Plant Circular RNA Database

Detail information of 1_circ_ag.4

			
						 General Information
					
						CircRNA Name
						1_circ_ag.4
					
						ID in PlantcircBase
						ath_circ_004890
					
						Alias
						1:10475164-10478859
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 10475164-10478859  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
						
							AT1G29910_circ_g.2 1_circ_ag.3 1_circ_ag.4 AT1G29910_circ_g.5 AT1G29910_circ_g.6 AT1G29910_circ_g.7 AT1G29910_circ_g.8 AT1G29910_circ_g.9 1_circ_ag.10 1_circ_ag.11 1_circ_ag.12 1_circ_ag.13 1_circ_ag.14 1_circ_ag.15 1_circ_ag.16 AT1G29920_circ_g.1 1_circ_ag.2 1_circ_ag.3 AT1G29920_circ_g.5 1_circ_ag.6 AT1G29920_circ_g.7 AT1G29920_circ_g.8 1_circ_ag.9 AT1G29920_circ_g.10 AT1G29930_circ_g.1 AT1G29930_circ_g.2 AT1G29930_circ_g.3 AT1G29930_circ_g.4 AT1G29930_circ_g.5 AT1G29930_circ_g.6 AT1G29930_circ_g.7 AT1G29930_circ_g.8 AT1G29930_circ_g.9 AT1G29930_circ_g.10 AT1G29930_circ_g.11 AT1G29930_circ_g.12 AT1G29930_circ_g.13 AT1G29930_circ_g.14 AT1G29930_circ_g.15 AT1G29930_circ_g.16 AT1G29930_circ_g.17 AT1G29930_circ_g.18 AT1G29930_circ_g.19 AT1G29930_circ_g.20 AT1G29930_circ_g.21 AT1G29930_circ_g.22 AT1G29930_circ_g.23 						
					
						Support reads
						2
					
						Tissues
						leaf
					
						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  
						
							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	1_circ_ag.4
ID in PlantcircBase	ath_circ_004890
Alias	1:10475164-10478859
Organism	Arabidpsis thaliana
Position	chr1: 10475164-10478859 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	AT1G29910_circ_g.2 1_circ_ag.3 1_circ_ag.4 AT1G29910_circ_g.5 AT1G29910_circ_g.6 AT1G29910_circ_g.7 AT1G29910_circ_g.8 AT1G29910_circ_g.9 1_circ_ag.10 1_circ_ag.11 1_circ_ag.12 1_circ_ag.13 1_circ_ag.14 1_circ_ag.15 1_circ_ag.16 AT1G29920_circ_g.1 1_circ_ag.2 1_circ_ag.3 AT1G29920_circ_g.5 1_circ_ag.6 AT1G29920_circ_g.7 AT1G29920_circ_g.8 1_circ_ag.9 AT1G29920_circ_g.10 AT1G29930_circ_g.1 AT1G29930_circ_g.2 AT1G29930_circ_g.3 AT1G29930_circ_g.4 AT1G29930_circ_g.5 AT1G29930_circ_g.6 AT1G29930_circ_g.7 AT1G29930_circ_g.8 AT1G29930_circ_g.9 AT1G29930_circ_g.10 AT1G29930_circ_g.11 AT1G29930_circ_g.12 AT1G29930_circ_g.13 AT1G29930_circ_g.14 AT1G29930_circ_g.15 AT1G29930_circ_g.16 AT1G29930_circ_g.17 AT1G29930_circ_g.18 AT1G29930_circ_g.19 AT1G29930_circ_g.20 AT1G29930_circ_g.21 AT1G29930_circ_g.22 AT1G29930_circ_g.23
Support reads	2
Tissues	leaf
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	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  
						
							CGTTCAAGCCATCGTCACTGGTAAGGGACCGATAGAGAACCTTGCTGACCATTTGGCCGATCCA
GTTAACAACAACGCATGGGCCTTCGCCACCAACTTTgttctctatcggtcccttaccagtgacg
atggcttgaacgaagaatccaaacatagagaacatagccaatcttccgttcttgagctccttta
ccttcaac

									
								

					

