Plant Circular RNA Database

Detail information of Solyc03g033540.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc03g033540.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_000952
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr3: 5077211-5081664  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						CIRI; find_circ
					
						Parent gene
						
							Solyc03g033540.2						
					
						Parent gene annotation
						
							Calcium-dependent protein kinase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc03g033540.2_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						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-AA							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
						Solyc03g033540.2.1:10

General Information
CircRNA Name	Solyc03g033540.2_circ_g.1
ID in PlantcircBase	sly_circ_000952
Alias	NA
Organism	Solanum lycopersicum
Position	chr3: 5077211-5081664 JBrowse»
Reference genome	SL2.50.38
Type	ei-circRNA
Identification method	CIRI; find_circ
Parent gene	Solyc03g033540.2
Parent gene annotation	Calcium-dependent protein kinase
Parent gene strand	-
Alternative splicing	Solyc03g033540.2_circ_g.2
Support reads	NA
Tissues	leaf
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-AA 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	Solyc03g033540.2.1:10

			
						 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  
						
							CGAATGAATTATAGAATTGAACCACATTCTCATGACCACCTAAGGCCTTCAATATCTTGACTTC
TCGTTTCACATCCTCAACCGCAATGGGAAGAACCATccattttaagttcttctggagtaatgaa
tccatctttatcaacatcaaatttctcaaaagcagcttgtgatctttgctgccactttgtagaa
ttatgctc

									
								

					

