Plant Circular RNA Database

Detail information of AT4G18960_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G18960_circ_g.3
					
						ID in PlantcircBase
						ath_circ_031623
					
						Alias
						4:10383912-10387706
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 10383912-10387706  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G18960						
					
						Parent gene annotation
						
							K-box region and MADS-box transcription factor family protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G18960_circ_g.1 AT4G18960_circ_g.2 						
					
						Support reads
						2
					
						Tissues
						flower
					
						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
						AT4G18960.1:5
AT4G18960.2:6
AT4G18960.3:6
AT4G18960.4:6

General Information
CircRNA Name	AT4G18960_circ_g.3
ID in PlantcircBase	ath_circ_031623
Alias	4:10383912-10387706
Organism	Arabidpsis thaliana
Position	chr4: 10383912-10387706 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G18960
Parent gene annotation	K-box region and MADS-box transcription factor family protein
Parent gene strand	+
Alternative splicing	AT4G18960_circ_g.1 AT4G18960_circ_g.2
Support reads	2
Tissues	flower
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	AT4G18960.1:5 AT4G18960.2:6 AT4G18960.3:6 AT4G18960.4:6

			
						 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  
						
							AATATAATATCAAATTAAATCTATATGCCTTGTTGCTAATTTTTGTTTAATTTTACAGAATGAG
CTCTTATTTTCTGAAATCGACTACATGCAGAAAAGAcaatcacggcgtaccaatcggagctagg
aggagattcctctcccttgaggaaatctgggagaggaaagatcgaaatcaaacggatcgagaac
acaacgaa

									
								

					