						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
						
							GTTCTCTATCGGTCCCTTACCAGTGACGATGGCTTGAACGAAGAATCCAAACATAGAGAACATA
GCCAATCTTCCGTTCTTGAGCTCCTTTACCTTCAACTCAGCGAAGGCCTCTGGGTCGGTAGCCA
AACCCAATGGGTCGAAACTGCCACCGGGGTAAAGCAAGTCCTCGGCCTCTCCCAATGGCCCATT
TCCTGCGACTCTGTAACCTTCAACGGCTCCCATCAAAATAACTTGTGTGGCCCAAATGGCCAAA
ATGCTCTGAGCGTGAACCAAGCTAGGGTTTCCCAAGTAATCGAGCCCTCCATCGCTGAAGATCT
GTGAACCAGCCTTGAACCAAACTGCCTCTCCAAACTTGACTCCGTTCCTGGCCAAAAGCTCAGG
GAAGACGCAGCCTAGGGCTCCGAGCATGGCCCACCTGCTGTGGATAACTTCTAGCTCACGGTTC
CTTGCGAATGTCTCGGGGTCAGCGGATAGACCAGCTGTGTCCCATCCGTAGTCTCCAGGGAACT
CTCCGGTAAGGTAGCTGGGTGACTCGCCAGAGAATGGACCCAAGTACTTGACTCGGTCGGATCC
GTACCATGGGCTGCCTGATGGACCCTTTGGCTTGGCAACAGTCTTCCTCATTGTCACACGGCCG
CTTCCAAGGACTTCTGATGCCGCAGGGGAAAGGTTCACAGCCTTTCCGGCGAAAGCAGGGGAGG
AGAGAGCCATTGTTGAGGCGGCCATTGAAACTTTTTTGTGTTTTTTTTTTTTTTATGACTAACT
TGTGAGTGAGAGTGATTAAAACTGGTTCGATAGTGTTGGATTATATAGGGATATTGTAACGTTT
GTTATATCTGAAGTAATCTTTATCTGTTCATTCATTGGATTTTAAGATTTTTGTTTTATCGTTT
AGTAGTCTTACGTGGCAATCTCTAGTCCACCAGCATTTGTTTTGATTTTTTCATTGCAGCCAAG
CGTTTTGTGACCACAAGTTATGAGCCACTGAATACTTCAACGGTTACACTTACTTACACCCTCG
TGACAAGAATGATTTTTGCTACAACCCAATAACTAAAACTTAAAGTATAACATTTTGAAAATAT
AGATTCTGATGATCGAAACATTAATATAAAGTAACATTATAAAAAGCATTTACCCACACATAAA
TATCAATATTTTCAATGGTAATTAGTTCATCATCACTACCAGTTTAATTTCAATTATGAATCGA
TTTCATCGTCACTTTATCCAATAACCAAAATAATCTCATGAATTATGTGATATCACCTTAAAAC
TTTGACGTTTTACTCTTTATCGAAGAAACACAACGATTAATGAAACACTGTTTTAACTTATCGA
CCATTTCTAAGAACATGAAAGAACTATATTAATTCATATGGCATGTTCATCATCATGGGTTTAG
ACTTTAGAGAACATATAGCTACTTTTTTTCTTATCATGATTCAAGTTATCTTTATTGTAAACTT
CAACAACCTTTTGAACAAACTTATTTATTCGCTTTTTCCGAATTCATCAACAAATTACTCCTCA
ATCACACTCCTATAGAAAACGGTTTAAGCTATCATTACATGTCTAGTTGGTTTTACTCAGCCCT
AGAAGTGTTGTTTATTGCATCACTTTCCACGAAGCACAATTTTTCTTTTTTACAATCACTAGAC
CTCACAGGCTCACACATATGCTTTAGAGCACATTCTAAACTTTGAACTATAAAAGCTGTTAACA
CTAATACACTATGCGTTCTTTTTTGCTCCAAACACTTTTGATCCATTATTAGGAGACACTCCAC
