Plant Circular RNA Database

Detail information of Solyc04g077120.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc04g077120.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_001528
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 62072849-62075052  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc04g077120.2						
					
						Parent gene annotation
						
							Inositol-tetrakisphosphate 1-kinase
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc04g077120.2_circ_g.2 						
					
						Support reads
						7
					
						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
						Solyc04g077120.2.1:6

General Information
CircRNA Name	Solyc04g077120.2_circ_g.1
ID in PlantcircBase	sly_circ_001528
Alias	NA
Organism	Solanum lycopersicum
Position	chr4: 62072849-62075052 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc04g077120.2
Parent gene annotation	Inositol-tetrakisphosphate 1-kinase
Parent gene strand	+
Alternative splicing	Solyc04g077120.2_circ_g.2
Support reads	7
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	Solyc04g077120.2.1:6

			
						 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  
						
							AAGCGTGAGCTGTCAACAAACCCTGGGGTTTTTAGATTCCCAAGAGTTTCTTGTGCTGCTGCAT
CTGCAGATGAAGCAGATTTAGACCCTTGTGTCGGGGgagtaaggggatattatttgttgctatt
gatcagagcaaacccctttcagatcaaggtccttttgacattgtgctccataaggttcccattt
tctacctt

									
								

					

						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: 614
Transcript exons: 62072849-62072930,62073291-62073323,62073997-62074117,62
074341-62074433,62074663-62074770,62074876-62075052
GAGTAAGGGGATATTATTTGTTGCTATTGATCAGAGCAAACCCCTTTCAGATCAAGGTCCTTTT
GACATTGTGCTCCATAAGTTGTCAGGAAGCAAGTGGCGGCGTATTCTTGAGGAATATAGGCTAA
CACATCCAGATGTGACAGTTCTTGACCCTCCGGAGGCCATACAACACATATACAACCGCCAATA
CATGCTTGAAGATGTTGCGGACCTGAATTTGTCGGACACCTATGGGGAAGTTGGTGTTCCCAGG
CAACTGGTTATTGAGAAAGATTCTTCATCTATTCCAGATGCAGTAGGTAAAGCTGAGCTGAGAC
TACCTATTGTTGCAAAGCCTTTGGCTGCCAAGTCCCATGAGTTGTCTCTAGCCTATGACAAATT
CTCTCTTCAGATGCTAGAACCCCCACTTGTGCTACAGGAATTTATCAACCACGGAGGAATTCTG
TTTAAAGTATACATTGTTGGGGAAGCAGTTAAGGTTGTTAGACGATTCAGTTTACCTGATATTA
GCAAGCGTGAGCTGTCAACAAACCCTGGGGTTTTTAGATTCCCAAGAGTTTCTTGTGCTGCTGC
ATCTGCAGATGAAGCAGATTTAGACCCTTGTGTCGGGG
						
					

