Plant Circular RNA Database

Detail information of 3_circ_ag.4

			
						 General Information
					
						CircRNA Name
						3_circ_ag.4
					
						ID in PlantcircBase
						ath_circ_025986
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 15984644-15988225  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						CIRI, KNIFE
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							3_circ_ag.2 3_circ_ag.3 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 AT3G44310_circ_g.1 AT3G44310_circ_g.2 3_circ_ag.3 AT3G44310_circ_g.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 AT3G44310_circ_g.8 						
					
						Support reads
						199
					
						Tissues
						root, aerial, inflorescences, 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.4
ID in PlantcircBase	ath_circ_025986
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 15984644-15988225 JBrowse»
Reference genome	TAIR10.38
Type	ag-circRNA
Identification method	CIRI, KNIFE
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	3_circ_ag.2 3_circ_ag.3 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 AT3G44310_circ_g.1 AT3G44310_circ_g.2 3_circ_ag.3 AT3G44310_circ_g.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 AT3G44310_circ_g.8
Support reads	199
Tissues	root, aerial, inflorescences, 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  
						
							TCAACCATCCCCGTTTACGACACTCCCATTGGAAAACTCGGTGCTGCTATTTGCTGGGAGAATA
GGATGCCCCTCTACAGAACTGCATTGTACGCCAAAGgcattgagctttattgtgcacctactgc
tgatggttcgaaagaatggcaatcgtcgatgcttcacattgcgatcgaaggtggatgtttcgta
ttgtcggc

									
								

					

