTGT
ACGTAGGACAAGCCCAAGATGGTATATCGGCTGTTAAGTTTGTATACGACAAAAGCCCTGAGGA
GGTCACAGGAGAAGAACATGGAAAGAGTACTCTACTCGGATTCGAAGAG
Transcript length: 438
Transcript exons: 5580423-5580658,5582368-5582569
TTCGTACTTGACTATCCAAGTGAATACATCACCGCAGTCGATGGCACTTATGATAAAATCTTTG
GGAGTGATGGCTCAGTCATAACTATGCTCAGGTTCAAGACTAATAAGCAAACGTCTCCTCCCTT
TGGACTTGAAGCTGGCACAGTCTTCGAACTCAAAGAGGAAGGCCACAAGATCGTTGGTTTCCAT
GGAAGAGCCGATGTTCTGCTCCACAAAATTGGAGTCCATGTTCGATTGACTCCTGCCAAGCCGC
TACCGGCACTTGGTAGTGATGATGGAACAGCATGGGATGATGGTGCTTACGTTGGGGTTAAGAA
GGTGTACGTAGGACAAGCCCAAGATGGTATATCGGCTGTTAAGTTTGTATACGACAAAAGCCCT
GAGGAGGTCACAGGAGAAGAACATGGAAAGAGTACTCTACTCGGATTCGAAGAG
						
					

						Genomic sequence
						
							TTCGTACTTGACTATCCAAGTGAATACATCACCGCAGTCGATGGCACTTATGATAAAATCTTTG
GGAGTGATGGCTCAGTCATAACTATGCTCAGGTTCAAGACTAATAAGCAAACGTCTCCTCCCTT
TGGACTTGAAGCTGGCACAGTCTTCGAACTCAAAGAGGAAGGCCACAAGATCGTTGGTTTCCAT
GGAAGAGCCGATGTTCTGCTCCACAAAATTGGAGTCCATGTTCGTCCTTTATCCAACTGATGAT
GGAGCTCTTTATCCTTGATTCCATGCATCTAATAAGTTATCAAATCTATCTTCTAAATTTCTCA
TATGAGGTCTCTTCATGCCTCTGGTGAATGGTGATCTTTGATAAGTGTTTTACGCGTTGTCTCT
TGCGATGTTGTTTTTTCTTTGTTCTTCTTGTGCTCTATTTTAATAAAGGAAGTTTGTTCCAATC
TGATCTTTAGTTTCCCTATATGTTCTATAATACTTACTTTTGCCATTATTTGGTTCTGATACTA
ATTTTACTTGCTATAATTCAAACTAAAATCTCAACGTATGAATTGTACAATTTAAAATGCAAAT
GTTAACTTTTTTGGATCAAATATATAGTTGTTCGTATTTTCTCAGTAAAAAAATCCTGCACAAA
GTTTTTATCTAGAATGTGTGACCATATTGAAGTTTTTGGCCTTCTCCAAACATAAAAAGTTATT
AGTTAAAAGTATATGAGTTGGCCAAAAAATACGAACCGGTTCTTGTTTCTAGATTGAGCGTTAC
AGAAAATTGTATTATATATATACTCTTGGTTCTAATTTCTCTTAGGTGATTTCAATTATACTTT
TACTGTTTGAAATAATGTACAATGCTGTGGAAACATGTTCTTACAAGACTTATCAAATCGTCAA
CCAATTAGAGTCCTAAAAAGGGGGTCACTAATTGTAGAATTCTGACTTATATAAATTGCAACTT
GCACCCTTTACAAGTAATAACGTATATAATAAAATTGACGACTCTGTGAATTTTAAAAGAACTA
ATTAGCTTGCTGCCATCGTTTCATTGGCCAACACCAATATAAAGACGATTAGTTGAGAAGCTGT
GGAAGTAAAAAAGGAGTATATGAATATTTGAACATGTATTTCTTCCGGTAATGTTTTAAATATG
CCTCGTGGATCACGAAATAATAGATTATTATTTCTGCTAGTACGATCAATGATCCTATATGCGG
ATATATGGTTATATGCAAGAAGTCAATATAAACACCTATGATTCACTTAAATCGATCACAATCT
ACTCACTTTTGAAGGTCATCTCTCTTTTCCTCTCTATTAGTACAAAATTGGTTAATAATTGAAA
ATTCACAATTTGTTTTTTTTTCCAATTATAGTAACTATAGTAAGATTGATCAGCAAGCAAAATA
TGGCTCAAAAGGTTGAAGCAAAAGGAGGGAAAGGAGGCAACCAATGGGACGATGGATCCGATCA
TGACGCCGTGACCAAGATTCAGGTTGCAGTAGGCGGAATGGGAATTCAATACATTCAGTTCGAT
TACGTCAAGAACGGACAAACCGAACAAACTCCTCTTCGTGGTATCAAAGGCAGTACCATTCCAA
CTGATCCGGTTCCTATACATTTTCCTTGCTTATTTGACTTCTTCTAATTTTTATAGAAAATCTA
TTGTTTTACGTTGAAGTATTGACATATTGAACTTGATCTCTACAGTTTGTGATTAACCATCCTG
AGGAGCATCTAGTTTCTATTGAAATTTGGTATAAACCTGATGGTCTTATTCAAGGGCTTAGGTT
CATATCCAACAAAAAGACTTCTCGTTTCATTGGATACGATCGTGGTACTAGATCATTTCTCCAA
GTTCAAGACAAGAAGATCATTGGCTTTCATGGGTCTGCCGGAGACAATCTTAATTCTCTTGGAG
CTTACTTTGCTCCGTTGACTATCCCATTGACTCCTGCCAAGCCGCTACCGGCACTTGGTAGTGA
TGATGGAACAGCATGGGATGATGGTGCTTACGTTGGGGTTAAGAAGGTGTACGTAGGACAAGCC
CAAGATGGTATATCGGCTGTTAAGTTTGTATACGACAAAAGCCCTGAGGAGGTCACAGGAGAAG
AACATGGAAAGAGTACTCTACTCGGATTCGAAGAG
						
