Plant Circular RNA Database

Detail information of Solyc02g050140.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc02g050140.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_000568
					
						Alias
						2:24523894|24525433, Slcirc040
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr2: 4089484-4091023  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc02g050140.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc02g050140.2_circ_g.1 						
					
						Support reads
						10/20
					
						Tissues
						fruit/leaf
					
						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
						Solyc02g050140.2.1:4

General Information
CircRNA Name	Solyc02g050140.2_circ_g.2
ID in PlantcircBase	sly_circ_000568
Alias	2:24523894\|24525433, Slcirc040
Organism	Solanum lycopersicum
Position	chr2: 4089484-4091023 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc02g050140.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc02g050140.2_circ_g.1
Support reads	10/20
Tissues	fruit/leaf
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	Solyc02g050140.2.1:4

			
						 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  
						
							CTCTCATCAAACCAATGAACCAACTTCAACTATTAGCTTCATGGAAAGATCCGTGGAAGTCGAT
TTTATTTATGGTGTTTGTAAGCTATGCTATAATCAGgaaggttgacattaactaaccatgctct
ctacttcgagtctgggatgggcttatacgacaaggcagtgcggtatgatctagcatccgacttg
aaacagat

									
								

					

						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: 724
Transcript exons: 4089484-4089658,4089731-4089929,4090089-4090325,4090911-
4091023
GAAGGTTGACATTAACTAACCATGCTCTCTACTTCGAGTCTGGGATGGGCTTATACGACAAGGC
AGTGCGGTATGATCTAGCATCCGACTTGAAACAGATCATTAAGCCTGAGCTTACTGGACCTTTA
GGTGCTCGCCTTTTTGATAAAGCTGTTATGTACAAGTCCTCATCTATGATGGATCCTGCATATT
TTGAATTTCCAGAATTTAAAGGAAGTTCAAGACGGGATTATTGGTTAGATATTTGTCTCGAGAT
TTTCCATGCTCACAACTTTGCTCGGAAGTATAAACTCAAAGAGGATCAGCAGTCCGAAGCACTT
GCTAGGGCTGTTCTTGGAATTTACAGATACAAGGCAGTCAGAGAGGCTTTTAAGGTGATACACC
CAGTATCACGGGTGTCACTTTGTAGACTTGGAATCATCTCATGCAAGGACGTCGATATAATTGG
AGAAGCAACAATGTTAGTAGGAGATGTCTTTGTTGGTGAGGTAAATCCTCTGGAAAATGCGGTC
AAGCAGTCAATGAAAAACATTGGAAGAGCTGAAGCTGCACAGGCGACAGTTGACCAAGTCAAAG
TTGAAGGAATTGATACTAATGTAGTGGTAATGAAGGAGCTGCTTTTTCCTCTCATCAAACCAAT
GAACCAACTTCAACTATTAGCTTCATGGAAAGATCCGTGGAAGTCGATTTTATTTATGGTGTTT
GTAAGCTATGCTATAATCAG
						
					