						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
						
							GCATTGAGCTTTATTGTGCACCTACTGCTGATGGTTCGAAAGAATGGCAATCGTCGATGCTTCA
CATTGCGATCGAAGGTGGATGTTTCGTATTGTCGGCTTGCCAGTTCTGCCTTCGTAAAGATTTC
CCTGATCATCCTGACTACTTGTTTACCGATTGGTACGACGACAAAGAGCCTGACTCTATTGTTT
CCCAAGGTGGAAGTGTTATTATTTCACCTTTGGGACAGGTTCTTGCGGGACCAAACTTTGAATC
AGAGGGTCTCATCACAGCTGATCTTGGTAAAAATATATATAATCTTCTTTAGTTTTTATCTTAG
GCTATAGAAAAGGATAATTTTTTTAGCTAATCATATTTTATTTTTGTCATCAAGATCTTGGTGA
TGTAGCAAGAGCTAAGTTGTACTTCGATTCGGTTGGACATTACTCGAGACCAGATGTTTTACAC
TTGACCGTAAATGAGCACCCGAAGAAACCGGTCACATTCATTTCGAAGGTGGAGAAAGCGGAAG
ATGACTCAAACAAGTAATCGGTTGTGATTCGTCAGTTCATGTCACTCCTATGAAGGAGTCAAGT
TCAAAATGTTATGTTGAGTTTCAAACTTTTATGCTAAACTTTTTTTCTTAATTTTCGTTAATAA
TGGAAGAGAACCAATTCTCTTGTATCTAAAGATTATCCATCTATCATCCAATTTGAGTGTTCAA
TTCTGGATGTTGTGTTACCCTACATTCTACAACCATGTAGCCAATTATTATGAATCTGGCTTTG
ATTTCAGTTGTGTTCTTTTCTTTTTTTTCTTTGCATATTTGCATTTAGAATGTTTAATAATTAA
GTTACTGTATTTCCACATACATTAGTTCCAAGAATATACATATATTAATTTATTTTTCTTAAAA
ATGTTTTGGAATGACTAATATTGACAACGAAAATAGAAGCTATGCTAAACCATTACGTATATGT
GACTTCACATGTTGTTGTTTTACATTCCCTATATATATGGATGGCTGTCACAATCAGAAACGTG
ATCGAAAAAAGACAAACAGTGTTTGCATAAAAAGACTATTTCGTTTCATTGACAATTTGTGTTT
ATTTGTAAAGAAAAGTGGCAAAGTGGAATTTGAGTTCCTGCAAGTAAGAAAGATGAAATAAAAG
ACTTGAGTGTGTGTTTTTTTCTTTTATCTGAAAGCTGCAATGAAATATTCCTACCAAGCCCGTT
TGATTATTAATTGGGGTTTGGTTTTCTTGATGCGAACTAATTGGTTATATAAGAAACTATACAA
TCCATGTTAATTCAAAAATTTTGATTTCTCTTGTAGGAATATGATTTACTATATGAGACTTTCT
TTTCGCCAATAATAGTAAATCCAAAGATATTTGACCGGACCAAAACACATTGATCTATTTTTTA
GTTTATTTAATCCAGTTTCTCTGAGATAATTCATTAAGGAAAACTTAGTATTAACCCATCCTAA
GATTAAATAGGAGCCAAACTCACATTTCAAATATTAAATAACATAAAATGGATTTAAAAAATCT
ATACGTCAAATTTTATTTATGACATTTCTTATTTAAATTTATATTTAATGAAATACAGCTAAGA
CAAACCAAAAAAAAAATACTTTCTAAGTGGTCCAAAACATCAATTCCGTTCAATATTATTAGGT
AGAATCGTACGACCAAAAAAGGTAGGTTAATACGAAATTACAAACATATCTATATACATAGTAT
ATATTATTACCTATTATGAGGAATCAAAATGCATCAAATATGGATTTAAGGAATCCATAAAAGA
ATAAATTCTACGGAAAAAAAAAAAAGAATAAATTCTTTTAAGTTTTTAATTTGTTTTTTATTTG
GTAGTTCTCCATTTTGTTTTATTTCGTTTGGATTTATTGTGTCCAAATACTTTGTAAACCACCG
TTGTAATTCTTAAACGGGGTTTTCACTTCTTTTTTATATTCAGACATAAAGCATCGGCTGGTTT
AATCAATCAATAGATTTTATTTTTCTTCTCAATTATTAGTAGGTTTGATGTGAACTTTACAAAA
AAAACAAAAACAAATCAATGCAGAGAAAAGAAACCACGTGGGCTAGTCCCACCTTGTTTCATTT
CCACCACAGGTTCGATCTTCGTTACCGTCTCCAATAGGAAAATAAACGTGACCACAAAAAAAAA
ACAAAAAAAAAGTCTATATATTGCTTCTCTCAAGTCTCTGAGTGTCATGAACCAAAGTAAAAAA
CAAAGACTCGAGTTGATATGTCTAGTACTAAAGATATGTCAACTGTCCAAAACGCAACTCCTTT
TAACGGCGTTGCCCCATCCACCACCGTGCGAGTTACAATCGTCCAATCCTCCACCGTCTATAAC
GATACTCCTGCCACTATAGGTAACCAATCCATTAATTCATCCTCTGACCTATTTTTATTTTTAT
TTTTTGATATGTAAAATTTATCGAAAACGTTCCATTTCAATATGTAGACAAAGCGGAGAAGTAT
ATTGTGGAGGCGGCAAGCAAGGGAGCAGAGCTAGTGTTGTTCCCGGAGGGGTTTATCGGTGGCT
ATCCTCGAGGTTTTAGGTTCGGTTTAGCGGTTGGCGTTCATAACGAAGAAGGGCGTGATGAGTT
TCGGAAGTACCATGCTTCTGCTATTCATGTTCCTGGTATTACTATTTACTTCCATTATTTGTAT
TCTTTTTATTATCATCTTATCTTGTATTTTATCCATAAAATGATTTTTGATACATTTTTAACCA
ATCAATGACTTTGAACCATATCCTCAATTATTGCATGCTTATCCTAGGCCGAGTGTATTCAAAG
TATACACCACCCGATCTCGGATCCAAGCCTACCAAAAATTTGGATATGCGGATCTAGATGACAA
TATTTATCCTGATCTTTATCTTTTAAATGTATAAATTACTATATGTTACATTAAATTTTATAAT
TTTTACACCAAAAAATATAATATTAAATCTCTTTAATTAAAGATTTTTTTTATTTCTCCTTTAT
TTGGTTGCTGGATTATGATTTTTAGTTGGCTATGGTTGGAGTCTTGGTGATGTGTATAAGTTTT
GGACAATTGAATTTTATTTGGAACAAAGTAAACTTAACTTTGAGGGAAAATATGTTTGATTTCG
AGTTCTCTTTTTTTTTGTCACGTTTAGATGAAATTTAATTGGAACAAGCATCTAATTAATGAGT
GTTCTTGCTCTAGTTTAAATTTAGTTGAGCACTCTCAATATCTTGGAACACAAAATGACTCTTT
TTGGTTTTTGTGATGAATCTTCAGGCCCTGAAGTAGCAAGATTGGCTGACGTGGCTAGGAAAAA
CCATGTGTACTTGGTAATGGGAGCCATAGAGAAGGAAGGGTATACCCTCTATTGCACAGTTCTT
TTCTTTAGTCCACAGGGTCAGTTCTTGGGCAAGCACCGTAAACTCATGCCCACAAGTTTGGAAC
GTTGCATTTGGGGCCAAGGGGACGGATCAACCATCCCCGTTTACGACACTCCCATTGGAAAACT
CGGTGCTGCTATTTGCTGGGAGAATAGGATGCCCCTCTACAGAACTGCATTGTACGCCAAAG
						
