Plant Circular RNA Database

Detail information of Solyc09g097960.2_circ_ag.1

			
						 General Information
					
						CircRNA Name
						Solyc09g097960.2_circ_ag.1
					
						ID in PlantcircBase
						sly_circ_003002
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr9: 71918669-71922258  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							Solyc09g097960.2_circ_ag.2 						
					
						Support reads
						3
					
						Tissues
						fruit
					
						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	Solyc09g097960.2_circ_ag.1
ID in PlantcircBase	sly_circ_003002
Alias	NA
Organism	Solanum lycopersicum
Position	chr9: 71918669-71922258 JBrowse»
Reference genome	SL2.50.38
Type	ag-circRNA
Identification method	CIRI
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	Solyc09g097960.2_circ_ag.2
Support reads	3
Tissues	fruit
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  
						
							AAGGGCAGCATGCGAGGCTAGCTTAAAGCGACTTGATGTTGACTGCATAGACTTGTACTACCAG
CACCGGATTGATACACGCGTGCCCATTGAAGTAACGgttggagaacttaagaagctggttgaag
agggtaaaataaaatatataggtctatcagaggcttcagcatcaacaattagaagagcacacgc
tgttcatc

									
								

					

						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
						
							GTTGGAGAACTTAAGAAGCTGGTTGAAGAGGGTAAAATAAAATATATAGGTCTATCAGAGGCTT
CAGCATCAACAATTAGAAGAGCACACGCTGTTCATCCAATAACAGCAGTACAATTAGAATGGTC
ACTATGGTCGAGAGATGTAGAGGAAGAAATAATCCCTACTTGCAGGTACTTTTTTTCTTCTTTC
TGTTAGTTTTTTTTGTGTTTGAGGTTTATACCAATGTGAGATCCTGATTTTTCCCGTCTGTTAA
CTGTTCAGAGAACTCGGAATTGGGATTGTAGCATACAGTCCACTAGGCCGGGGCTTTTTGTCAT
CCGGTCCAAAGCTGGTTGAGGACTTGACAAATGAAGATTTCCGAAAGGTTCAGATTATATTTAT
TGTTTGTTTTGAGGTCCAATATGTTCACATTATGTTTAATTGCAGTGCATTTGACTTGAAAAGA
TCTCCAACTTTGCAGCATCTACCGAGGTTTCAGGGCGAGAATCTTGAGCATAACAAAAAATTGT
ACGAGAGGATTTGTGAATTGGCAACTAAGAAGGGATGCACCCCGTCTCAACTGGCGTTGGCGTG
GGTACATCACCAAGGAAACGACGTGTGTCCCATCCCGGGCACCACTAAGATTGAAAATTTCAAT
CAGAACATTGGAGCTCTGTCCATAAAGCTAACATCAGAAGACATGGCAGAGCTTGAATCTATTG
CTTCAGCTAATGCAGTCCAGGGTGATAGGTACGGTTCGGCTGCAGCAACCTACAAAGATTCAGA
AACTCCTCCTATTTCAGCATGGAAGGCTACATAAATATAGAGTTGTTCTTGTGTTGTGCACTGT
ATGTAATGAGGTTTCTTTTTTCCTGTTTCAAAACTATTGTGCCACTTACTGATGGTTCAAATAA
TAAAATCAATTCTCTGTTTGTGGACTTTTTCCTATGGAGTAAAATATTGATATCTATTGGCTTT
CTATTTAGTTATGCATAAATTAGTTATATTTCTGTTAGTTATTCGATTTTCTATATGTAACTTT
TACTAAATTCAGATTTGCATAAAGTTACAGAAACAATTTCACATGCAAAATTCGAACATAACTA
ATTTAGATTTGTACAAAGTTACGAAGTGATTTCATATTCAAAGTTCAAATATACGTACTTTGCA
AAAAATTTACAAAAGCGATTTCATATCCATACTGATTCAAATTTGCACAAAGTTACAAAAATGA
