Plant Circular RNA Database

Detail information of AT4G15340_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT4G15340_circ_g.1
					
						ID in PlantcircBase
						ath_circ_031066
					
						Alias
						Chr4:8756898|8758635
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 8756898-8758635  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						CIRCexplorer; CIRI
					
						Parent gene
						
							AT4G15340						
					
						Parent gene annotation
						
							Arabidiol synthase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						6
					
						Tissues
						seedling
					
						Exon boundary  
						
							No-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  
						
							CT-TA							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
						AT4G15340.2:5
AT4G15340.1:5

General Information
CircRNA Name	AT4G15340_circ_g.1
ID in PlantcircBase	ath_circ_031066
Alias	Chr4:8756898\|8758635
Organism	Arabidpsis thaliana
Position	chr4: 8756898-8758635 JBrowse»
Reference genome	TAIR10.38
Type	ei-circRNA
Identification method	CIRCexplorer; CIRI
Parent gene	AT4G15340
Parent gene annotation	Arabidiol synthase
Parent gene strand	-
Alternative splicing	NA
Support reads	6
Tissues	seedling
Exon boundary	No-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	CT-TA 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	AT4G15340.2:5 AT4G15340.1:5

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							YES							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   
						
							Convergent:(F):ACTCCAACACCTCTCATCCTCCAG
(R):TCTTCCTCCTTTGCACATCGGTTTC.Divergent:(F):GTGGAGAAACTCTTTGATGCCGTTG
(R)GGATGAGAGGTGTTGGAGTTGC
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	YES 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	Convergent:(F):ACTCCAACACCTCTCATCCTCCAG (R):TCTTCCTCCTTTGCACATCGGTTTC.Divergent:(F):GTGGAGAAACTCTTTGATGCCGTTG (R)GGATGAGAGGTGTTGGAGTTGC 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  
						
							TGGAGCTGGAGGATGAGAGGTGTTGGAGTTGCAACAAATTTTTTACCATACAAGTATGACAACC
CCATGAAAATATCCCGTAAATAAATCCATAGAGTTCcctgcaagtagagaagaaaatcaacggc
atcaaagagtttctccacatccattttctggccaacaaactccgacggcatcctctcaaataat
agacagca

									
								

					

						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
						
							CCTGCAAGTAGAGAAGAAAATCAACGGCATCAAAGAGTTTCTCCACATCCATTTTCTGGCCAAC
AAACTCCGACGGCATCCTCTCAAATAATAGACAGCACTGAGAGTTTGAGCAAATCATTTGTTTA
GACTTTAGACTAATGACTAAATTTAATTAGTAGAGATATTTTTATCTCTTACTTTTAAACTCTC
AGCAGTGCAGTCTGAAACAGGCCATCCTTGATCTTTGTCCGAAAACGTCCATCCACCTTTCGAA
ATATGGCGGAACATTTTTATGTGATCACTAGGAGGATTCTCTGTAACTTGAGATTTCTTCAAGT
AATCGTATCCTTTAACGAGCGTGGATCTAATTTCATCATCGACATCATCCTCAACACCGTCTAA
CAGGAAATGTAGCGACATGACTGTATCCCACAATTGGCTGCCAAAAGACTGCAAGAGTTGTATG
TATATATGTGTTATTATTATTTATTCGTCAACCAAATAGAGATGGTATAGAGTTGGGATTTTAT
TCCATGGAGGATCTACAAACTAGAAAAGTCAAGAGCTAGAATTCAAAGTCAAAAGCATGAAGAA
TAAACCTGAATTTTGAGGCCATCCTCGCCAATCCATATGAAATCAGAGACTCGAGCAAGATGCT
TTTTAAAATATTCACCCTCTGGGTCTTCTACCCAACATGCAAGCATATGAAAGGCCTATTAAAC
AAAAAAAAGGAAACAAAGATTATTCCAAGAAAAAAAAAAAAAAAAAAACAACAAAATTACCTTT
GGCACTGATCCGCCTGTAATGTATCTATTGGCTTCATCTTGATAGTGAAGGAGTTTCATAGTGG
TTCGAAGAGCTGCTTGTCTTATGAGCTTGTTGAAAGGCCATCGATTTAGAATACTCTCTGAGAA
GATATGAACACCTTTCCAAAACAAATCTTGTAAAAATGAGGATGGATAACAGAGATCTTCCTGC
ATGATCATAATCACATTTCTTTAATATCAAAAAAGTATTTGGTAATTTAACACTTCTTTTGCAC
TAATTTGCAAACTAACCGATTTTTAAAAGCATCCAAAGAACACATTTTCTTGTAAAAAAGACGG
ATTTACCTAAAATTAGTGGATATGTGAGGCTTGGGAGCTTTTTATGCGAATATTTGCTTACCAA
ATTGTTTTGTTTTGTTTTTCTTACAAATATAGGTTCACGGATAACATATAAAATTGTCAATACG
AGTAAAAAGTGTTACGTCTTTAGTTAATATCCAAAGGTGCTACGAACATAAAATAAACTTTTAA
AATGCTAATTTGCCACCAAAAAGGGATCAACGCATCGTGACGAAAAAAAAAACAAAAACAAAAG
GGACCTAAGCATCGATAATAAATAAATGGTGTACCTAATATTTATTTTTATAAGCGTACCATTG
GCGTAAGCAAATAAATTGTTGTACCTAATATTAGATTGTGTGTAAGATAAACTAAAATTTAGTG
TATACATGCTGTTCTCAATAGAATAAGACATGCATACATAAACCTTAGTACTATTTTTTTTCTA
ATGTATATGACATGTGATTTGTATTTACAACTTGCCTTTGCACATCGGTTTCTGGTAAGCCTCC
AATTGATTTTGGTGTAAGGCTCTGGATAAAGCTCTTCTTGGAGCTGGAGGATGAGAGGTGTTGG
AGTTGCAACAAATTTTTTACCATACAAGTATGACAACCCCATGAAAATATCCCGTAAATAAATC
CATAGAGTTC
						