					

			
		

Sequences
Splice junction sequence	TCAACCATCCCCGTTTACGACACTCCCATTGGAAAACTCGGTGCTGCTATTTGCTGGGAGAATA GGATGCCCCTCTACAGAACTGCATTGTACGCCAAAGgcattgagctttattgtgcacctactgc tgatggttcgaaagaatggcaatcgtcgatgcttcacattgcgatcgaaggtggatgtttcgta ttgtcggc
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	GCATTGAGCTTTATTGTGCACCTACTGCTGATGGTTCGAAAGAATGGCAATCGTCGATGCTTCA CATTGCGATCGAAGGTGGATGTTTCGTATTGTCGGCTTGCCAGTTCTGCCTTCGTAAAGATTTC CCTGATCATCCTGACTACTTGTTTACCGATTGGTACGACGACAAAGAGCCTGACTCTATTGTTT CCCAAGGTGGAAGTGTTATTATTTCACCTTTGGGACAGGTTCTTGCGGGACCAAACTTTGAATC AGAGGGTCTCATCACAGCTGATCTTGGTAAAAATATATATAATCTTCTTTAGTTTTTATCTTAG GCTATAGAAAAGGATAATTTTTTTAGCTAATCATATTTTATTTTTGTCATCAAGATCTTGGTGA TGTAGCAAGAGCTAAGTTGTACTTCGATTCGGTTGGACATTACTCGAGACCAGATGTTTTACAC TTGACCGTAAATGAGCACCCGAAGAAACCGGTCACATTCATTTCGAAGGTGGAGAAAGCGGAAG ATGACTCAAACAAGTAATCGGTTGTGATTCGTCAGTTCATGTCACTCCTATGAAGGAGTCAAGT TCAAAATGTTATGTTGAGTTTCAAACTTTTATGCTAAACTTTTTTTCTTAATTTTCGTTAATAA TGGAAGAGAACCAATTCTCTTGTATCTAAAGATTATCCATCTATCATCCAATTTGAGTGTTCAA TTCTGGATGTTGTGTTACCCTACATTCTACAACCATGTAGCCAATTATTATGAATCTGGCTTTG ATTTCAGTTGTGTTCTTTTCTTTTTTTTCTTTGCATATTTGCATTTAGAATGTTTAATAATTAA GTTACTGTATTTCCACATACATTAGTTCCAAGAATATACATATATTAATTTATTTTTCTTAAAA ATGTTTTGGAATGACTAATATTGACAACGAAAATAGAAGCTATGCTAAACCATTACGTATATGT GACTTCACATGTTGTTGTTTTACATTCCCTATATATATGGATGGCTGTCACAATCAGAAACGTG ATCGAAAAAAGACAAACAGTGTTTGCATAAAAAGACTATTTCGTTTCATTGACAATTTGTGTTT ATTTGTAAAGAAAAGTGGCAAAGTGGAATTTGAGTTCCTGCAAGTAAGAAAGATGAAATAAAAG ACTTGAGTGTGTGTTTTTTTCTTTTATCTGAAAGCTGCAATGAAATATTCCTACCAAGCCCGTT TGATTATTAATTGGGGTTTGGTTTTCTTGATGCGAACTAATTGGTTATATAAGAAACTATACAA TCCATGTTAATTCAAAAATTTTGATTTCTCTTGTAGGAATATGATTTACTATATGAGACTTTCT TTTCGCCAATAATAGTAAATCCAAAGATATTTGACCGGACCAAAACACATTGATCTATTTTTTA GTTTATTTAATCCAGTTTCTCTGAGATAATTCATTAAGGAAAACTTAGTATTAACCCATCCTAA GATTAAATAGGAGCCAAACTCACATTTCAAATATTAAATAACATAAAATGGATTTAAAAAATCT ATACGTCAAATTTTATTTATGACATTTCTTATTTAAATTTATATTTAATGAAATACAGCTAAGA CAAACCAAAAAAAAAATACTTTCTAAGTGGTCCAAAACATCAATTCCGTTCAATATTATTAGGT AGAATCGTACGACCAAAAAAGGTAGGTTAATACGAAATTACAAACATATCTATATACATAGTAT ATATTATTACCTATTATGAGGAATCAAAATGCATCAAATATGGATTTAAGGAATCCATAAAAGA