TTCCATAGCCGAGATTCAAAGTTCAAATATACATACTAATTTAAATTTGCATAAAAGTTATTTC
ATATACAAGATTAGAACGAACATAAATATTCAAATTCACGTAAAGTTATATAAACGATTTCATA
TCCAGAATTCAATCCTACACAATAATTTAAATTTACACAAATTTATAAAAACAATTTTATATTC
GGGATTCGAACTTTCCGAATGAAAGATTAACACATAACCACAACTTTGGTGTTTGTCATTTGTC
AATACCATATCTAATTAGCAACCTCTATATATACAAAACAATATCCACTTGCTCAATTATGTGC
ATATTTGCAGAGTAGTAAGCTTAAGCTGAATCACAACAATGGCGGCAGAGGGAACAAAAGTGGG
AAGAATCAAATTGGGTTCAGAGGGTCTTGAAGTATCTGCTCAAGGACTTGGTTGTATGGGTATG
TCCGCTTTTTACGGGCCTCCCAAACCCGATTCCGATATGGTCCAACTCATCCACCACGCCATTA
ACTCCGGCGTCACATTTCTCGATACTTCCGATGTATATGGGCCCCACACTAATGAAATCCTCCT
CGGCAAGGTACTTAACTTCTTAATTTTTGGGATTTTCTCTGCCTTTTATGCATTGATTATTGTA
CGCTATGCTTGTTGATTTTGGAATCTTGGTGTTTGAGCTGGAATTGTTGTAACATATGCAAATG
TGCTGGTTCATAAAGCTTAAAAGGCTTGCACTTTTCGCATCCTTGTAGCCTAGGGATCTGTTAA
ATGAGTCGAGAACATGAGGTTTAAGGTTCAGCTAAGACACCATGGTTATCAATAAAAAAGAAAA
GACTCTACTTTTTGTTTTAGGTTGAATTGGGTTGGATTTGGTGCTATTCTTTACACGTTTTAGC
TCCTTTGAGGTGGACCTTAGCAAGAAATGTTGTTCATGGTTCTTCAAAACATGTATATCTTTTG
GAGGTGTTGACCTAAGTTGCTCGGACTCAGGTGCGGGTGTCCGATACGTGTGTGGATCTAAAGG
TCGGATTCATCATGATCGATCTAATTTTTAAGATTCAGGAATATGGATCCATATGAGTGCGGGG
ACTCGCCTAAAAATAATTAGAATATTTAAAAAATAGAGCTATAAAACCTAAATTATGAGATATT
ATGTGGAGAACTTGAGGAGAATCCAGGAAGGAGATCAAAGGAAAAGGAGGGATATCGAAATTTC
TATATAAAAGGTATTCCATTTCCTTCAATTTCACCTTAGCTTTTGTATTGATTACAAAAATCAT
TAAAATTGTCCAGACTTTCCCCATCGATTTTGGTCAAAATACCCAAAATCGGTTGACCGAATCG
GACACAGATCCCTCACTTTCACCCATGCGGCACCAAAAGTGAAGAGTCTGAGCAACTTAGGTGT
TGAGAAAGGCGAATTCAAAATTTGAAACTTAATGGGTTCGCACCAAAATTTTATCATTTGCCGT
CTAATTTAGTGGTTCAAAAATCTATTACTTGTACTAATTTATTGAGCTTTTTAACGCATATAGA
TGGTCTAAGCCAAAGCTATTGGGTTCGGATGAGTCCATAGGTTCTTTACTAGGTCCTCCCTGGG
TGTTCGGGATGGTTTTCCCTGGGTGCTTGAAATTTGAAGGTTCCAATGAAGTCAGTGCTAGTAT
GCAGAGTTTATCTTTACTTGTAATAGCTAGTTCCAACAATTTCATTCTTAATATGCTAAATAAT
CTGATTATTTAGATGCTAAAATCTATCGAGGTCAGGATAAGGGCAAATGTAGCGAGAATCGAAG
TGAAATGACAGAAAACGGAAAGCTCAGAGACAGAATTGTTTTATTGTTGAACCACTGTCCAGTC
GAAAAAGAAAAGAAACCTCTTGTCGATACAAAGTCAGCCAAGTCTAAGAACAAGAATACAAGTA
ATGAAAGAAAGAGCTTTAGTGAGTGTTATGTAGTAGTTGCAGTGAATAATTGATGATTGATGTC
CTTGTTTGTAGGGATGAGGCTCCTTTTACAGGGTAAAGAAGAGGGTCTCTATGTAATTTTTTAA
TTCTTTTTTCAAATGATGAGAGTCATGGTCAGTTGCTAAGAGCGTGGCTGTCGGTTCTTGGGTT
GGTTGAGAGTCTGTTGGTCCTCAAGGTTATATGATAATCAATGATCATTGTATTTATGCAGGCT
CTGATGGGCGGGATGAGGGAACGAGTTGAGTTAGCAACAAAATTTGCTGTAAGTTTTGCAGAAG
GAAAAATGCAAGTGCGCGGAGAGCCAGCCTATGTAAGGGCAGCATGCGAGGCTAGCTTAAAGCG
ACTTGATGTTGACTGCATAGACTTGTACTACCAGCACCGGATTGATACACGCGTGCCCATTGAA
GTAACG
						