						Genomic sequence
						
							GAGTAAGGGGATATTATTTGTTGCTATTGATCAGAGCAAACCCCTTTCAGATCAAGGTCCTTTT
GACATTGTGCTCCATAAGGTTCCCATTTTCTACCTTTTCTAATTCCTGTGTATTTCTCCCTCTT
GGGGGAATGTATACTTTGTGATCTAATAGTAATCCTTTAATTCGTAAACTATCTACCTCCCAAG
GTAGGGGCAAGGTCATGATATACTCTATAGTCTACCCTCTCGAGACACCACTCGTGGGATTACA
CTTTGTTAAATGTTGTTTGTTTGTAATATCTTATAAGGGCATATCACCAAATATCTGTTCTGAA
ACATGTTACTTGTCTGTATATGCTCGCATACTTAATCCATTATAGCTTGTCCCTGGGAGATGTC
ATTCTGTAATATGATGCCCTCTGTCTCTATCTGACATTTTTGTGCTCCTTTCTCGCAGTTGTCA
GGAAGCAAGTGGCGGCGTATTCTTGAGGTTGGTTCATTGGGAAGCTTTCTATGTGTATGTATGT
GTGCGTTTTACAGAATCCTGTTGATTACAGCTAGCATGCATCGTTCAGGCAAATCTGTAATTAG
TGTAGGCTAAAATACACATAATTACTTGATGTGGATTAGACATGCGTTAGCAGTGATTGGTGAG
ATGAGCTGTCTTTTTGCTTAAACTTGCTCTATCTGGCATAACTTGCAGACTTCTAGCTCTTTCC
TCTGTCATGAATCATTACTTGGTAATTGTGTCAAAAGCCTTGAGCTTTGTGGGTAGAGTAGCTG
ATTGATTGCAGATAGGATTCCTGGTTTCCATATATGGATCTTATTTGTTCCGCGGCTTATCATA
ATCCTCATATCAGCTCAGGAGAGAACTTACCTAGTCAATGCCTTTTAATCTTCGGTATATTTCC
TTTTAAGTGCCACTCCAATGCTTCCCAAGTTGTTTGGATTAAGGCATATTAGTAGTTGGGATCA
TTCTAGTTTTGTCGGAGACTAGTTGTTGGAAAAGGTAAATTCATATTGTGCTCTGTTCACCTTA
TTTTTATTCTGCTTTTTAAGTGCTGTTTGCTTCTTTAGAGCCTATTTGTAGTTTAATCAACTGA
GTGTATTGGAAGAACCTCTAGTATTTTTCTCCTTACCTCTTCTCTTTGCTCTCTGTGTAGGAAT
ATAGGCTAACACATCCAGATGTGACAGTTCTTGACCCTCCGGAGGCCATACAACACATATACAA
CCGCCAATACATGCTTGAAGATGTTGCGGACCTGAATTTGTCGGACACCTATGGTAATATTTCC
CGTCTGTTCATGGTTATTTGAGAACAATTGATTGCAGTAATTTTAGCCCTGGGAAGCTGTGTGA
ACTGGGATTGCCACGTTTTCTTTTTCTTCTTGGCTTGAAGAAGTGGGGAGAGGACCAAATGCTG
GGCAGCTGGGTAAGGGAGATTGAGGGGTGGGGTTTACTACATCAGTGAAAAAAATGGATTAACT
TATTTTTGATTGCATGACAGGGGAAGTTGGTGTTCCCAGGCAACTGGTTATTGAGAAAGATTCT
TCATCTATTCCAGATGCAGTAGGTAAAGCTGAGCTGAGACTACCTATTGGTACGTTTTTTCTCT
TCACATTCGTCTTTAATCAACTGATCCTTGGGCAGTTGACACTTTAAAACTCAAGATCTGTACC
TCTCTTGTAGCCATCAAAGTTGCAACTGTGTAACTTACATGTGACAAGCATCTGAATAATTTGA
AAGTGATCTCTTTCAAACTTGAGCAGTATGTGAACAATGTAATCTGTTCATGAAATCCCTGAAT
TGAGCTTCTTTTATCTTCTCAGTTGCAAAGCCTTTGGCTGCCAAGTCCCATGAGTTGTCTCTAG
CCTATGACAAATTCTCTCTTCAGATGCTAGAACCCCCACTTGTGCTACAGGAATTTATCAACCA
CGGTACGTATATTATTTGAGATATTGAACTTGTGCCTTCCATTCCATGTGCAAATGTTTATAAG
TCGTCGTGTTGATGATTATGTATTTTTTGTCTTGTGGTTGTAGGAGGAATTCTGTTTAAAGTAT
ACATTGTTGGGGAAGCAGTTAAGGTTGTTAGACGATTCAGTTTACCTGATATTAGCAAGCGTGA
GCTGTCAACAAACCCTGGGGTTTTTAGATTCCCAAGAGTTTCTTGTGCTGCTGCATCTGCAGAT
GAAGCAGATTTAGACCCTTGTGTCGGGG
						
					

			
		