ATAAATTCTACGGAAAAAAAAAAAAGAATAAATTCTTTTAAGTTTTTAATTTGTTTTTTATTTG GTAGTTCTCCATTTTGTTTTATTTCGTTTGGATTTATTGTGTCCAAATACTTTGTAAACCACCG TTGTAATTCTTAAACGGGGTTTTCACTTCTTTTTTATATTCAGACATAAAGCATCGGCTGGTTT AATCAATCAATAGATTTTATTTTTCTTCTCAATTATTAGTAGGTTTGATGTGAACTTTACAAAA AAAACAAAAACAAATCAATGCAGAGAAAAGAAACCACGTGGGCTAGTCCCACCTTGTTTCATTT CCACCACAGGTTCGATCTTCGTTACCGTCTCCAATAGGAAAATAAACGTGACCACAAAAAAAAA ACAAAAAAAAAGTCTATATATTGCTTCTCTCAAGTCTCTGAGTGTCATGAACCAAAGTAAAAAA CAAAGACTCGAGTTGATATGTCTAGTACTAAAGATATGTCAACTGTCCAAAACGCAACTCCTTT TAACGGCGTTGCCCCATCCACCACCGTGCGAGTTACAATCGTCCAATCCTCCACCGTCTATAAC GATACTCCTGCCACTATAGGTAACCAATCCATTAATTCATCCTCTGACCTATTTTTATTTTTAT TTTTTGATATGTAAAATTTATCGAAAACGTTCCATTTCAATATGTAGACAAAGCGGAGAAGTAT ATTGTGGAGGCGGCAAGCAAGGGAGCAGAGCTAGTGTTGTTCCCGGAGGGGTTTATCGGTGGCT ATCCTCGAGGTTTTAGGTTCGGTTTAGCGGTTGGCGTTCATAACGAAGAAGGGCGTGATGAGTT TCGGAAGTACCATGCTTCTGCTATTCATGTTCCTGGTATTACTATTTACTTCCATTATTTGTAT TCTTTTTATTATCATCTTATCTTGTATTTTATCCATAAAATGATTTTTGATACATTTTTAACCA ATCAATGACTTTGAACCATATCCTCAATTATTGCATGCTTATCCTAGGCCGAGTGTATTCAAAG TATACACCACCCGATCTCGGATCCAAGCCTACCAAAAATTTGGATATGCGGATCTAGATGACAA TATTTATCCTGATCTTTATCTTTTAAATGTATAAATTACTATATGTTACATTAAATTTTATAAT TTTTACACCAAAAAATATAATATTAAATCTCTTTAATTAAAGATTTTTTTTATTTCTCCTTTAT TTGGTTGCTGGATTATGATTTTTAGTTGGCTATGGTTGGAGTCTTGGTGATGTGTATAAGTTTT GGACAATTGAATTTTATTTGGAACAAAGTAAACTTAACTTTGAGGGAAAATATGTTTGATTTCG AGTTCTCTTTTTTTTTGTCACGTTTAGATGAAATTTAATTGGAACAAGCATCTAATTAATGAGT GTTCTTGCTCTAGTTTAAATTTAGTTGAGCACTCTCAATATCTTGGAACACAAAATGACTCTTT TTGGTTTTTGTGATGAATCTTCAGGCCCTGAAGTAGCAAGATTGGCTGACGTGGCTAGGAAAAA CCATGTGTACTTGGTAATGGGAGCCATAGAGAAGGAAGGGTATACCCTCTATTGCACAGTTCTT TTCTTTAGTCCACAGGGTCAGTTCTTGGGCAAGCACCGTAAACTCATGCCCACAAGTTTGGAAC GTTGCATTTGGGGCCAAGGGGACGGATCAACCATCCCCGTTTACGACACTCCCATTGGAAAACT CGGTGCTGCTATTTGCTGGGAGAATAGGATGCCCCTCTACAGAACTGCATTGTACGCCAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.991210953

Conservation Information
Conserved circRNAs	NA
PMCS	0.991210953

			
						 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 3_circ_ag.4

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