						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
						
							CAATCACGGCGTACCAATCGGAGCTAGGAGGAGATTCCTCTCCCTTGAGGAAATCTGGGAGAGG
AAAGATCGAAATCAAACGGATCGAGAACACAACGAATCGTCAAGTCACTTTTTGCAAACGTAGA
AATGGTTTGCTCAAGAAAGCTTACGAGCTCTCTGTTCTTTGTGATGCTGAAGTCGCACTCATCG
TCTTCTCTAGCCGTGGTCGTCTCTATGAGTACTCTAACAACAGGTTTCTTCTTCTTCTCGTGCT
CTGTTCTTACTTTATTAATAATTAAATTATTTTTAAAGTCCGATTTAGGGTTTTATGTTTATGT
TAAAGCATAAATCTTTTACGAGGGTTTTCGATCTTCTAAGCTAGATTTGATTCTCTTCTTCTTG
AATGCTCTTATGGGTAGGATTATTTTTCACTTTTTTCCTTCATATTCCACACACATATATATAT
AAACACACTAACATTAGTGGGAATATTTGTTTGATATGTTTATTTTATTTACTTCGGGGGTTTT
TGTAACAATTTTGTAGATCTAATTTCTTGTTCTTCATGTGTATATTAATTTTCCCTTAAGACTT
AAATAAAAAGAGAGAATTTGTTATATATAGATATATGAAGTGAGGGAAATGGTACAAAGTTAAA
GGAGATCTGAGTGAGAGTTAGATAATAAATGAAAAGAAATAAGAAACCATCAGGGTTTTTTCTA
ATGTGGAGTTTTAGATTCAGTTTTGTAGAACTAAGATTCACTTTGTTGGGTGTTCTTTCTTCAC
TCATTTCTGTTATTATAATAATAATAAAATCTTATATCTTTCTATTTTCCTTACTAACAAGTAC
TTGAAGATTTAGATATATTTATAGATCTGGTGTTGTAATAGGTAAAAACTTGATTTTTATGACT
ATAAAAGTAAGTTTTGGGAAACAAATTGGGGAGAGAGTAAGGAAGGACTATGAGGTCATATCTT
CTGTTTTGTGATCATCCATCCTCCATTGTTGTTAATGTCTGTGTCTCTCTTTTTCTTCTCTTCT
TTCTCTTACTTTCCTTTCTTATCTCTAGCTCTCTTTCTCTCTCATGAATTATATCATATCATAT
ATTTGATACAAACACATGTGATGGTAAGTGAGAGTGAATAAGGTGAAACTAGCTAGATTTTTGA
GTTTTCATGAAATTTTAACTTATATGAGTGATAGAAAATAATGGAACTTATACGTACATGTAGG
ACAATTTAGATGGTTATCTAAGTTTTTGTTTTTGTTTTCTCTTGAGAATGTTAAATGTTAGTGT
TATTTTTGTAGTTTTGGAAAATTATATATGAGCTAAGATTAGTTTAGAAGTGGTCAAAAGAAAC
ATAGATTTGAAATTTCAACTGAATTTTCAAGATTTCAAATAGTCAATGAAACAAGGAGGTAATT
AAGACAAATTAGCTTATGGGGACTCTTTTTTGTTATTCCTTAAAATTACTCTTTTTAAAATTAA
AAATAACTAATCTCATTTCGAACTACATTACTCAAACTAGTAATCTCTAATTCGACACGCAATT
TCCAAATACTTATTAGTAGAGAGTCCCACGTGATTACTTTCTTCTCCACCAAAACATAAAACAT
GTCAAGATTAAATGGTGTTTGAAAATTAAAAGATCAATTTTCTTAATCGTTTACAGTTGTCAAC
TCTCATGTCCTGAAATATATAATTCTCATGTCCAAAACAAGAAAAGCTAACAACGACTTCAAAT
TAAATCAGTCAATCAAAATTAGTCTTCATTTACCTACTAATTTCTTTTTATATATCCGATGGGT
ACTCTACGAAATCAGAGTTTCGTTTCTTTATTTATTTTCTTTTATAAGATTTTTGAGGTTTTTT
CAGAGGTTGGAATTGAGCGCAAGATTAGGTTTTGGGTCTGTAAGATTTGTTGTCTTTGTTAAAG
AATCTTTGATCACGTCATCACTCAGATATTATTTCTTTTTATTTTTCACTTGTATTTTTACTAA
TTTATTATAAAGTTTTGTTAGTTTCAGTTCTTGACTTCTGACAAGAAGGTTTTATGTCATAATG
AATTAATTTGTAACCTATTTATAAATTCAAAAATGTCATCATATTACTACTTTTGACCATTTAA
TATTAGATTTCTCATTTGGTCAATACCCAATGTTCATATTACATATATAGAGACAAAAATTATA
AGGATACTAAATTGTTCATATTTCTTGGAAGTAAAAAGATTAATGATCACTGAATAAATAGATT
TGGCATAGAAGTATAGCATTGGAATTGCTTCAACATCTTTGGTGTAGATAGATTTATGCAATTT
CTCTTTCTTTTTGAAGTATCTTTTTTTTTTCTAGAGAGAGAATAATGTTAGGGATTTTTATCAT
TTTCTCTCTCATTATGGGTACTGAGAGGAAAGTGAGATTTTTAGTACGGATCCAATAGTTTAAG
AGTTTGGTCTGCCTTCTACGATCCAAAAAAATCTACGGTCATGATCTCTCCATCGAGAAGGTTG
AGAGTTCAGACATCAAAGTCTATAATATGTCATTGTAATACGTATTTGTGTATATATATCTATG
TACAAGTACATATACAGGAAACTCAAGAAAAAAGAATAAATGGTAAATTTAATTATATTCCAAA
TAAGGAAAGTATGGAACGTTGTGATGTTACTCGGACAAGTCATTTAGTTACATCCATCACGTTT
AAATTTAATCCAATGGTTACAATTTTAATACTATCAAATGTCTATTGGATTTATACCCAATGTG
TTAATGGGTTGTTGACACATGTCACATGTCTGAAACCCTAGACATGTTCAGACCAATCATGTCA
CTCTAATTTTGCCAGCATGGCAGTTGGCAGCCAATCACTAGCTCGATAAATTTAAGGTTTCAGA
GGAATTTTAATTTATTTAGGGTTCATATTGTTTCATAAAATGATTCTTTATTTGTTACAACTTT
AAGGAAATATTTTATTAACTATTTAATTGTTCCCTTTTCTTATATTACTTTTGTTTTTTCTTCA
CATCATGTGTCACATTAAGTTGCATTTCTTCTGACTCAAAAGAACCGATGTTTGCTTTTAAGGT
TTCGTATTAGAATCACTTAACTGTGCAAGTGGTCGATTTGACCCTATCAATTTTATTTTTTATT
ACTTATCAAAATGCAGATTTAAGCGTAGATTAAGTTTAGAAAATAGGTAGTTAATAGGTCTAAT
TAACTTATTAATTCCTTTAAAAAAATTATTGCAGTGTAAAAGGGACTATTGAGAGGTACAAGAA
GGCAATATCGGACAATTCTAACACCGGATCGGTGGCAGAAATTAATGCACAGGTAAGTGGTAAC
TTAATATTACACGAATGATTTTAATTAATATATGATGACATGACAACATTGTTCATTCTTTTAC
TCTTTTTTTTTTTGTTGTTGTTGTAGTATTATCAACAAGAATCAGCCAAATTGCGTCAACAAAT
AATCAGCATACAAAACTCCAACAGGTTAATTATCTAACTGACTTGAAATATTTGATTACTTGGT
TGTTATTAACTATTTGATATATTAACATATGTTGATAAATCAATTAGGCAATTGATGGGTGAGA
CGATAGGGTCAATGTCTCCCAAAGAGCTCAGGAACTTGGAAGGCAGATTAGAGAGAAGTATTAC
CCGAATCCGATCCAAGAAGGTAATTCTATTTTTTTTATAAATGCTTCAATATAATATCAAATTA
AATCTATATGCCTTGTTGCTAATTTTTGTTTAATTTTACAGAATGAGCTCTTATTTTCTGAAAT
CGACTACATGCAGAAAAGA
						