						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
						
							CCATTTTAAGTTCTTCTGGAGTAATGAATCCATCTTTATCAACATCAAATTTCTCAAAAGCAGC
TTGTGATCTTTGCTGCCACTTTGTAGAATTATGCTCCTCCAACTGATGGACATGTAGAGTGGCA
GCCACAAACTCCGGGAAATCAACAAGCCCATCCGTGTTACTGTCAATCTGCCAAGCAATGAACA
AAATACTTTAGGTCCCGGAACTGCAGAAGAGACCATATAGTAGAAAGTAATGAACATGCATATG
ATGAAAACTATAAAGATTATTATATTAGTTGGCACTTGGCAGCAATATTAGCATTGACAATTGA
GTAAAGTTTGTAACAAGGATTATGGTGCAGGAAAAATTTGGAATATACAATCTGACACAAAGAA
ATCCCCAAATATTTGGTCACCAATTTAAAAATGGTGTAGTACAAGCTTGCACACACATTAACTA
TTCCATCGAGTGTCTCTAACTCCCACCATCGCAAGTACCAAGTAATTTTGCCTCAATAAGGCTC
AAGCAGATGGGAAGAAGTCAGTCAACGTGTTCTGTCACTTACTGGATTTGAACTCTAGTCTTTC
ATGATTTTCATCCCACTTCGTTAACATCTAGGTAACACTCTTGGGTGCATTTGATAACCAATTT
CTTCTAAGGAACTTGCACTTATGAGCTATCCTTTGCTATGATCTTCTTGCACACACCTCAACTA
TTTCATTGAATATCTCCATCTACCACCATCACAAGTACCGGGTAACTTCGCCCCAATAATGCTC
AGACAGAGAGGAAGAAATCACCTAACATGTTTGGCCTCTTACCGGATATGAACTCTAGTCTTTC
ATGGTTTTCATTCCACTTCACTGACTGCTACACAACACTGTTGGGTGCATTTGATAACCAATTC
TTCAAAGGAACTTGCTTCCTAATCCTTGCTATTATCTTCCTTTTTTTGAATATGCTTCTTTTTT
TATATTATTAAAGTAGTTTCAAACATGCAACAGCCTAAGGCAACAAAAGCGTTTTATACTTGGT
AATAATTATCTTATTATTTATTAGATGTCATGTTCTGCTCTGATGCTTCATTACTAGATAAATA
AGTTTACCGCTTGAAGAATCTCAAGAACTCGTGATTCTTTCATTTTCCATGGGAGATCCTTTGC
AAGGGCCTGCATTGGAAATGAACGTGGTAAGTCACCAAAAATATGACGACCATATGCATACACA
ATGTTTTTGATCAAGGCATATATACAATTTTTTTGCATCAAGATAACACAAAATAGAGATGTCT
CCAATGTTTGCCAATGGCCATTGAGAGTTGTAAGTACGAAACTAGCTCCAACTCGAAAGATGAG
CAATACCTGTCTCATTTCTTCGAGACTGATGACACCATTCTTATCCACATCAATTGCAGAAAAT
TGATCCCGCAGATCAGCGATCTCCTCCTCATCAAGTGTGCTAGCTAACGCCTGCAAGTAGTGGA
ACAGCATCCAGAAATTTATGTTTTGTATACTGAAGTTACCTTATCACAAAAGGTTTAAGAAATA
AGAAAGCAATGAGCTTACACGTAAAGCAAACTGTTTTAGACGACTGTATTTGACAAATTGCCGC
ATGTTGGATAAAACAGAAATGTCCAGTGGAATCTCAGATGCATCCCCTCCTTCTCGGACCCATG
GATGTGCTGAAGATGTTCAAGTAGATGATTTTCAAAACAATTGCTCATTATATCAATAAATTTA
AAGGAATGACCACAGTAACATTTGTTTACTAATTTATTTGAACACTACGACATAATGTTCTTAT
TTCCAAGAACTACAAACAAGTAAGCATATGCTGCATATCTGATGTTGTGCTATAAGTTATCAAA
ATGTAGAAGCTGTACATCTGGACAGAGAACCATGATTGATATCTATTACCAAACATTGCTGATG
AAGTAGGTGAATGAAATGGATAAAGCGAAGTGTACAAATCTTTTTAAGTGAACCTTGAGCTACT
GTCGATACATCAGTTTCATCACATAACACCTTACAATCACTAAGAAAAATTGGTGCTTGTGAAA
GAACGTGAAGAGCCAATTGGAAACCTTAAGACAGATGATGAGTATAGACCCTTTCAGATGCTCT
TGTATTGCAGGTGTGGGGATTTTAAGGTTTAACGCCCTTCTGTTGTGCAGTGTTGTCAAAGGTG