TTAGAAAGATTTTCTAATCCTTTGGTCAACTAGGAAGTTCAAGGTTTTTCTAAACAGAAATTCA
TTTCACAAGTAATTTAATTTATAAGGAAATGAATAGAGAAATCAAATCATTGAAGAACTACAAA
ATATAGATTCAAGGTCAGGTCTAAGAAAATATTCCTGAAGCTCAAAAAAGAGTTTTCCTCTCAC
ATTATAGAATTGGCCTTTACTTCAACATTTTCCCACCTATTCCACATTTGGTCAGAACATTTTT
AATTACTTGTGGATCAATTTCCGGTTGAAATGGGTTTGGTGAATATCCGGTTCAGTTATATGGT
GGCCGTTGGAATTGGCTTATTAGTTGTGGCCGTTGTTGAAGCCGTTGGTATTGGTAAGGGAGAA
GCAGACTTGTGGCTATGAGTCTATGACCATGACTCGTGATTATGGAGCTGTCTTATGACCCTGA
CCATCACCTTGATCTGGTGGATTCCAATGTTTTCTTCTTCTTCTAATAAAATATTATGGTCAAT
ACAGGTGCTAATTAAGATGGTAATAATTTCTTATGTTTCTGTGGTAAAGTTTGATTCAATTCCG
TAGTTTTAGATAATCTTATTTCCATACATAAATTTTATAGTTTTATCTACTTTGTTCTTATGTT
TTATCTCTAGCCAAGAGTTATTATTATTATCAGAAGAAGAAAAAAAAAAGAAGCATATATACAA
AAGGTTTAATAAAATGTATTATACAAGGCAATTATCCAAATTTTTTTTGTTTTGGTTTACATTG
ATGCTCTCAGGATTTCATAAGGATAGAGAGATCTATTCGTATACGTGTCACGTCATGAGTGGGT
GTTTCGCCAATCCATGAAACGCACCTAGATATCTAAAACACATATCAATTGCGAATCTGCGAAG
TGCGAGCCATTAACCACGTAAGCAAACAAACAATCTAAACCCCAAAAAAAATCTATGACTAGCC
AATAGCAACCTCAGAGATTGATATTTCAAGATAAGACAGTATTTAGATTTCTGTATTATATATA
GCGAAAATCGCATCAATACCAAACCACCCATTTCTTGGCTTACAACAACAAATCTTAAACGTTT
TACTTTGTGCTGCACTACTCAACCTCAATGGCCGCCTCAACAATGGCTCTCTCCTCCCCTGCCT
TCGCCGGTAAGGCCGTCAAGCTTTCCCCCGCGGCATCTGAAGTCCTTGGAAGCGGCCGTGTGAC
AATGAGGAAGACTGTTGCCAAGCCAAAGGGCCCATCAGGCAGCCCATGGTACGGATCTGACCGT
GTCAAGTACTTGGGTCCATTCTCTGGCGAATCACCGAGCTACCTTACCGGAGAGTTCCCCGGAG
ACTACGGATGGGACACCGCCGGACTTTCAGCTGACCCCGAGACATTCGCAAGGAACCGTGAACT
AGAAGTTATCCACAGCAGGTGGGCCATGCTCGGAGCCCTAGGCTGCGTCTTCCCTGAGCTTTTG
GCTAGAAACGGAGTCAAGTTCGGAGAGGCGGTTTGGTTCAAGGCCGGTTCACAGATCTTCAGCG
ATGGAGGGCTCGATTACTTGGGAAACCCTAGCTTGGTTCACGCTCAGAGCATTTTGGCCATTTG
GGCCACACAAGTTATTTTGATGGGAGCCGTTGAAGGCTACAGAGTCGCAGGAAATGGGCCATTG
GGAGAGGCCGAGGACTTGCTTTACCCCGGTGGCAGCTTCGACCCATTGGGTTTGGCTACCGACC
CAGAGGCATTCGCTGAGTTGAAGGTGAAGGAGCTCAAGAACGGAAGATTGGCTATGTTCTCTAT
GTTTGGATTCTTCGTTCAAGCCATCGTCACTGGTAAGGGACCGATAGAGAACCTTGCTGACCAT
TTGGCCGATCCAGTTAACAACAACGCATGGGCCTTCGCCACCAACTTT
						