					

			
		

Sequences
Splice junction sequence	CCAAGATGGTATATCGGCTGTTAAGTTTGTATACGACAAAAGCCCTGAGGAGGTCACAGGAGAA GAACATGGAAAGAGTACTCTACTCGGATTCGAAGAGttcgtacttgactatccaagtgaataca tcaccgcagtcgatggcacttatgataaaatctttgggagtgatggctcagtcataactatgct caggttca
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: 433 Transcript exons: 5580423-5580653,5582368-5582569 TTCGTACTTGACTATCCAAGTGAATACATCACCGCAGTCGATGGCACTTATGATAAAATCTTTG GGAGTGATGGCTCAGTCATAACTATGCTCAGGTTCAAGACTAATAAGCAAACGTCTCCTCCCTT TGGACTTGAAGCTGGCACAGTCTTCGAACTCAAAGAGGAAGGCCACAAGATCGTTGGTTTCCAT GGAAGAGCCGATGTTCTGCTCCACAAAATTGGAGTCCATATTGACTCCTGCCAAGCCGCTACCG GCACTTGGTAGTGATGATGGAACAGCATGGGATGATGGTGCTTACGTTGGGGTTAAGAAGGTGT ACGTAGGACAAGCCCAAGATGGTATATCGGCTGTTAAGTTTGTATACGACAAAAGCCCTGAGGA GGTCACAGGAGAAGAACATGGAAAGAGTACTCTACTCGGATTCGAAGAG Transcript length: 438 Transcript exons: 5580423-5580658,5582368-5582569 TTCGTACTTGACTATCCAAGTGAATACATCACCGCAGTCGATGGCACTTATGATAAAATCTTTG GGAGTGATGGCTCAGTCATAACTATGCTCAGGTTCAAGACTAATAAGCAAACGTCTCCTCCCTT TGGACTTGAAGCTGGCACAGTCTTCGAACTCAAAGAGGAAGGCCACAAGATCGTTGGTTTCCAT GGAAGAGCCGATGTTCTGCTCCACAAAATTGGAGTCCATGTTCGATTGACTCCTGCCAAGCCGC TACCGGCACTTGGTAGTGATGATGGAACAGCATGGGATGATGGTGCTTACGTTGGGGTTAAGAA GGTGTACGTAGGACAAGCCCAAGATGGTATATCGGCTGTTAAGTTTGTATACGACAAAAGCCCT GAGGAGGTCACAGGAGAAGAACATGGAAAGAGTACTCTACTCGGATTCGAAGAG
Genomic sequence	TTCGTACTTGACTATCCAAGTGAATACATCACCGCAGTCGATGGCACTTATGATAAAATCTTTG GGAGTGATGGCTCAGTCATAACTATGCTCAGGTTCAAGACTAATAAGCAAACGTCTCCTCCCTT TGGACTTGAAGCTGGCACAGTCTTCGAACTCAAAGAGGAAGGCCACAAGATCGTTGGTTTCCAT GGAAGAGCCGATGTTCTGCTCCACAAAATTGGAGTCCATGTTCGTCCTTTATCCAACTGATGAT GGAGCTCTTTATCCTTGATTCCATGCATCTAATAAGTTATCAAATCTATCTTCTAAATTTCTCA TATGAGGTCTCTTCATGCCTCTGGTGAATGGTGATCTTTGATAAGTGTTTTACGCGTTGTCTCT TGCGATGTTGTTTTTTCTTTGTTCTTCTTGTGCTCTATTTTAATAAAGGAAGTTTGTTCCAATC TGATCTTTAGTTTCCCTATATGTTCTATAATACTTACTTTTGCCATTATTTGGTTCTGATACTA ATTTTACTTGCTATAATTCAAACTAAAATCTCAACGTATGAATTGTACAATTTAAAATGCAAAT