Sequences
Splice junction sequence	AAGCGTGAGCTGTCAACAAACCCTGGGGTTTTTAGATTCCCAAGAGTTTCTTGTGCTGCTGCAT CTGCAGATGAAGCAGATTTAGACCCTTGTGTCGGGGgagtaaggggatattatttgttgctatt gatcagagcaaacccctttcagatcaaggtccttttgacattgtgctccataaggttcccattt tctacctt
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: 614 Transcript exons: 62072849-62072930,62073291-62073323,62073997-62074117,62 074341-62074433,62074663-62074770,62074876-62075052 GAGTAAGGGGATATTATTTGTTGCTATTGATCAGAGCAAACCCCTTTCAGATCAAGGTCCTTTT GACATTGTGCTCCATAAGTTGTCAGGAAGCAAGTGGCGGCGTATTCTTGAGGAATATAGGCTAA CACATCCAGATGTGACAGTTCTTGACCCTCCGGAGGCCATACAACACATATACAACCGCCAATA CATGCTTGAAGATGTTGCGGACCTGAATTTGTCGGACACCTATGGGGAAGTTGGTGTTCCCAGG CAACTGGTTATTGAGAAAGATTCTTCATCTATTCCAGATGCAGTAGGTAAAGCTGAGCTGAGAC TACCTATTGTTGCAAAGCCTTTGGCTGCCAAGTCCCATGAGTTGTCTCTAGCCTATGACAAATT CTCTCTTCAGATGCTAGAACCCCCACTTGTGCTACAGGAATTTATCAACCACGGAGGAATTCTG TTTAAAGTATACATTGTTGGGGAAGCAGTTAAGGTTGTTAGACGATTCAGTTTACCTGATATTA GCAAGCGTGAGCTGTCAACAAACCCTGGGGTTTTTAGATTCCCAAGAGTTTCTTGTGCTGCTGC ATCTGCAGATGAAGCAGATTTAGACCCTTGTGTCGGGG
Genomic sequence	GAGTAAGGGGATATTATTTGTTGCTATTGATCAGAGCAAACCCCTTTCAGATCAAGGTCCTTTT GACATTGTGCTCCATAAGGTTCCCATTTTCTACCTTTTCTAATTCCTGTGTATTTCTCCCTCTT GGGGGAATGTATACTTTGTGATCTAATAGTAATCCTTTAATTCGTAAACTATCTACCTCCCAAG GTAGGGGCAAGGTCATGATATACTCTATAGTCTACCCTCTCGAGACACCACTCGTGGGATTACA CTTTGTTAAATGTTGTTTGTTTGTAATATCTTATAAGGGCATATCACCAAATATCTGTTCTGAA ACATGTTACTTGTCTGTATATGCTCGCATACTTAATCCATTATAGCTTGTCCCTGGGAGATGTC ATTCTGTAATATGATGCCCTCTGTCTCTATCTGACATTTTTGTGCTCCTTTCTCGCAGTTGTCA GGAAGCAAGTGGCGGCGTATTCTTGAGGTTGGTTCATTGGGAAGCTTTCTATGTGTATGTATGT GTGCGTTTTACAGAATCCTGTTGATTACAGCTAGCATGCATCGTTCAGGCAAATCTGTAATTAG TGTAGGCTAAAATACACATAATTACTTGATGTGGATTAGACATGCGTTAGCAGTGATTGGTGAG ATGAGCTGTCTTTTTGCTTAAACTTGCTCTATCTGGCATAACTTGCAGACTTCTAGCTCTTTCC TCTGTCATGAATCATTACTTGGTAATTGTGTCAAAAGCCTTGAGCTTTGTGGGTAGAGTAGCTG ATTGATTGCAGATAGGATTCCTGGTTTCCATATATGGATCTTATTTGTTCCGCGGCTTATCATA ATCCTCATATCAGCTCAGGAGAGAACTTACCTAGTCAATGCCTTTTAATCTTCGGTATATTTCC TTTTAAGTGCCACTCCAATGCTTCCCAAGTTGTTTGGATTAAGGCATATTAGTAGTTGGGATCA TTCTAGTTTTGTCGGAGACTAGTTGTTGGAAAAGGTAAATTCATATTGTGCTCTGTTCACCTTA