Plant Circular RNA Database

Detail information of Solyc01g100860.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc01g100860.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_000407
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr1: 90766597-90771135  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc01g100860.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc01g100860.2_circ_g.1 Solyc01g100860.2_circ_g.2 						
					
						Support reads
						4
					
						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  
						
							CT-AC							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
						Solyc01g100860.2.1:1

General Information
CircRNA Name	Solyc01g100860.2_circ_g.3
ID in PlantcircBase	sly_circ_000407
Alias	NA
Organism	Solanum lycopersicum
Position	chr1: 90766597-90771135 JBrowse»
Reference genome	SL2.50.38
Type	ei-circRNA
Identification method	CIRI
Parent gene	Solyc01g100860.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc01g100860.2_circ_g.1 Solyc01g100860.2_circ_g.2
Support reads	4
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	CT-AC 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	Solyc01g100860.2.1:1

			
						 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  
						
							ATAGTACTTTGTTTTAAGGCACTAAGTACCTTGTCCTGACCCCCGACATCCCAGACGGTGAAGC
TTATGTTCTTGTATTCAACAGTCTCCACATTGAATCcaatggtaggaatagtggtaacaatctc
tcccagcttgagcttgtacaatattgtggttttaccagctgcatcaagaccaaccatcagaata
cgcatctc

									
								

					