					

			
		

Sequences
Splice junction sequence	CGTTCAAGCCATCGTCACTGGTAAGGGACCGATAGAGAACCTTGCTGACCATTTGGCCGATCCA GTTAACAACAACGCATGGGCCTTCGCCACCAACTTTgttctctatcggtcccttaccagtgacg atggcttgaacgaagaatccaaacatagagaacatagccaatcttccgttcttgagctccttta ccttcaac
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	GTTCTCTATCGGTCCCTTACCAGTGACGATGGCTTGAACGAAGAATCCAAACATAGAGAACATA GCCAATCTTCCGTTCTTGAGCTCCTTTACCTTCAACTCAGCGAAGGCCTCTGGGTCGGTAGCCA AACCCAATGGGTCGAAACTGCCACCGGGGTAAAGCAAGTCCTCGGCCTCTCCCAATGGCCCATT TCCTGCGACTCTGTAACCTTCAACGGCTCCCATCAAAATAACTTGTGTGGCCCAAATGGCCAAA ATGCTCTGAGCGTGAACCAAGCTAGGGTTTCCCAAGTAATCGAGCCCTCCATCGCTGAAGATCT GTGAACCAGCCTTGAACCAAACTGCCTCTCCAAACTTGACTCCGTTCCTGGCCAAAAGCTCAGG GAAGACGCAGCCTAGGGCTCCGAGCATGGCCCACCTGCTGTGGATAACTTCTAGCTCACGGTTC CTTGCGAATGTCTCGGGGTCAGCGGATAGACCAGCTGTGTCCCATCCGTAGTCTCCAGGGAACT CTCCGGTAAGGTAGCTGGGTGACTCGCCAGAGAATGGACCCAAGTACTTGACTCGGTCGGATCC GTACCATGGGCTGCCTGATGGACCCTTTGGCTTGGCAACAGTCTTCCTCATTGTCACACGGCCG CTTCCAAGGACTTCTGATGCCGCAGGGGAAAGGTTCACAGCCTTTCCGGCGAAAGCAGGGGAGG AGAGAGCCATTGTTGAGGCGGCCATTGAAACTTTTTTGTGTTTTTTTTTTTTTTATGACTAACT TGTGAGTGAGAGTGATTAAAACTGGTTCGATAGTGTTGGATTATATAGGGATATTGTAACGTTT GTTATATCTGAAGTAATCTTTATCTGTTCATTCATTGGATTTTAAGATTTTTGTTTTATCGTTT AGTAGTCTTACGTGGCAATCTCTAGTCCACCAGCATTTGTTTTGATTTTTTCATTGCAGCCAAG CGTTTTGTGACCACAAGTTATGAGCCACTGAATACTTCAACGGTTACACTTACTTACACCCTCG TGACAAGAATGATTTTTGCTACAACCCAATAACTAAAACTTAAAGTATAACATTTTGAAAATAT AGATTCTGATGATCGAAACATTAATATAAAGTAACATTATAAAAAGCATTTACCCACACATAAA TATCAATATTTTCAATGGTAATTAGTTCATCATCACTACCAGTTTAATTTCAATTATGAATCGA TTTCATCGTCACTTTATCCAATAACCAAAATAATCTCATGAATTATGTGATATCACCTTAAAAC TTTGACGTTTTACTCTTTATCGAAGAAACACAACGATTAATGAAACACTGTTTTAACTTATCGA CCATTTCTAAGAACATGAAAGAACTATATTAATTCATATGGCATGTTCATCATCATGGGTTTAG ACTTTAGAGAACATATAGCTACTTTTTTTCTTATCATGATTCAAGTTATCTTTATTGTAAACTT CAACAACCTTTTGAACAAACTTATTTATTCGCTTTTTCCGAATTCATCAACAAATTACTCCTCA ATCACACTCCTATAGAAAACGGTTTAAGCTATCATTACATGTCTAGTTGGTTTTACTCAGCCCT AGAAGTGTTGTTTATTGCATCACTTTCCACGAAGCACAATTTTTCTTTTTTACAATCACTAGAC CTCACAGGCTCACACATATGCTTTAGAGCACATTCTAAACTTTGAACTATAAAAGCTGTTAACA CTAATACACTATGCGTTCTTTTTTGCTCCAAACACTTTTGATCCATTATTAGGAGACACTCCAC