CGCTTAAGCCATGAAGTGAGGCTCATAACGTGTTGAGTGCTTTGTCTCATTTAATGCACTTCAA
TGTCATCATCAAAGTTCTAAGGCACCCTTGCCAATGAGCCTATTCTTAAAAAAGAGGCAACACT
AAGCCATTGATGTTTTACTATATTGTAAAAAAGATTCAATTCTTTTGTACAAATATTTGGCATT
CATGCTCATAATCATTGGTCTTGGACTAAACATATACACTTTTCTGTTTTCTCCATTTGCACCT
TTTTTTAATTAAAGCCCGTGCTTTTTTTGCGTTTAGCACTTAAAGCCCCAACGAACCTTAGAAC
TTTTATGCGCTTTTTGTTTTTGACAACACTCCCAATTCTAGGTTTCCTACACCAACTTTAATGT
GGATGAGGCTCGCTAAAGTTGGTGCCTATACCATGTGAAAGAATCTGAGCATCCAATCCAAAAC
CATAAGGAAATGGGTGGAGTGGTCCAACATTTTTATGTACCCCTTGAAAGCCCTTAGCTGATAT
GAGAAACTTTATACAACTTAACAGTACAAATTCAGGATGATATTACTTACATAGGGCCTGAGCA
GCAGTAAGTCTAGCGCGAGGATCCTTCACCAGTATTTTCTTTACAAAATCTTTAGCACTGTTGC
TTATGTTAGACCATGGCTTGCGACGAAAATCAGGCTTGTTCCGTAGGACCTTAACATTTTGGAA
GCAAAGTTAGAGAAACTATTCAAAACCAGGCAAATCACAAAGAATTTACACAATATAAATGTTG
TTCTTCTTGAAGTAAAAGTACTTAAATGTCTTGTAGGAAGAACAATTCTTTGGATAAGAGCCTC
TCCAAGGAAGCATCAACCAAAAGTGAATTATGAACAAAATAAATAGCAGTAACTTCTTTGGACA
CAAAAGAGAAAACGATGAAAACATAAGATCAAAATCACTCAATAATGAAATGAAACAAACTAAA
ATGTCCACAAAGAAAAAAATATCACAGTATCATAGTTAAGATGTTTACGAGAGCATGCAACAAA
AAGTGAATGGAAAATCTGAAATTCCAAGAGAGATGAGATTTATTAAGTGAGTGTTAACTTCAAA
AAACCACTTAAAGGTATAAACAAACCTGATACACACTATTGAAAAGACAAACAAAGGCAAACAT
ATAAACTTTTATACAAAATCTGCAAGTTCATGACCCCATTAGAGCCCTAAAATTGTGATATCCT
TTCTTTAGGTTTCCCAAGTTGAAACAATAATTGAAATCTTTCTAAATTACACTTGATATATTAG
CAACTCACCTCTTTGAATATACCATCCTCAGTTTTGTCCCAGAAAGGCCGACGACCACATAGCA
AAATGTATGTAATTACGCCAATACTCCATACATCTGATTCAGGTCCTGATCTACGCTTTAATAC
CTCTGGAGCTACATAATATGCACTGCCGACAATGTCTTGGAACTTTTTCCCTGCATATATAAGT
TTCCTATGATAAGCTCATAACTTTACGAGAGAAAACCACAATAATAGCCTCCAAGATCATTAAA
GAACTTGACAGATGTATTAAGAATATTAGTACTTCAGCAAGACCAAAATCTGTGGCAGAGAATC
CAATCACCTGGTCTGATGAAGTCTGAAAGACCAAAATCCGTCGCTTTTAATGGTGAATCCTCCT
TTGTAGACTTAAAGAGAAAATTCTACAAGGAAAAAAGTTTGTTTCAGAAAAGCAATATCAAGAA
GCATTACCAAGTCAAAGTAGTATCGAACTGCTTGCACACCTCAGGTTTCATATCACGATGCACC
AAACCATGTAAATGACACTCAGCTGCCACTTTTAGCATCTGGCGTACAACTATTGCTGCATCTT
TCTCGGTATACCGACTGTCTTTTCTGATTAGACAAATTATGTCAACCCTTATCAGTAAAACTTC
ATAATCAGCAATTTGAATAAAGAGCCGGGATTCTGCAACTCACAAATAATCAACTGAAACTGGT
AATTTCAGAATACTTACTTGGACAAAATTCGGTCCAATAGTTCTCCACCTTCACATAACCTAAA
AGAAAACAAAAACTGAATACTCTTAACTTGCCATTCAAGTGGAAGGATTAGTAGTAGGGAAATA
AACTAGGACCAGAGAGATTTTAAAAAAAAACTTACTCCATCACAATGTAGACATAATTATCATC
CTCGAATGAATTATAGAATTGAACCACATTCTCATGACCACCTAAGGCCTTCAATATCTTGACT
TCTCGTTTCACATCCTCAACCGCAATGGGAAGAACCAT
						