						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
						
							CAATGGTAGGAATAGTGGTAACAATCTCTCCCAGCTTGAGCTTGTACAATATTGTGGTTTTACC
AGCTGCATCAAGACCAACCATCAGAATACGCATCTCCTTCTTGGCAAACAACCGGCTGAAAAGC
TTCCCGAATGATAAACCCATCTTTTTTTCAATGCCTGTCAGGACCAAAATTAAGATTCAAATTA
CCACACAAATTCACCCGTTAAGCTTAAGCCAACAGATTAGGTTACATAAATGCACAATCATGAA
CAAAATTATGATCTGAAGCCAACAAAAATCCAAATTATGGTGTCTGATCTTCAGGCTTCATTTT
CGCTGCATTAGATGTATCAAAAAAACCAACTATTGGATCCTTTTCAAAAGATCTCATCATAAAT
TTCAATTATCCATGAGAGATGCATCGCAACAGGTTTAAAAATCGATAGAATCGACGACCAATCG
GATCTTACATAACTAATAAAAATCCGGATCCAGAAGAAGAACCCAAATCAAGATCCAAAAAGAA
AGAAGAACCCAAATCATACGGAGATTAAATCAGTCGAATAAAAATACAAGAAATCAAAGAAAGA
TGAAAACTTTATCAAATTCCCAGATCTAAAAGGCCAAATTCCAGATCTCCAATTCAGTAAACTC
TTCAATGAAGAAAGAGATACATACATAAACTCTGTCAAAATCAATTGTTATGAACCAAATCGAC
GTGTGTGTGAAAGATAGATGCAATTCAAAGGGGGAAAGAGAGATCTTACAATGATGAAGAAGGA
ATCACAGAGAGAGAGAGGGGGGGCAGTAGATCTAGAAAAAACTGCCCTTTGTATATAATTGACA
AGAAATGGGAACCTTTGGATGTTCTCTTGTTGTTTTAGAAGCCTCTAATATTTTAATGTCAACC
CTATTATTAAATTGTCACAATTTTGAATTTTCAAATACTCTATTTAGGATTCTTTTACTAACGT
AAATAATAAAGTTGGTGTTATATTATAAATTGTATAGGTTAAAATTGTTGTAAACACATTGTGA
CCCCAAATGTTTTCCTGAGTTGTGATTCTTCTTGGTTTTTTATGGAACACGTGTACGATATTAC
GTTAGTTACAAAATTCTCTAAGAAATTCAATCAAGCGATTGAACAATGGAAAAGAAATTAGTGA
ACAGATTCATATAAAAGTAAAACACAATTATATAGACATTCAACTTTCAAAATTATTATGTAGC
TCCATAAATGTTTTATTAATGCATTAAGTAGTTCAAAATGAGTACTTTTTCTCAAACTTTTTTT
ATGTTTAGCTAAGAAATTATTCAAATTGGAGATTTTCATTTACCATTATATCATAATTTTTTTT
TCCAATTAGTGTTAAATATGAAAAATCGACCTACCGAACTACTGAATTATTATTGTGATGAATT
AATTATTATGTTATGTATTGTATTATGTTTTATATTTAAATTATTATGTTATGTATGTAATTTT
AAATTAAAGTTTTCATCTTATCATTTTAATTTTGTTCATTTTTTATAGTGAAAATTAATAATAA
AATAAAGCTATACTATTGACTAAAATTAGAAAAAAAATCAAAATATTTTAATTTGGGATGAAAG
TAATATATATAAATAATCTATTTTAAAAATTATTGTGTTACATTGAAAAATAATTATGAATATT
AGATATTTAATCAATGACATTATATATAAAATAATATGTTAATTAAAAAATAATAATAAAATAT
TAAAAAAGTGAAAATTTTCTAGAAATAAAGAGTAGAGTCTAAAATAGAGAGGATTGGGGTGTCC
ATTCTCTATTTCATGCTATTGCTTTAAGAGGAGCTTTCCTACTACTGACTCGTCTGCTGGTGGA
GATCCAACCTCTCACCAACTAGGTAAAATGAAGTAGTCAACTGATTAAACTAGTAAAATTCCTC
CTCGAGTCGAATTTGGAAGACTAAAAAATACTCCTATTAAATAACATTTGGTTTAAATCATATG
CAGCTCTTCAAAGTTGTTTGCATACTTCACTTAGACAACTATAGGATGTCCCTATTGAACACCT
CAGTGGTTCAAAAGTCATGCATATTTGACACAAAATGTTTACATGTCAATAAACGTGTGGTTTA
CTCTCTTTAAGCGCATAAATGTACCAAAATATTTTTTTATTATTAATTTTTACAACAAAATTAA
TATTTTTTTAAAAAGGAAATAATTAACAAAAAGAAAAGGAAGAAAGAGTCGTCTTCTTCCACTG