					

			
		

Sequences
Splice junction sequence	AAGGGCAGCATGCGAGGCTAGCTTAAAGCGACTTGATGTTGACTGCATAGACTTGTACTACCAG CACCGGATTGATACACGCGTGCCCATTGAAGTAACGgttggagaacttaagaagctggttgaag agggtaaaataaaatatataggtctatcagaggcttcagcatcaacaattagaagagcacacgc tgttcatc
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	GTTGGAGAACTTAAGAAGCTGGTTGAAGAGGGTAAAATAAAATATATAGGTCTATCAGAGGCTT CAGCATCAACAATTAGAAGAGCACACGCTGTTCATCCAATAACAGCAGTACAATTAGAATGGTC ACTATGGTCGAGAGATGTAGAGGAAGAAATAATCCCTACTTGCAGGTACTTTTTTTCTTCTTTC TGTTAGTTTTTTTTGTGTTTGAGGTTTATACCAATGTGAGATCCTGATTTTTCCCGTCTGTTAA CTGTTCAGAGAACTCGGAATTGGGATTGTAGCATACAGTCCACTAGGCCGGGGCTTTTTGTCAT CCGGTCCAAAGCTGGTTGAGGACTTGACAAATGAAGATTTCCGAAAGGTTCAGATTATATTTAT TGTTTGTTTTGAGGTCCAATATGTTCACATTATGTTTAATTGCAGTGCATTTGACTTGAAAAGA TCTCCAACTTTGCAGCATCTACCGAGGTTTCAGGGCGAGAATCTTGAGCATAACAAAAAATTGT ACGAGAGGATTTGTGAATTGGCAACTAAGAAGGGATGCACCCCGTCTCAACTGGCGTTGGCGTG GGTACATCACCAAGGAAACGACGTGTGTCCCATCCCGGGCACCACTAAGATTGAAAATTTCAAT CAGAACATTGGAGCTCTGTCCATAAAGCTAACATCAGAAGACATGGCAGAGCTTGAATCTATTG CTTCAGCTAATGCAGTCCAGGGTGATAGGTACGGTTCGGCTGCAGCAACCTACAAAGATTCAGA AACTCCTCCTATTTCAGCATGGAAGGCTACATAAATATAGAGTTGTTCTTGTGTTGTGCACTGT ATGTAATGAGGTTTCTTTTTTCCTGTTTCAAAACTATTGTGCCACTTACTGATGGTTCAAATAA TAAAATCAATTCTCTGTTTGTGGACTTTTTCCTATGGAGTAAAATATTGATATCTATTGGCTTT CTATTTAGTTATGCATAAATTAGTTATATTTCTGTTAGTTATTCGATTTTCTATATGTAACTTT TACTAAATTCAGATTTGCATAAAGTTACAGAAACAATTTCACATGCAAAATTCGAACATAACTA ATTTAGATTTGTACAAAGTTACGAAGTGATTTCATATTCAAAGTTCAAATATACGTACTTTGCA AAAAATTTACAAAAGCGATTTCATATCCATACTGATTCAAATTTGCACAAAGTTACAAAAATGA TTCCATAGCCGAGATTCAAAGTTCAAATATACATACTAATTTAAATTTGCATAAAAGTTATTTC ATATACAAGATTAGAACGAACATAAATATTCAAATTCACGTAAAGTTATATAAACGATTTCATA TCCAGAATTCAATCCTACACAATAATTTAAATTTACACAAATTTATAAAAACAATTTTATATTC GGGATTCGAACTTTCCGAATGAAAGATTAACACATAACCACAACTTTGGTGTTTGTCATTTGTC AATACCATATCTAATTAGCAACCTCTATATATACAAAACAATATCCACTTGCTCAATTATGTGC ATATTTGCAGAGTAGTAAGCTTAAGCTGAATCACAACAATGGCGGCAGAGGGAACAAAAGTGGG AAGAATCAAATTGGGTTCAGAGGGTCTTGAAGTATCTGCTCAAGGACTTGGTTGTATGGGTATG TCCGCTTTTTACGGGCCTCCCAAACCCGATTCCGATATGGTCCAACTCATCCACCACGCCATTA ACTCCGGCGTCACATTTCTCGATACTTCCGATGTATATGGGCCCCACACTAATGAAATCCTCCT CGGCAAGGTACTTAACTTCTTAATTTTTGGGATTTTCTCTGCCTTTTATGCATTGATTATTGTA