TTTTTATTCTGCTTTTTAAGTGCTGTTTGCTTCTTTAGAGCCTATTTGTAGTTTAATCAACTGA GTGTATTGGAAGAACCTCTAGTATTTTTCTCCTTACCTCTTCTCTTTGCTCTCTGTGTAGGAAT ATAGGCTAACACATCCAGATGTGACAGTTCTTGACCCTCCGGAGGCCATACAACACATATACAA CCGCCAATACATGCTTGAAGATGTTGCGGACCTGAATTTGTCGGACACCTATGGTAATATTTCC CGTCTGTTCATGGTTATTTGAGAACAATTGATTGCAGTAATTTTAGCCCTGGGAAGCTGTGTGA ACTGGGATTGCCACGTTTTCTTTTTCTTCTTGGCTTGAAGAAGTGGGGAGAGGACCAAATGCTG GGCAGCTGGGTAAGGGAGATTGAGGGGTGGGGTTTACTACATCAGTGAAAAAAATGGATTAACT TATTTTTGATTGCATGACAGGGGAAGTTGGTGTTCCCAGGCAACTGGTTATTGAGAAAGATTCT TCATCTATTCCAGATGCAGTAGGTAAAGCTGAGCTGAGACTACCTATTGGTACGTTTTTTCTCT TCACATTCGTCTTTAATCAACTGATCCTTGGGCAGTTGACACTTTAAAACTCAAGATCTGTACC TCTCTTGTAGCCATCAAAGTTGCAACTGTGTAACTTACATGTGACAAGCATCTGAATAATTTGA AAGTGATCTCTTTCAAACTTGAGCAGTATGTGAACAATGTAATCTGTTCATGAAATCCCTGAAT TGAGCTTCTTTTATCTTCTCAGTTGCAAAGCCTTTGGCTGCCAAGTCCCATGAGTTGTCTCTAG CCTATGACAAATTCTCTCTTCAGATGCTAGAACCCCCACTTGTGCTACAGGAATTTATCAACCA CGGTACGTATATTATTTGAGATATTGAACTTGTGCCTTCCATTCCATGTGCAAATGTTTATAAG TCGTCGTGTTGATGATTATGTATTTTTTGTCTTGTGGTTGTAGGAGGAATTCTGTTTAAAGTAT ACATTGTTGGGGAAGCAGTTAAGGTTGTTAGACGATTCAGTTTACCTGATATTAGCAAGCGTGA GCTGTCAACAAACCCTGGGGTTTTTAGATTCCCAAGAGTTTCTTGTGCTGCTGCATCTGCAGAT GAAGCAGATTTAGACCCTTGTGTCGGGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.356047889

Conservation Information
Conserved circRNAs	NA
PMCS	0.356047889

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							62074076-62074006(+)
						
						Potential amino acid sequence
						
							MLEDVADLNLSDTYGEVGVPRQLVIEKDSSSIPDAVGKAELRLPIVAKPLAAKSHELSLAYDKF
SLQMLEPPLVLQEFINHGGILFKVYIVGEAVKVVRRFSLPDISKRELSTNPGVFRFPRVSCAAA
SADEADLDPCVGGVRGYYLLLLIRANPFQIKVLLTLCSISCQEASGGVFLRNIG*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	62074076-62074006(+)
Potential amino acid sequence	MLEDVADLNLSDTYGEVGVPRQLVIEKDSSSIPDAVGKAELRLPIVAKPLAAKSHELSLAYDKF SLQMLEPPLVLQEFINHGGILFKVYIVGEAVKVVRRFSLPDISKRELSTNPGVFRFPRVSCAAA SADEADLDPCVGGVRGYYLLLLIRANPFQIKVLLTLCSISCQEASGGVFLRNIG*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc04g077120.2_circ_g.1

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