CATCCCAATATTCCCTAACGTATAACTATGCTCAATTCTCATCCACCATTTTCATCAATTATTT
ACGCACATGCACAACCCACCCCATTCCCTGCCCCTCTCTCTTTCTCTCACACTTTATGGTTCTT
CTCTTGCTTTTTTTTTTTCTTATGTAGATCTATGTCTCAAATATTGATCCGGCAAATTATTTGT
TACCAAAAAATGTTATGATCATAATCATTCCACAACCAAAGACACAAAGGTGATGCAGCTTATG
CCGGCGAAAGGAATAAAAATGAATGAAGGAGAAGAAAGAGGTAAGGCCATGATTTGTTGGCGTC
GTAATTGCCATCGACGCCGATTAAGAGGAAATGGGTCTGGCGGGGGGTTAAATAAAAAAAATAA
AATTATTTCTAAGTTATTTAAATAGAGCTTTTTAAAAAAATTGAACTCAAACCACGTGTCATCA
TTTTACTGGTGGGTAGTTTTTTTGGAAAATTCTTTTTATTTATTTTTTAGTTAATAAATAAACC
AAAATAGTTATTTTTTAAAATATCATTTTTAATTAATTTTTGAATTCAAATCACACATCTCATA
TATTTGGCTGATTGTCAAAAATTGTCAAATAGATATAAATTTTAAGGGGTACAAATATTCCATA
GATATAAGCCCTAGTTGAAGTGTGTAAATGAATTATGCAGACAACCCTTTAAGATTTTGTTATA
AAGTTGTGGAGGCCTAAACTTCTTAACCAAACAAAATAGTTCAAACTCCAGCAGTATCGAAAAG
CAGCATTAACTAAAACCAACGAAGACTGGGAGGGAATCTCGAGTCTTAACTAAAACAAAATATC
GAAAGCAGAGTCATTGAGAATATGTAAACCCAGAATGTAAAATATTACATGAATTCAACTAAAG
TTACTGTAAAGTAACATTCTTTTAAAGAAATGAAAATGTACTGAAATAAAAAATAGTGATAAGT
GGATCCATTCAGCAGGTGCACAAGTGCTCTAGACATTGTTTGAAGTCTATATTGACAAAAATAT
AGCTGCAAAAATCATGGATCTCGTGTTCAACCCTGCAAAAACAAGGTCATTGGAAGATGAGAGC
AAAATTAAAGTGTCAAATAAAATCTAATACGATATGCCTCACTCCCATACCTTGTTTGCAATGT
TGTTTGAGAGCCAGTCAAGCCCCTCATACAACCCTTCTCCAGAGGTAGCACATGTGCTCTGAAT
GTACCTGTTATAGAAAGTCATAGATTCAGCATTTGGTAGCACATGCAAGTCCTATCAATCTCCA
GCACCATACTAAATAAACACATATACTTGAACATCTTACAAATAAGGTAACACAAAATAGTACA
TACCAGTGACGTTGACGGAGGGAGTGCAAACCAAGCTTGTCAGTGATCTCAGCAGCATTCATAG
CATTTGGAAGATCTTGCTTGTTAGCAAACACAAGCAGCACAGCATCTCTCAGTTCATCCTATGC
ATACATTGCAAAATTTATTCAAAATAGGGTACGAGTGAAAAGAACCAACTACAAGTTAATTAGA
ACAGAAAGTTGGTAAATAGTAAATACAGATCATTTCAGACTTTTAAATGCTCCATGGGGCCTAT
TCTGGATGTATCTTGTGTATTGCACCAGACATGGGCCACCCCAAGACACAATATAATCTTAACC
GAAAGAATGAGAGGTGTGTGTTGCATACCTCATTCAACATCCGATGCAGCTCGTCTCTGGCCTC
AACAACACGATCACGATCATTACTATCAACCACAAAGATAAGTCCTTGTGTGTTTTGGAAGTAA
TGCCTCCACAATGGTCTGATCTGGAAGTGCCAAAAAATTGACAAGGAACAACAGACAACAAAAA
GTAAGTCAATATCCGAAAGAAGTCATTGCATGACTGCAGATTCCAGATAAGTATATGTACTTGA
CAGCAGCAAAGAACGCTAGAAGTCAATGAACAGAAGAAAAGATCATTTCTTGGTTTTATATTTC
TGTTATTCTGGTGGCTGGTGGGTACGAACATTTTGCAAAAAAATCGGAAAAATAGGCATGGTGA
ATTTGAAAACTAGTAATAGAAAGAAAATATAATTTCAAAACCAGAAATGCTCTTTCTATAACTC
GCAGCTTAGTAAGGTCAGTATGAAGTCAGACAAACTCAAAGTAGAAGAACTTGCAATCATCTTT
TAATGTCAGATACTAAAAAGAGCATAGTACTTTGTTTTAAGGCACTAAGTACCTTGTCCTGACC
CCCGACATCCCAGACGGTGAAGCTTATGTTCTTGTATTCAACAGTCTCCACATTGAATC
						