CGCTATGCTTGTTGATTTTGGAATCTTGGTGTTTGAGCTGGAATTGTTGTAACATATGCAAATG TGCTGGTTCATAAAGCTTAAAAGGCTTGCACTTTTCGCATCCTTGTAGCCTAGGGATCTGTTAA ATGAGTCGAGAACATGAGGTTTAAGGTTCAGCTAAGACACCATGGTTATCAATAAAAAAGAAAA GACTCTACTTTTTGTTTTAGGTTGAATTGGGTTGGATTTGGTGCTATTCTTTACACGTTTTAGC TCCTTTGAGGTGGACCTTAGCAAGAAATGTTGTTCATGGTTCTTCAAAACATGTATATCTTTTG GAGGTGTTGACCTAAGTTGCTCGGACTCAGGTGCGGGTGTCCGATACGTGTGTGGATCTAAAGG TCGGATTCATCATGATCGATCTAATTTTTAAGATTCAGGAATATGGATCCATATGAGTGCGGGG ACTCGCCTAAAAATAATTAGAATATTTAAAAAATAGAGCTATAAAACCTAAATTATGAGATATT ATGTGGAGAACTTGAGGAGAATCCAGGAAGGAGATCAAAGGAAAAGGAGGGATATCGAAATTTC TATATAAAAGGTATTCCATTTCCTTCAATTTCACCTTAGCTTTTGTATTGATTACAAAAATCAT TAAAATTGTCCAGACTTTCCCCATCGATTTTGGTCAAAATACCCAAAATCGGTTGACCGAATCG GACACAGATCCCTCACTTTCACCCATGCGGCACCAAAAGTGAAGAGTCTGAGCAACTTAGGTGT TGAGAAAGGCGAATTCAAAATTTGAAACTTAATGGGTTCGCACCAAAATTTTATCATTTGCCGT CTAATTTAGTGGTTCAAAAATCTATTACTTGTACTAATTTATTGAGCTTTTTAACGCATATAGA TGGTCTAAGCCAAAGCTATTGGGTTCGGATGAGTCCATAGGTTCTTTACTAGGTCCTCCCTGGG TGTTCGGGATGGTTTTCCCTGGGTGCTTGAAATTTGAAGGTTCCAATGAAGTCAGTGCTAGTAT GCAGAGTTTATCTTTACTTGTAATAGCTAGTTCCAACAATTTCATTCTTAATATGCTAAATAAT CTGATTATTTAGATGCTAAAATCTATCGAGGTCAGGATAAGGGCAAATGTAGCGAGAATCGAAG TGAAATGACAGAAAACGGAAAGCTCAGAGACAGAATTGTTTTATTGTTGAACCACTGTCCAGTC GAAAAAGAAAAGAAACCTCTTGTCGATACAAAGTCAGCCAAGTCTAAGAACAAGAATACAAGTA ATGAAAGAAAGAGCTTTAGTGAGTGTTATGTAGTAGTTGCAGTGAATAATTGATGATTGATGTC CTTGTTTGTAGGGATGAGGCTCCTTTTACAGGGTAAAGAAGAGGGTCTCTATGTAATTTTTTAA TTCTTTTTTCAAATGATGAGAGTCATGGTCAGTTGCTAAGAGCGTGGCTGTCGGTTCTTGGGTT GGTTGAGAGTCTGTTGGTCCTCAAGGTTATATGATAATCAATGATCATTGTATTTATGCAGGCT CTGATGGGCGGGATGAGGGAACGAGTTGAGTTAGCAACAAAATTTGCTGTAAGTTTTGCAGAAG GAAAAATGCAAGTGCGCGGAGAGCCAGCCTATGTAAGGGCAGCATGCGAGGCTAGCTTAAAGCG ACTTGATGTTGACTGCATAGACTTGTACTACCAGCACCGGATTGATACACGCGTGCCCATTGAA GTAACG

			
						 Conservation Information
					
						Conserved circRNAs
						
							stu_circ_001199 ath_circ_008181 ath_circ_008179  
						
						PMCS
						0.919581385

Conservation Information
Conserved circRNAs	stu_circ_001199 ath_circ_008181 ath_circ_008179
PMCS	0.919581385

			
						 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
						Zuo et al., 2016

circRNA

Detail information of Solyc09g097960.2_circ_ag.1

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