TTAGAAAGATTTTCTAATCCTTTGGTCAACTAGGAAGTTCAAGGTTTTTCTAAACAGAAATTCA TTTCACAAGTAATTTAATTTATAAGGAAATGAATAGAGAAATCAAATCATTGAAGAACTACAAA ATATAGATTCAAGGTCAGGTCTAAGAAAATATTCCTGAAGCTCAAAAAAGAGTTTTCCTCTCAC ATTATAGAATTGGCCTTTACTTCAACATTTTCCCACCTATTCCACATTTGGTCAGAACATTTTT AATTACTTGTGGATCAATTTCCGGTTGAAATGGGTTTGGTGAATATCCGGTTCAGTTATATGGT GGCCGTTGGAATTGGCTTATTAGTTGTGGCCGTTGTTGAAGCCGTTGGTATTGGTAAGGGAGAA GCAGACTTGTGGCTATGAGTCTATGACCATGACTCGTGATTATGGAGCTGTCTTATGACCCTGA CCATCACCTTGATCTGGTGGATTCCAATGTTTTCTTCTTCTTCTAATAAAATATTATGGTCAAT ACAGGTGCTAATTAAGATGGTAATAATTTCTTATGTTTCTGTGGTAAAGTTTGATTCAATTCCG TAGTTTTAGATAATCTTATTTCCATACATAAATTTTATAGTTTTATCTACTTTGTTCTTATGTT TTATCTCTAGCCAAGAGTTATTATTATTATCAGAAGAAGAAAAAAAAAAGAAGCATATATACAA AAGGTTTAATAAAATGTATTATACAAGGCAATTATCCAAATTTTTTTTGTTTTGGTTTACATTG ATGCTCTCAGGATTTCATAAGGATAGAGAGATCTATTCGTATACGTGTCACGTCATGAGTGGGT GTTTCGCCAATCCATGAAACGCACCTAGATATCTAAAACACATATCAATTGCGAATCTGCGAAG TGCGAGCCATTAACCACGTAAGCAAACAAACAATCTAAACCCCAAAAAAAATCTATGACTAGCC AATAGCAACCTCAGAGATTGATATTTCAAGATAAGACAGTATTTAGATTTCTGTATTATATATA GCGAAAATCGCATCAATACCAAACCACCCATTTCTTGGCTTACAACAACAAATCTTAAACGTTT TACTTTGTGCTGCACTACTCAACCTCAATGGCCGCCTCAACAATGGCTCTCTCCTCCCCTGCCT TCGCCGGTAAGGCCGTCAAGCTTTCCCCCGCGGCATCTGAAGTCCTTGGAAGCGGCCGTGTGAC AATGAGGAAGACTGTTGCCAAGCCAAAGGGCCCATCAGGCAGCCCATGGTACGGATCTGACCGT GTCAAGTACTTGGGTCCATTCTCTGGCGAATCACCGAGCTACCTTACCGGAGAGTTCCCCGGAG ACTACGGATGGGACACCGCCGGACTTTCAGCTGACCCCGAGACATTCGCAAGGAACCGTGAACT AGAAGTTATCCACAGCAGGTGGGCCATGCTCGGAGCCCTAGGCTGCGTCTTCCCTGAGCTTTTG GCTAGAAACGGAGTCAAGTTCGGAGAGGCGGTTTGGTTCAAGGCCGGTTCACAGATCTTCAGCG ATGGAGGGCTCGATTACTTGGGAAACCCTAGCTTGGTTCACGCTCAGAGCATTTTGGCCATTTG GGCCACACAAGTTATTTTGATGGGAGCCGTTGAAGGCTACAGAGTCGCAGGAAATGGGCCATTG GGAGAGGCCGAGGACTTGCTTTACCCCGGTGGCAGCTTCGACCCATTGGGTTTGGCTACCGACC CAGAGGCATTCGCTGAGTTGAAGGTGAAGGAGCTCAAGAACGGAAGATTGGCTATGTTCTCTAT GTTTGGATTCTTCGTTCAAGCCATCGTCACTGGTAAGGGACCGATAGAGAACCTTGCTGACCAT TTGGCCGATCCAGTTAACAACAACGCATGGGCCTTCGCCACCAACTTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.258809139

Conservation Information
Conserved circRNAs	NA
PMCS	0.258809139

			
						 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 1_circ_ag.4

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