					

			
		

Sequences
Splice junction sequence	ATAGTACTTTGTTTTAAGGCACTAAGTACCTTGTCCTGACCCCCGACATCCCAGACGGTGAAGC TTATGTTCTTGTATTCAACAGTCTCCACATTGAATCcaatggtaggaatagtggtaacaatctc tcccagcttgagcttgtacaatattgtggttttaccagctgcatcaagaccaaccatcagaata cgcatctc
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	CAATGGTAGGAATAGTGGTAACAATCTCTCCCAGCTTGAGCTTGTACAATATTGTGGTTTTACC AGCTGCATCAAGACCAACCATCAGAATACGCATCTCCTTCTTGGCAAACAACCGGCTGAAAAGC TTCCCGAATGATAAACCCATCTTTTTTTCAATGCCTGTCAGGACCAAAATTAAGATTCAAATTA CCACACAAATTCACCCGTTAAGCTTAAGCCAACAGATTAGGTTACATAAATGCACAATCATGAA CAAAATTATGATCTGAAGCCAACAAAAATCCAAATTATGGTGTCTGATCTTCAGGCTTCATTTT CGCTGCATTAGATGTATCAAAAAAACCAACTATTGGATCCTTTTCAAAAGATCTCATCATAAAT TTCAATTATCCATGAGAGATGCATCGCAACAGGTTTAAAAATCGATAGAATCGACGACCAATCG GATCTTACATAACTAATAAAAATCCGGATCCAGAAGAAGAACCCAAATCAAGATCCAAAAAGAA AGAAGAACCCAAATCATACGGAGATTAAATCAGTCGAATAAAAATACAAGAAATCAAAGAAAGA TGAAAACTTTATCAAATTCCCAGATCTAAAAGGCCAAATTCCAGATCTCCAATTCAGTAAACTC TTCAATGAAGAAAGAGATACATACATAAACTCTGTCAAAATCAATTGTTATGAACCAAATCGAC GTGTGTGTGAAAGATAGATGCAATTCAAAGGGGGAAAGAGAGATCTTACAATGATGAAGAAGGA ATCACAGAGAGAGAGAGGGGGGGCAGTAGATCTAGAAAAAACTGCCCTTTGTATATAATTGACA AGAAATGGGAACCTTTGGATGTTCTCTTGTTGTTTTAGAAGCCTCTAATATTTTAATGTCAACC CTATTATTAAATTGTCACAATTTTGAATTTTCAAATACTCTATTTAGGATTCTTTTACTAACGT AAATAATAAAGTTGGTGTTATATTATAAATTGTATAGGTTAAAATTGTTGTAAACACATTGTGA CCCCAAATGTTTTCCTGAGTTGTGATTCTTCTTGGTTTTTTATGGAACACGTGTACGATATTAC GTTAGTTACAAAATTCTCTAAGAAATTCAATCAAGCGATTGAACAATGGAAAAGAAATTAGTGA ACAGATTCATATAAAAGTAAAACACAATTATATAGACATTCAACTTTCAAAATTATTATGTAGC TCCATAAATGTTTTATTAATGCATTAAGTAGTTCAAAATGAGTACTTTTTCTCAAACTTTTTTT ATGTTTAGCTAAGAAATTATTCAAATTGGAGATTTTCATTTACCATTATATCATAATTTTTTTT TCCAATTAGTGTTAAATATGAAAAATCGACCTACCGAACTACTGAATTATTATTGTGATGAATT AATTATTATGTTATGTATTGTATTATGTTTTATATTTAAATTATTATGTTATGTATGTAATTTT AAATTAAAGTTTTCATCTTATCATTTTAATTTTGTTCATTTTTTATAGTGAAAATTAATAATAA AATAAAGCTATACTATTGACTAAAATTAGAAAAAAAATCAAAATATTTTAATTTGGGATGAAAG TAATATATATAAATAATCTATTTTAAAAATTATTGTGTTACATTGAAAAATAATTATGAATATT AGATATTTAATCAATGACATTATATATAAAATAATATGTTAATTAAAAAATAATAATAAAATAT TAAAAAAGTGAAAATTTTCTAGAAATAAAGAGTAGAGTCTAAAATAGAGAGGATTGGGGTGTCC ATTCTCTATTTCATGCTATTGCTTTAAGAGGAGCTTTCCTACTACTGACTCGTCTGCTGGTGGA GATCCAACCTCTCACCAACTAGGTAAAATGAAGTAGTCAACTGATTAAACTAGTAAAATTCCTC CTCGAGTCGAATTTGGAAGACTAAAAAATACTCCTATTAAATAACATTTGGTTTAAATCATATG CAGCTCTTCAAAGTTGTTTGCATACTTCACTTAGACAACTATAGGATGTCCCTATTGAACACCT CAGTGGTTCAAAAGTCATGCATATTTGACACAAAATGTTTACATGTCAATAAACGTGTGGTTTA CTCTCTTTAAGCGCATAAATGTACCAAAATATTTTTTTATTATTAATTTTTACAACAAAATTAA TATTTTTTTAAAAAGGAAATAATTAACAAAAAGAAAAGGAAGAAAGAGTCGTCTTCTTCCACTG