					

			
		

Sequences
Splice junction sequence	CGAATGAATTATAGAATTGAACCACATTCTCATGACCACCTAAGGCCTTCAATATCTTGACTTC TCGTTTCACATCCTCAACCGCAATGGGAAGAACCATccattttaagttcttctggagtaatgaa tccatctttatcaacatcaaatttctcaaaagcagcttgtgatctttgctgccactttgtagaa ttatgctc
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	CCATTTTAAGTTCTTCTGGAGTAATGAATCCATCTTTATCAACATCAAATTTCTCAAAAGCAGC TTGTGATCTTTGCTGCCACTTTGTAGAATTATGCTCCTCCAACTGATGGACATGTAGAGTGGCA GCCACAAACTCCGGGAAATCAACAAGCCCATCCGTGTTACTGTCAATCTGCCAAGCAATGAACA AAATACTTTAGGTCCCGGAACTGCAGAAGAGACCATATAGTAGAAAGTAATGAACATGCATATG ATGAAAACTATAAAGATTATTATATTAGTTGGCACTTGGCAGCAATATTAGCATTGACAATTGA GTAAAGTTTGTAACAAGGATTATGGTGCAGGAAAAATTTGGAATATACAATCTGACACAAAGAA ATCCCCAAATATTTGGTCACCAATTTAAAAATGGTGTAGTACAAGCTTGCACACACATTAACTA TTCCATCGAGTGTCTCTAACTCCCACCATCGCAAGTACCAAGTAATTTTGCCTCAATAAGGCTC AAGCAGATGGGAAGAAGTCAGTCAACGTGTTCTGTCACTTACTGGATTTGAACTCTAGTCTTTC ATGATTTTCATCCCACTTCGTTAACATCTAGGTAACACTCTTGGGTGCATTTGATAACCAATTT CTTCTAAGGAACTTGCACTTATGAGCTATCCTTTGCTATGATCTTCTTGCACACACCTCAACTA TTTCATTGAATATCTCCATCTACCACCATCACAAGTACCGGGTAACTTCGCCCCAATAATGCTC AGACAGAGAGGAAGAAATCACCTAACATGTTTGGCCTCTTACCGGATATGAACTCTAGTCTTTC ATGGTTTTCATTCCACTTCACTGACTGCTACACAACACTGTTGGGTGCATTTGATAACCAATTC TTCAAAGGAACTTGCTTCCTAATCCTTGCTATTATCTTCCTTTTTTTGAATATGCTTCTTTTTT TATATTATTAAAGTAGTTTCAAACATGCAACAGCCTAAGGCAACAAAAGCGTTTTATACTTGGT AATAATTATCTTATTATTTATTAGATGTCATGTTCTGCTCTGATGCTTCATTACTAGATAAATA AGTTTACCGCTTGAAGAATCTCAAGAACTCGTGATTCTTTCATTTTCCATGGGAGATCCTTTGC AAGGGCCTGCATTGGAAATGAACGTGGTAAGTCACCAAAAATATGACGACCATATGCATACACA ATGTTTTTGATCAAGGCATATATACAATTTTTTTGCATCAAGATAACACAAAATAGAGATGTCT CCAATGTTTGCCAATGGCCATTGAGAGTTGTAAGTACGAAACTAGCTCCAACTCGAAAGATGAG CAATACCTGTCTCATTTCTTCGAGACTGATGACACCATTCTTATCCACATCAATTGCAGAAAAT TGATCCCGCAGATCAGCGATCTCCTCCTCATCAAGTGTGCTAGCTAACGCCTGCAAGTAGTGGA ACAGCATCCAGAAATTTATGTTTTGTATACTGAAGTTACCTTATCACAAAAGGTTTAAGAAATA AGAAAGCAATGAGCTTACACGTAAAGCAAACTGTTTTAGACGACTGTATTTGACAAATTGCCGC ATGTTGGATAAAACAGAAATGTCCAGTGGAATCTCAGATGCATCCCCTCCTTCTCGGACCCATG GATGTGCTGAAGATGTTCAAGTAGATGATTTTCAAAACAATTGCTCATTATATCAATAAATTTA AAGGAATGACCACAGTAACATTTGTTTACTAATTTATTTGAACACTACGACATAATGTTCTTAT TTCCAAGAACTACAAACAAGTAAGCATATGCTGCATATCTGATGTTGTGCTATAAGTTATCAAA ATGTAGAAGCTGTACATCTGGACAGAGAACCATGATTGATATCTATTACCAAACATTGCTGATG AAGTAGGTGAATGAAATGGATAAAGCGAAGTGTACAAATCTTTTTAAGTGAACCTTGAGCTACT GTCGATACATCAGTTTCATCACATAACACCTTACAATCACTAAGAAAAATTGGTGCTTGTGAAA GAACGTGAAGAGCCAATTGGAAACCTTAAGACAGATGATGAGTATAGACCCTTTCAGATGCTCT TGTATTGCAGGTGTGGGGATTTTAAGGTTTAACGCCCTTCTGTTGTGCAGTGTTGTCAAAGGTG CGCTTAAGCCATGAAGTGAGGCTCATAACGTGTTGAGTGCTTTGTCTCATTTAATGCACTTCAA