					

			
		

Sequences
Splice junction sequence	TGGAGCTGGAGGATGAGAGGTGTTGGAGTTGCAACAAATTTTTTACCATACAAGTATGACAACC CCATGAAAATATCCCGTAAATAAATCCATAGAGTTCcctgcaagtagagaagaaaatcaacggc atcaaagagtttctccacatccattttctggccaacaaactccgacggcatcctctcaaataat agacagca
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	CCTGCAAGTAGAGAAGAAAATCAACGGCATCAAAGAGTTTCTCCACATCCATTTTCTGGCCAAC AAACTCCGACGGCATCCTCTCAAATAATAGACAGCACTGAGAGTTTGAGCAAATCATTTGTTTA GACTTTAGACTAATGACTAAATTTAATTAGTAGAGATATTTTTATCTCTTACTTTTAAACTCTC AGCAGTGCAGTCTGAAACAGGCCATCCTTGATCTTTGTCCGAAAACGTCCATCCACCTTTCGAA ATATGGCGGAACATTTTTATGTGATCACTAGGAGGATTCTCTGTAACTTGAGATTTCTTCAAGT AATCGTATCCTTTAACGAGCGTGGATCTAATTTCATCATCGACATCATCCTCAACACCGTCTAA CAGGAAATGTAGCGACATGACTGTATCCCACAATTGGCTGCCAAAAGACTGCAAGAGTTGTATG TATATATGTGTTATTATTATTTATTCGTCAACCAAATAGAGATGGTATAGAGTTGGGATTTTAT TCCATGGAGGATCTACAAACTAGAAAAGTCAAGAGCTAGAATTCAAAGTCAAAAGCATGAAGAA TAAACCTGAATTTTGAGGCCATCCTCGCCAATCCATATGAAATCAGAGACTCGAGCAAGATGCT TTTTAAAATATTCACCCTCTGGGTCTTCTACCCAACATGCAAGCATATGAAAGGCCTATTAAAC AAAAAAAAGGAAACAAAGATTATTCCAAGAAAAAAAAAAAAAAAAAAACAACAAAATTACCTTT GGCACTGATCCGCCTGTAATGTATCTATTGGCTTCATCTTGATAGTGAAGGAGTTTCATAGTGG TTCGAAGAGCTGCTTGTCTTATGAGCTTGTTGAAAGGCCATCGATTTAGAATACTCTCTGAGAA GATATGAACACCTTTCCAAAACAAATCTTGTAAAAATGAGGATGGATAACAGAGATCTTCCTGC ATGATCATAATCACATTTCTTTAATATCAAAAAAGTATTTGGTAATTTAACACTTCTTTTGCAC TAATTTGCAAACTAACCGATTTTTAAAAGCATCCAAAGAACACATTTTCTTGTAAAAAAGACGG ATTTACCTAAAATTAGTGGATATGTGAGGCTTGGGAGCTTTTTATGCGAATATTTGCTTACCAA ATTGTTTTGTTTTGTTTTTCTTACAAATATAGGTTCACGGATAACATATAAAATTGTCAATACG AGTAAAAAGTGTTACGTCTTTAGTTAATATCCAAAGGTGCTACGAACATAAAATAAACTTTTAA AATGCTAATTTGCCACCAAAAAGGGATCAACGCATCGTGACGAAAAAAAAAACAAAAACAAAAG GGACCTAAGCATCGATAATAAATAAATGGTGTACCTAATATTTATTTTTATAAGCGTACCATTG GCGTAAGCAAATAAATTGTTGTACCTAATATTAGATTGTGTGTAAGATAAACTAAAATTTAGTG TATACATGCTGTTCTCAATAGAATAAGACATGCATACATAAACCTTAGTACTATTTTTTTTCTA ATGTATATGACATGTGATTTGTATTTACAACTTGCCTTTGCACATCGGTTTCTGGTAAGCCTCC AATTGATTTTGGTGTAAGGCTCTGGATAAAGCTCTTCTTGGAGCTGGAGGATGAGAGGTGTTGG AGTTGCAACAAATTTTTTACCATACAAGTATGACAACCCCATGAAAATATCCCGTAAATAAATC CATAGAGTTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.108278423

Conservation Information
Conserved circRNAs	NA
PMCS	0.108278423

			
						 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
						responsive to methyl jasmonate (validated)

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	responsive to methyl jasmonate (validated)

			
						 Other Information
					
						References
						Zhang et al., 2020

circRNA

Detail information of AT4G15340_circ_g.1

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