						Genomic sequence
						
							GAAGGTTGACATTAACTAACCATGCTCTCTACTTCGAGTCTGGGATGGGCTTATACGACAAGGC
AGTGCGGTATGATCTAGCATCCGACTTGAAACAGATCATTAAGCCTGAGCTTACTGGACCTTTA
GGTGCTCGCCTTTTTGATAAAGCTGTTATGTACAAGTCCTCATCTATGTAAGCTTAATGTTTTC
AGTTGAAGCTATATACTTAAATTCACCAGGAACTTCTAACTTTAAGTTAGTACAGGATGGATCC
TGCATATTTTGAATTTCCAGAATTTAAAGGAAGTTCAAGACGGGATTATTGGTTAGATATTTGT
CTCGAGATTTTCCATGCTCACAACTTTGCTCGGAAGTATAAACTCAAAGAGGATCAGCAGTCCG
AAGCACTTGCTAGGGCTGTTCTTGGAATTTACAGATACAAGGCAGTCAGAGAGGCTTTTAAGGT
ATCTTCTTCCAATTACAAAACCGTACTATGTTTTAACTTAGCAGAAAGTCTTCCTAGAGGAGAT
GCGATCTTGGAAACTTTATCAAGCCGCTTGAAACTCATGAACTCTGCCGGCAATCGACGTAGAT
TATTGGGTTCTCCTAGTGCAAGGAGACAGGTGATACACCCAGTATCACGGGTGTCACTTTGTAG
ACTTGGAATCATCTCATGCAAGGACGTCGATATAATTGGAGAAGCAACAATGTTAGTAGGAGAT
GTCTTTGTTGGTGAGGTAAATCCTCTGGAAAATGCGGTCAAGCAGTCAATGAAAAACATTGGAA
GAGCTGAAGCTGCACAGGCGACAGTTGACCAAGTCAAAGTTGAAGGAATTGATACTAATGTAGT
GGTAATGAAGGTATAAATAAAACCCTTAACCTTTTTCTTTTTTTTTTGCTTAATGTATCATTCC
TCTGTTCAGGAGATTGCTGCTGCTTGTTCTCTTATTGATAGTTGATCCTGCTAAGTACACTTCT
GCATACAGGAAGACTGTTTTATGTAGTGAGTTACTTCAGCTCATCCTATGTTTAAAAGCTGTGC
AAAGTTGGAATACTGCACTCTTTTTTCCTAGGGAACTAAGAAGGTAGCATGATTGTTCTTCAGC
CGTTCGTATGTCTTCTGTACATCTTTTATTTTAGAGTAGTAAGTAGTTAGCTGCTCCACTTATT
TGTGGCTCCCTTTGTTGCATTTGCTTATTATTCTTAAATTAGAACTAAGGAGTTCCTGCACCCT
ACCTTTGAAAGTATCACATCATAAATGGGGTATTTTGTATCTTTGCTTCTTACTGTAAAATGTG
AATTTTGAGATGAGTAGTACTACATGATCTTTCTTCATTCCTCAGGATGACATAATGTTTGAGT
TGTGATATGTTGTTGCCGCTTACTGCTTAGAAGCTTATTTAGTTGCTTCATTCCTCAAGATTAC
ACTTATTTTTTTCCCGCAGGAGCTGCTTTTTCCTCTCATCAAACCAATGAACCAACTTCAACTA
TTAGCTTCATGGAAAGATCCGTGGAAGTCGATTTTATTTATGGTGTTTGTAAGCTATGCTATAA
TCAG
						
					

			
		

