Plant Circular RNA Database

Detail information of AT3G14840_circ_g.6

			
						 General Information
					
						CircRNA Name
						AT3G14840_circ_g.6
					
						ID in PlantcircBase
						ath_circ_021822
					
						Alias
						Ath_circ_FC5677
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 4991846-4992519  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, circRNA_finder
					
						Parent gene
						
							AT3G14840						
					
						Parent gene annotation
						
							Probable leucine-rich repeat receptor-like serine/threonine-prot
ein kinase At3g14840
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G14840_circ_g.4 AT3G14840_circ_g.5 AT3G14840_circ_g.7 						
					
						Support reads
						2
					
						Tissues
						root
					
						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
						AT3G14840.2:3

General Information
CircRNA Name	AT3G14840_circ_g.6
ID in PlantcircBase	ath_circ_021822
Alias	Ath_circ_FC5677
Organism	Arabidpsis thaliana
Position	chr3: 4991846-4992519 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, circRNA_finder
Parent gene	AT3G14840
Parent gene annotation	Probable leucine-rich repeat receptor-like serine/threonine-prot ein kinase At3g14840
Parent gene strand	+
Alternative splicing	AT3G14840_circ_g.4 AT3G14840_circ_g.5 AT3G14840_circ_g.7
Support reads	2
Tissues	root
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	AT3G14840.2:3

			
						 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  
						
							CCAGATCAGTTCGTTCTCCTTGAGGCAAATCAAAGTTGCCACGGATAACTTTGATCCTGCAAAC
AAGATCGGAGAAGGTGGTTTTGGTCCTGTACACAAGggtaaacgtgaagtgaaagatttcaata
tcgttgatgaagcaaaaggtgtgggaaaagctgttgttaagaaatttcctgtcatggttacaaa
tgggaaac

						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: 477
Transcript exons: 4991846-4992041,4992138-4992299,4992401-4992519
GGTAAACGTGAAGTGAAAGATTTCAATATCGTTGATGAAGCAAAAGGTGTGGGAAAAGCTGTTG
TTAAGAAATTTCCTGTCATGGTTACAAATGGGAAACTGGAAATAAGATTGCAGTGGGCTGGGAA
AGGAACTCAAGCTATTCCTGTGAGAGGTGTCTATGGTCCTCTCATATCTGCTGTATCGGTAGAT
CCAGATTTTATTCCACCAAAGGAACCGGGCACTGGAACTGGTGGTGGAAGTTCTGTTGGTACAG
TGGTTGGTAGTGTAATCGCTTCTACGGTGTTTCTTGTGCTTTTAATCGGCGGTATATTATGGTG
GAGAGGCTGCTTAAGACCCAAGAGTCAGATGGAAAAAGATTTCAAGAACTTAGATTTCCAGATC
AGTTCGTTCTCCTTGAGGCAAATCAAAGTTGCCACGGATAACTTTGATCCTGCAAACAAGATCG
GAGAAGGTGGTTTTGGTCCTGTACACAAG
						
						Genomic sequence
						
							GGTAAACGTGAAGTGAAAGATTTCAATATCGTTGATGAAGCAAAAGGTGTGGGAAAAGCTGTTG
TTAAGAAATTTCCTGTCATGGTTACAAATGGGAAACTGGAAATAAGATTGCAGTGGGCTGGGAA
AGGAACTCAAGCTATTCCTGTGAGAGGTGTCTATGGTCCTCTCATATCTGCTGTATCGGTAGAT
CCAGGTAAACTTTGCTAAACCTCAAACTATTTACGAGAGACTTCTCCTTTGTTTGAGTGTTTTT
GTCTCTTGACTTTACTCCCATGGTCTTGCTTTCTAGATTTTATTCCACCAAAGGAACCGGGCAC
TGGAACTGGTGGTGGAAGTTCTGTTGGTACAGTGGTTGGTAGTGTAATCGCTTCTACGGTGTTT
CTTGTGCTTTTAATCGGCGGTATATTATGGTGGAGAGGCTGCTTAAGACCCAAGAGTCAGATGG
AAAAAGGTACATAGTTTGAGTTGCTTAAATAGTATTTCAACATTCCAATTCCTTTTGAGTTCTG
TCTCTTTGTATCTTTCTAACTCAGCTGTGTTTCTTCACCTCAGATTTCAAGAACTTAGATTTCC
AGATCAGTTCGTTCTCCTTGAGGCAAATCAAAGTTGCCACGGATAACTTTGATCCTGCAAACAA
GATCGGAGAAGGTGGTTTTGGTCCTGTACACAAG