					

			
		

Sequences
Splice junction sequence	AATATAATATCAAATTAAATCTATATGCCTTGTTGCTAATTTTTGTTTAATTTTACAGAATGAG CTCTTATTTTCTGAAATCGACTACATGCAGAAAAGAcaatcacggcgtaccaatcggagctagg aggagattcctctcccttgaggaaatctgggagaggaaagatcgaaatcaaacggatcgagaac acaacgaa
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	CAATCACGGCGTACCAATCGGAGCTAGGAGGAGATTCCTCTCCCTTGAGGAAATCTGGGAGAGG AAAGATCGAAATCAAACGGATCGAGAACACAACGAATCGTCAAGTCACTTTTTGCAAACGTAGA AATGGTTTGCTCAAGAAAGCTTACGAGCTCTCTGTTCTTTGTGATGCTGAAGTCGCACTCATCG TCTTCTCTAGCCGTGGTCGTCTCTATGAGTACTCTAACAACAGGTTTCTTCTTCTTCTCGTGCT CTGTTCTTACTTTATTAATAATTAAATTATTTTTAAAGTCCGATTTAGGGTTTTATGTTTATGT TAAAGCATAAATCTTTTACGAGGGTTTTCGATCTTCTAAGCTAGATTTGATTCTCTTCTTCTTG AATGCTCTTATGGGTAGGATTATTTTTCACTTTTTTCCTTCATATTCCACACACATATATATAT AAACACACTAACATTAGTGGGAATATTTGTTTGATATGTTTATTTTATTTACTTCGGGGGTTTT TGTAACAATTTTGTAGATCTAATTTCTTGTTCTTCATGTGTATATTAATTTTCCCTTAAGACTT AAATAAAAAGAGAGAATTTGTTATATATAGATATATGAAGTGAGGGAAATGGTACAAAGTTAAA GGAGATCTGAGTGAGAGTTAGATAATAAATGAAAAGAAATAAGAAACCATCAGGGTTTTTTCTA ATGTGGAGTTTTAGATTCAGTTTTGTAGAACTAAGATTCACTTTGTTGGGTGTTCTTTCTTCAC TCATTTCTGTTATTATAATAATAATAAAATCTTATATCTTTCTATTTTCCTTACTAACAAGTAC TTGAAGATTTAGATATATTTATAGATCTGGTGTTGTAATAGGTAAAAACTTGATTTTTATGACT ATAAAAGTAAGTTTTGGGAAACAAATTGGGGAGAGAGTAAGGAAGGACTATGAGGTCATATCTT CTGTTTTGTGATCATCCATCCTCCATTGTTGTTAATGTCTGTGTCTCTCTTTTTCTTCTCTTCT TTCTCTTACTTTCCTTTCTTATCTCTAGCTCTCTTTCTCTCTCATGAATTATATCATATCATAT ATTTGATACAAACACATGTGATGGTAAGTGAGAGTGAATAAGGTGAAACTAGCTAGATTTTTGA GTTTTCATGAAATTTTAACTTATATGAGTGATAGAAAATAATGGAACTTATACGTACATGTAGG ACAATTTAGATGGTTATCTAAGTTTTTGTTTTTGTTTTCTCTTGAGAATGTTAAATGTTAGTGT TATTTTTGTAGTTTTGGAAAATTATATATGAGCTAAGATTAGTTTAGAAGTGGTCAAAAGAAAC ATAGATTTGAAATTTCAACTGAATTTTCAAGATTTCAAATAGTCAATGAAACAAGGAGGTAATT AAGACAAATTAGCTTATGGGGACTCTTTTTTGTTATTCCTTAAAATTACTCTTTTTAAAATTAA AAATAACTAATCTCATTTCGAACTACATTACTCAAACTAGTAATCTCTAATTCGACACGCAATT TCCAAATACTTATTAGTAGAGAGTCCCACGTGATTACTTTCTTCTCCACCAAAACATAAAACAT GTCAAGATTAAATGGTGTTTGAAAATTAAAAGATCAATTTTCTTAATCGTTTACAGTTGTCAAC TCTCATGTCCTGAAATATATAATTCTCATGTCCAAAACAAGAAAAGCTAACAACGACTTCAAAT TAAATCAGTCAATCAAAATTAGTCTTCATTTACCTACTAATTTCTTTTTATATATCCGATGGGT ACTCTACGAAATCAGAGTTTCGTTTCTTTATTTATTTTCTTTTATAAGATTTTTGAGGTTTTTT