GTTAACTTTTTTGGATCAAATATATAGTTGTTCGTATTTTCTCAGTAAAAAAATCCTGCACAAA GTTTTTATCTAGAATGTGTGACCATATTGAAGTTTTTGGCCTTCTCCAAACATAAAAAGTTATT AGTTAAAAGTATATGAGTTGGCCAAAAAATACGAACCGGTTCTTGTTTCTAGATTGAGCGTTAC AGAAAATTGTATTATATATATACTCTTGGTTCTAATTTCTCTTAGGTGATTTCAATTATACTTT TACTGTTTGAAATAATGTACAATGCTGTGGAAACATGTTCTTACAAGACTTATCAAATCGTCAA CCAATTAGAGTCCTAAAAAGGGGGTCACTAATTGTAGAATTCTGACTTATATAAATTGCAACTT GCACCCTTTACAAGTAATAACGTATATAATAAAATTGACGACTCTGTGAATTTTAAAAGAACTA ATTAGCTTGCTGCCATCGTTTCATTGGCCAACACCAATATAAAGACGATTAGTTGAGAAGCTGT GGAAGTAAAAAAGGAGTATATGAATATTTGAACATGTATTTCTTCCGGTAATGTTTTAAATATG CCTCGTGGATCACGAAATAATAGATTATTATTTCTGCTAGTACGATCAATGATCCTATATGCGG ATATATGGTTATATGCAAGAAGTCAATATAAACACCTATGATTCACTTAAATCGATCACAATCT ACTCACTTTTGAAGGTCATCTCTCTTTTCCTCTCTATTAGTACAAAATTGGTTAATAATTGAAA ATTCACAATTTGTTTTTTTTTCCAATTATAGTAACTATAGTAAGATTGATCAGCAAGCAAAATA TGGCTCAAAAGGTTGAAGCAAAAGGAGGGAAAGGAGGCAACCAATGGGACGATGGATCCGATCA TGACGCCGTGACCAAGATTCAGGTTGCAGTAGGCGGAATGGGAATTCAATACATTCAGTTCGAT TACGTCAAGAACGGACAAACCGAACAAACTCCTCTTCGTGGTATCAAAGGCAGTACCATTCCAA CTGATCCGGTTCCTATACATTTTCCTTGCTTATTTGACTTCTTCTAATTTTTATAGAAAATCTA TTGTTTTACGTTGAAGTATTGACATATTGAACTTGATCTCTACAGTTTGTGATTAACCATCCTG AGGAGCATCTAGTTTCTATTGAAATTTGGTATAAACCTGATGGTCTTATTCAAGGGCTTAGGTT CATATCCAACAAAAAGACTTCTCGTTTCATTGGATACGATCGTGGTACTAGATCATTTCTCCAA GTTCAAGACAAGAAGATCATTGGCTTTCATGGGTCTGCCGGAGACAATCTTAATTCTCTTGGAG CTTACTTTGCTCCGTTGACTATCCCATTGACTCCTGCCAAGCCGCTACCGGCACTTGGTAGTGA TGATGGAACAGCATGGGATGATGGTGCTTACGTTGGGGTTAAGAAGGTGTACGTAGGACAAGCC CAAGATGGTATATCGGCTGTTAAGTTTGTATACGACAAAAGCCCTGAGGAGGTCACAGGAGAAG AACATGGAAAGAGTACTCTACTCGGATTCGAAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.802243691

Conservation Information
Conserved circRNAs	NA
PMCS	0.802243691

			
						 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
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of 3_circ_ag.15

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