TGTCATCATCAAAGTTCTAAGGCACCCTTGCCAATGAGCCTATTCTTAAAAAAGAGGCAACACT AAGCCATTGATGTTTTACTATATTGTAAAAAAGATTCAATTCTTTTGTACAAATATTTGGCATT CATGCTCATAATCATTGGTCTTGGACTAAACATATACACTTTTCTGTTTTCTCCATTTGCACCT TTTTTTAATTAAAGCCCGTGCTTTTTTTGCGTTTAGCACTTAAAGCCCCAACGAACCTTAGAAC TTTTATGCGCTTTTTGTTTTTGACAACACTCCCAATTCTAGGTTTCCTACACCAACTTTAATGT GGATGAGGCTCGCTAAAGTTGGTGCCTATACCATGTGAAAGAATCTGAGCATCCAATCCAAAAC CATAAGGAAATGGGTGGAGTGGTCCAACATTTTTATGTACCCCTTGAAAGCCCTTAGCTGATAT GAGAAACTTTATACAACTTAACAGTACAAATTCAGGATGATATTACTTACATAGGGCCTGAGCA GCAGTAAGTCTAGCGCGAGGATCCTTCACCAGTATTTTCTTTACAAAATCTTTAGCACTGTTGC TTATGTTAGACCATGGCTTGCGACGAAAATCAGGCTTGTTCCGTAGGACCTTAACATTTTGGAA GCAAAGTTAGAGAAACTATTCAAAACCAGGCAAATCACAAAGAATTTACACAATATAAATGTTG TTCTTCTTGAAGTAAAAGTACTTAAATGTCTTGTAGGAAGAACAATTCTTTGGATAAGAGCCTC TCCAAGGAAGCATCAACCAAAAGTGAATTATGAACAAAATAAATAGCAGTAACTTCTTTGGACA CAAAAGAGAAAACGATGAAAACATAAGATCAAAATCACTCAATAATGAAATGAAACAAACTAAA ATGTCCACAAAGAAAAAAATATCACAGTATCATAGTTAAGATGTTTACGAGAGCATGCAACAAA AAGTGAATGGAAAATCTGAAATTCCAAGAGAGATGAGATTTATTAAGTGAGTGTTAACTTCAAA AAACCACTTAAAGGTATAAACAAACCTGATACACACTATTGAAAAGACAAACAAAGGCAAACAT ATAAACTTTTATACAAAATCTGCAAGTTCATGACCCCATTAGAGCCCTAAAATTGTGATATCCT TTCTTTAGGTTTCCCAAGTTGAAACAATAATTGAAATCTTTCTAAATTACACTTGATATATTAG CAACTCACCTCTTTGAATATACCATCCTCAGTTTTGTCCCAGAAAGGCCGACGACCACATAGCA AAATGTATGTAATTACGCCAATACTCCATACATCTGATTCAGGTCCTGATCTACGCTTTAATAC CTCTGGAGCTACATAATATGCACTGCCGACAATGTCTTGGAACTTTTTCCCTGCATATATAAGT TTCCTATGATAAGCTCATAACTTTACGAGAGAAAACCACAATAATAGCCTCCAAGATCATTAAA GAACTTGACAGATGTATTAAGAATATTAGTACTTCAGCAAGACCAAAATCTGTGGCAGAGAATC CAATCACCTGGTCTGATGAAGTCTGAAAGACCAAAATCCGTCGCTTTTAATGGTGAATCCTCCT TTGTAGACTTAAAGAGAAAATTCTACAAGGAAAAAAGTTTGTTTCAGAAAAGCAATATCAAGAA GCATTACCAAGTCAAAGTAGTATCGAACTGCTTGCACACCTCAGGTTTCATATCACGATGCACC AAACCATGTAAATGACACTCAGCTGCCACTTTTAGCATCTGGCGTACAACTATTGCTGCATCTT TCTCGGTATACCGACTGTCTTTTCTGATTAGACAAATTATGTCAACCCTTATCAGTAAAACTTC ATAATCAGCAATTTGAATAAAGAGCCGGGATTCTGCAACTCACAAATAATCAACTGAAACTGGT AATTTCAGAATACTTACTTGGACAAAATTCGGTCCAATAGTTCTCCACCTTCACATAACCTAAA AGAAAACAAAAACTGAATACTCTTAACTTGCCATTCAAGTGGAAGGATTAGTAGTAGGGAAATA AACTAGGACCAGAGAGATTTTAAAAAAAAACTTACTCCATCACAATGTAGACATAATTATCATC CTCGAATGAATTATAGAATTGAACCACATTCTCATGACCACCTAAGGCCTTCAATATCTTGACT TCTCGTTTCACATCCTCAACCGCAATGGGAAGAACCAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.186653016

Conservation Information
Conserved circRNAs	NA
PMCS	0.186653016

			
						 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
						Yang et al., 2020

circRNA

Detail information of Solyc03g033540.2_circ_g.1

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