CATCCCAATATTCCCTAACGTATAACTATGCTCAATTCTCATCCACCATTTTCATCAATTATTT ACGCACATGCACAACCCACCCCATTCCCTGCCCCTCTCTCTTTCTCTCACACTTTATGGTTCTT CTCTTGCTTTTTTTTTTTCTTATGTAGATCTATGTCTCAAATATTGATCCGGCAAATTATTTGT TACCAAAAAATGTTATGATCATAATCATTCCACAACCAAAGACACAAAGGTGATGCAGCTTATG CCGGCGAAAGGAATAAAAATGAATGAAGGAGAAGAAAGAGGTAAGGCCATGATTTGTTGGCGTC GTAATTGCCATCGACGCCGATTAAGAGGAAATGGGTCTGGCGGGGGGTTAAATAAAAAAAATAA AATTATTTCTAAGTTATTTAAATAGAGCTTTTTAAAAAAATTGAACTCAAACCACGTGTCATCA TTTTACTGGTGGGTAGTTTTTTTGGAAAATTCTTTTTATTTATTTTTTAGTTAATAAATAAACC AAAATAGTTATTTTTTAAAATATCATTTTTAATTAATTTTTGAATTCAAATCACACATCTCATA TATTTGGCTGATTGTCAAAAATTGTCAAATAGATATAAATTTTAAGGGGTACAAATATTCCATA GATATAAGCCCTAGTTGAAGTGTGTAAATGAATTATGCAGACAACCCTTTAAGATTTTGTTATA AAGTTGTGGAGGCCTAAACTTCTTAACCAAACAAAATAGTTCAAACTCCAGCAGTATCGAAAAG CAGCATTAACTAAAACCAACGAAGACTGGGAGGGAATCTCGAGTCTTAACTAAAACAAAATATC GAAAGCAGAGTCATTGAGAATATGTAAACCCAGAATGTAAAATATTACATGAATTCAACTAAAG TTACTGTAAAGTAACATTCTTTTAAAGAAATGAAAATGTACTGAAATAAAAAATAGTGATAAGT GGATCCATTCAGCAGGTGCACAAGTGCTCTAGACATTGTTTGAAGTCTATATTGACAAAAATAT AGCTGCAAAAATCATGGATCTCGTGTTCAACCCTGCAAAAACAAGGTCATTGGAAGATGAGAGC AAAATTAAAGTGTCAAATAAAATCTAATACGATATGCCTCACTCCCATACCTTGTTTGCAATGT TGTTTGAGAGCCAGTCAAGCCCCTCATACAACCCTTCTCCAGAGGTAGCACATGTGCTCTGAAT GTACCTGTTATAGAAAGTCATAGATTCAGCATTTGGTAGCACATGCAAGTCCTATCAATCTCCA GCACCATACTAAATAAACACATATACTTGAACATCTTACAAATAAGGTAACACAAAATAGTACA TACCAGTGACGTTGACGGAGGGAGTGCAAACCAAGCTTGTCAGTGATCTCAGCAGCATTCATAG CATTTGGAAGATCTTGCTTGTTAGCAAACACAAGCAGCACAGCATCTCTCAGTTCATCCTATGC ATACATTGCAAAATTTATTCAAAATAGGGTACGAGTGAAAAGAACCAACTACAAGTTAATTAGA ACAGAAAGTTGGTAAATAGTAAATACAGATCATTTCAGACTTTTAAATGCTCCATGGGGCCTAT TCTGGATGTATCTTGTGTATTGCACCAGACATGGGCCACCCCAAGACACAATATAATCTTAACC GAAAGAATGAGAGGTGTGTGTTGCATACCTCATTCAACATCCGATGCAGCTCGTCTCTGGCCTC AACAACACGATCACGATCATTACTATCAACCACAAAGATAAGTCCTTGTGTGTTTTGGAAGTAA TGCCTCCACAATGGTCTGATCTGGAAGTGCCAAAAAATTGACAAGGAACAACAGACAACAAAAA GTAAGTCAATATCCGAAAGAAGTCATTGCATGACTGCAGATTCCAGATAAGTATATGTACTTGA CAGCAGCAAAGAACGCTAGAAGTCAATGAACAGAAGAAAAGATCATTTCTTGGTTTTATATTTC TGTTATTCTGGTGGCTGGTGGGTACGAACATTTTGCAAAAAAATCGGAAAAATAGGCATGGTGA ATTTGAAAACTAGTAATAGAAAGAAAATATAATTTCAAAACCAGAAATGCTCTTTCTATAACTC GCAGCTTAGTAAGGTCAGTATGAAGTCAGACAAACTCAAAGTAGAAGAACTTGCAATCATCTTT TAATGTCAGATACTAAAAAGAGCATAGTACTTTGTTTTAAGGCACTAAGTACCTTGTCCTGACC CCCGACATCCCAGACGGTGAAGCTTATGTTCTTGTATTCAACAGTCTCCACATTGAATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						1.0204837

Conservation Information
Conserved circRNAs	NA
PMCS	1.0204837

			
						 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 Solyc01g100860.2_circ_g.3

Address

Any questions?

Supported by