Sequences
Splice junction sequence	CCAGATCAGTTCGTTCTCCTTGAGGCAAATCAAAGTTGCCACGGATAACTTTGATCCTGCAAAC AAGATCGGAGAAGGTGGTTTTGGTCCTGTACACAAGggtaaacgtgaagtgaaagatttcaata tcgttgatgaagcaaaaggtgtgggaaaagctgttgttaagaaatttcctgtcatggttacaaa tgggaaac
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: 477 Transcript exons: 4991846-4992041,4992138-4992299,4992401-4992519 GGTAAACGTGAAGTGAAAGATTTCAATATCGTTGATGAAGCAAAAGGTGTGGGAAAAGCTGTTG TTAAGAAATTTCCTGTCATGGTTACAAATGGGAAACTGGAAATAAGATTGCAGTGGGCTGGGAA AGGAACTCAAGCTATTCCTGTGAGAGGTGTCTATGGTCCTCTCATATCTGCTGTATCGGTAGAT CCAGATTTTATTCCACCAAAGGAACCGGGCACTGGAACTGGTGGTGGAAGTTCTGTTGGTACAG TGGTTGGTAGTGTAATCGCTTCTACGGTGTTTCTTGTGCTTTTAATCGGCGGTATATTATGGTG GAGAGGCTGCTTAAGACCCAAGAGTCAGATGGAAAAAGATTTCAAGAACTTAGATTTCCAGATC AGTTCGTTCTCCTTGAGGCAAATCAAAGTTGCCACGGATAACTTTGATCCTGCAAACAAGATCG GAGAAGGTGGTTTTGGTCCTGTACACAAG
Genomic sequence	GGTAAACGTGAAGTGAAAGATTTCAATATCGTTGATGAAGCAAAAGGTGTGGGAAAAGCTGTTG TTAAGAAATTTCCTGTCATGGTTACAAATGGGAAACTGGAAATAAGATTGCAGTGGGCTGGGAA AGGAACTCAAGCTATTCCTGTGAGAGGTGTCTATGGTCCTCTCATATCTGCTGTATCGGTAGAT CCAGGTAAACTTTGCTAAACCTCAAACTATTTACGAGAGACTTCTCCTTTGTTTGAGTGTTTTT GTCTCTTGACTTTACTCCCATGGTCTTGCTTTCTAGATTTTATTCCACCAAAGGAACCGGGCAC TGGAACTGGTGGTGGAAGTTCTGTTGGTACAGTGGTTGGTAGTGTAATCGCTTCTACGGTGTTT CTTGTGCTTTTAATCGGCGGTATATTATGGTGGAGAGGCTGCTTAAGACCCAAGAGTCAGATGG AAAAAGGTACATAGTTTGAGTTGCTTAAATAGTATTTCAACATTCCAATTCCTTTTGAGTTCTG TCTCTTTGTATCTTTCTAACTCAGCTGTGTTTCTTCACCTCAGATTTCAAGAACTTAGATTTCC AGATCAGTTCGTTCTCCTTGAGGCAAATCAAAGTTGCCACGGATAACTTTGATCCTGCAAACAA GATCGGAGAAGGTGGTTTTGGTCCTGTACACAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.262408047

Conservation Information
Conserved circRNAs	NA
PMCS	0.262408047

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4991927-4992516(+)
						
						Potential amino acid sequence
						
							MVTNGKLEIRLQWAGKGTQAIPVRGVYGPLISAVSVDPDFIPPKEPGTGTGGGSSVGTVVGSVI
ASTVFLVLLIGGILWWRGCLRPKSQMEKDFKNLDFQISSFSLRQIKVATDNFDPANKIGEGGFG
PVHKGKREVKDFNIVDEAKGVGKAVVKKFPVMVTNGKLEIRLQWAGKGTQAIPVRGVYGPLISA
VSVDPDFIPPKEPGTGTGGGSSVGTVVGSVIASTVFLVLLIGGILWWRGCLRPKSQMEKDFKNL
DFQISSFSLRQIKVATDNFDPANKIGEGGFGPVHKGKREVKDFNIVDEAKGVGKAVVKKFPVMV
TNGKLEIRLQWAGKGTQAIPVRGVYGPLISAVSVDPDFIPPKEPGTGTGGGSSVGTVVGSVIAS
TVFLVLLIGGILWWRGCLRPKSQMEKDFKNLDFQISSFSLRQIKVATDNFDPANKIGEGGFGPV
HKGKREVKDFNIVDEAKGVGKAVVKKFPVMVTNGKLEIRLQWAGKGTQAIPVRGVYGPLISAVS
VDPDFIPPKEPGTGTGGGSSVGTVVGSVIASTVFLVLLIGGILWWRGCLRPKSQMEKDFKNLDF
QISSFSLRQIKVATDNFDPANKIGEGGFGPVHK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4991927-4992516(+)
Potential amino acid sequence	MVTNGKLEIRLQWAGKGTQAIPVRGVYGPLISAVSVDPDFIPPKEPGTGTGGGSSVGTVVGSVI ASTVFLVLLIGGILWWRGCLRPKSQMEKDFKNLDFQISSFSLRQIKVATDNFDPANKIGEGGFG PVHKGKREVKDFNIVDEAKGVGKAVVKKFPVMVTNGKLEIRLQWAGKGTQAIPVRGVYGPLISA VSVDPDFIPPKEPGTGTGGGSSVGTVVGSVIASTVFLVLLIGGILWWRGCLRPKSQMEKDFKNL DFQISSFSLRQIKVATDNFDPANKIGEGGFGPVHKGKREVKDFNIVDEAKGVGKAVVKKFPVMV TNGKLEIRLQWAGKGTQAIPVRGVYGPLISAVSVDPDFIPPKEPGTGTGGGSSVGTVVGSVIAS TVFLVLLIGGILWWRGCLRPKSQMEKDFKNLDFQISSFSLRQIKVATDNFDPANKIGEGGFGPV HKGKREVKDFNIVDEAKGVGKAVVKKFPVMVTNGKLEIRLQWAGKGTQAIPVRGVYGPLISAVS VDPDFIPPKEPGTGTGGGSSVGTVVGSVIASTVFLVLLIGGILWWRGCLRPKSQMEKDFKNLDF QISSFSLRQIKVATDNFDPANKIGEGGFGPVHK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT3G14840_circ_g.6

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