CAGAGGTTGGAATTGAGCGCAAGATTAGGTTTTGGGTCTGTAAGATTTGTTGTCTTTGTTAAAG AATCTTTGATCACGTCATCACTCAGATATTATTTCTTTTTATTTTTCACTTGTATTTTTACTAA TTTATTATAAAGTTTTGTTAGTTTCAGTTCTTGACTTCTGACAAGAAGGTTTTATGTCATAATG AATTAATTTGTAACCTATTTATAAATTCAAAAATGTCATCATATTACTACTTTTGACCATTTAA TATTAGATTTCTCATTTGGTCAATACCCAATGTTCATATTACATATATAGAGACAAAAATTATA AGGATACTAAATTGTTCATATTTCTTGGAAGTAAAAAGATTAATGATCACTGAATAAATAGATT TGGCATAGAAGTATAGCATTGGAATTGCTTCAACATCTTTGGTGTAGATAGATTTATGCAATTT CTCTTTCTTTTTGAAGTATCTTTTTTTTTTCTAGAGAGAGAATAATGTTAGGGATTTTTATCAT TTTCTCTCTCATTATGGGTACTGAGAGGAAAGTGAGATTTTTAGTACGGATCCAATAGTTTAAG AGTTTGGTCTGCCTTCTACGATCCAAAAAAATCTACGGTCATGATCTCTCCATCGAGAAGGTTG AGAGTTCAGACATCAAAGTCTATAATATGTCATTGTAATACGTATTTGTGTATATATATCTATG TACAAGTACATATACAGGAAACTCAAGAAAAAAGAATAAATGGTAAATTTAATTATATTCCAAA TAAGGAAAGTATGGAACGTTGTGATGTTACTCGGACAAGTCATTTAGTTACATCCATCACGTTT AAATTTAATCCAATGGTTACAATTTTAATACTATCAAATGTCTATTGGATTTATACCCAATGTG TTAATGGGTTGTTGACACATGTCACATGTCTGAAACCCTAGACATGTTCAGACCAATCATGTCA CTCTAATTTTGCCAGCATGGCAGTTGGCAGCCAATCACTAGCTCGATAAATTTAAGGTTTCAGA GGAATTTTAATTTATTTAGGGTTCATATTGTTTCATAAAATGATTCTTTATTTGTTACAACTTT AAGGAAATATTTTATTAACTATTTAATTGTTCCCTTTTCTTATATTACTTTTGTTTTTTCTTCA CATCATGTGTCACATTAAGTTGCATTTCTTCTGACTCAAAAGAACCGATGTTTGCTTTTAAGGT TTCGTATTAGAATCACTTAACTGTGCAAGTGGTCGATTTGACCCTATCAATTTTATTTTTTATT ACTTATCAAAATGCAGATTTAAGCGTAGATTAAGTTTAGAAAATAGGTAGTTAATAGGTCTAAT TAACTTATTAATTCCTTTAAAAAAATTATTGCAGTGTAAAAGGGACTATTGAGAGGTACAAGAA GGCAATATCGGACAATTCTAACACCGGATCGGTGGCAGAAATTAATGCACAGGTAAGTGGTAAC TTAATATTACACGAATGATTTTAATTAATATATGATGACATGACAACATTGTTCATTCTTTTAC TCTTTTTTTTTTTGTTGTTGTTGTAGTATTATCAACAAGAATCAGCCAAATTGCGTCAACAAAT AATCAGCATACAAAACTCCAACAGGTTAATTATCTAACTGACTTGAAATATTTGATTACTTGGT TGTTATTAACTATTTGATATATTAACATATGTTGATAAATCAATTAGGCAATTGATGGGTGAGA CGATAGGGTCAATGTCTCCCAAAGAGCTCAGGAACTTGGAAGGCAGATTAGAGAGAAGTATTAC CCGAATCCGATCCAAGAAGGTAATTCTATTTTTTTTATAAATGCTTCAATATAATATCAAATTA AATCTATATGCCTTGTTGCTAATTTTTGTTTAATTTTACAGAATGAGCTCTTATTTTCTGAAAT CGACTACATGCAGAAAAGA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.12763782

Conservation Information
Conserved circRNAs	NA
PMCS	0.12763782

			
						 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 AT4G18960_circ_g.3

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