Sequences
Splice junction sequence	CTCTCATCAAACCAATGAACCAACTTCAACTATTAGCTTCATGGAAAGATCCGTGGAAGTCGAT TTTATTTATGGTGTTTGTAAGCTATGCTATAATCAGgaaggttgacattaactaaccatgctct ctacttcgagtctgggatgggcttatacgacaaggcagtgcggtatgatctagcatccgacttg aaacagat
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: 724 Transcript exons: 4089484-4089658,4089731-4089929,4090089-4090325,4090911- 4091023 GAAGGTTGACATTAACTAACCATGCTCTCTACTTCGAGTCTGGGATGGGCTTATACGACAAGGC AGTGCGGTATGATCTAGCATCCGACTTGAAACAGATCATTAAGCCTGAGCTTACTGGACCTTTA GGTGCTCGCCTTTTTGATAAAGCTGTTATGTACAAGTCCTCATCTATGATGGATCCTGCATATT TTGAATTTCCAGAATTTAAAGGAAGTTCAAGACGGGATTATTGGTTAGATATTTGTCTCGAGAT TTTCCATGCTCACAACTTTGCTCGGAAGTATAAACTCAAAGAGGATCAGCAGTCCGAAGCACTT GCTAGGGCTGTTCTTGGAATTTACAGATACAAGGCAGTCAGAGAGGCTTTTAAGGTGATACACC CAGTATCACGGGTGTCACTTTGTAGACTTGGAATCATCTCATGCAAGGACGTCGATATAATTGG AGAAGCAACAATGTTAGTAGGAGATGTCTTTGTTGGTGAGGTAAATCCTCTGGAAAATGCGGTC AAGCAGTCAATGAAAAACATTGGAAGAGCTGAAGCTGCACAGGCGACAGTTGACCAAGTCAAAG TTGAAGGAATTGATACTAATGTAGTGGTAATGAAGGAGCTGCTTTTTCCTCTCATCAAACCAAT GAACCAACTTCAACTATTAGCTTCATGGAAAGATCCGTGGAAGTCGATTTTATTTATGGTGTTT GTAAGCTATGCTATAATCAG
Genomic sequence	GAAGGTTGACATTAACTAACCATGCTCTCTACTTCGAGTCTGGGATGGGCTTATACGACAAGGC AGTGCGGTATGATCTAGCATCCGACTTGAAACAGATCATTAAGCCTGAGCTTACTGGACCTTTA GGTGCTCGCCTTTTTGATAAAGCTGTTATGTACAAGTCCTCATCTATGTAAGCTTAATGTTTTC AGTTGAAGCTATATACTTAAATTCACCAGGAACTTCTAACTTTAAGTTAGTACAGGATGGATCC TGCATATTTTGAATTTCCAGAATTTAAAGGAAGTTCAAGACGGGATTATTGGTTAGATATTTGT CTCGAGATTTTCCATGCTCACAACTTTGCTCGGAAGTATAAACTCAAAGAGGATCAGCAGTCCG AAGCACTTGCTAGGGCTGTTCTTGGAATTTACAGATACAAGGCAGTCAGAGAGGCTTTTAAGGT ATCTTCTTCCAATTACAAAACCGTACTATGTTTTAACTTAGCAGAAAGTCTTCCTAGAGGAGAT GCGATCTTGGAAACTTTATCAAGCCGCTTGAAACTCATGAACTCTGCCGGCAATCGACGTAGAT TATTGGGTTCTCCTAGTGCAAGGAGACAGGTGATACACCCAGTATCACGGGTGTCACTTTGTAG ACTTGGAATCATCTCATGCAAGGACGTCGATATAATTGGAGAAGCAACAATGTTAGTAGGAGAT GTCTTTGTTGGTGAGGTAAATCCTCTGGAAAATGCGGTCAAGCAGTCAATGAAAAACATTGGAA GAGCTGAAGCTGCACAGGCGACAGTTGACCAAGTCAAAGTTGAAGGAATTGATACTAATGTAGT GGTAATGAAGGTATAAATAAAACCCTTAACCTTTTTCTTTTTTTTTTGCTTAATGTATCATTCC TCTGTTCAGGAGATTGCTGCTGCTTGTTCTCTTATTGATAGTTGATCCTGCTAAGTACACTTCT GCATACAGGAAGACTGTTTTATGTAGTGAGTTACTTCAGCTCATCCTATGTTTAAAAGCTGTGC AAAGTTGGAATACTGCACTCTTTTTTCCTAGGGAACTAAGAAGGTAGCATGATTGTTCTTCAGC CGTTCGTATGTCTTCTGTACATCTTTTATTTTAGAGTAGTAAGTAGTTAGCTGCTCCACTTATT TGTGGCTCCCTTTGTTGCATTTGCTTATTATTCTTAAATTAGAACTAAGGAGTTCCTGCACCCT ACCTTTGAAAGTATCACATCATAAATGGGGTATTTTGTATCTTTGCTTCTTACTGTAAAATGTG AATTTTGAGATGAGTAGTACTACATGATCTTTCTTCATTCCTCAGGATGACATAATGTTTGAGT TGTGATATGTTGTTGCCGCTTACTGCTTAGAAGCTTATTTAGTTGCTTCATTCCTCAAGATTAC ACTTATTTTTTTCCCGCAGGAGCTGCTTTTTCCTCTCATCAAACCAATGAACCAACTTCAACTA TTAGCTTCATGGAAAGATCCGTGGAAGTCGATTTTATTTATGGTGTTTGTAAGCTATGCTATAA TCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.827749389

Conservation Information
Conserved circRNAs	NA
PMCS	0.827749389

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4090965-4089489(+)
4089529-4089499(+)
						
						Potential amino acid sequence
						
							MERSVEVDFIYGVCKLCYNQEG*(+)
MGLYDKAVRYDLASDLKQIIKPELTGPLGARLFDKAVMYKSSSMMDPAYFEFPEFKGSSRRDYW
LDICLEIFHAHNFARKYKLKEDQQSEALARAVLGIYRYKAVREAFKVIHPVSRVSLCRLGIISC
KDVDIIGEATMLVGDVFVGEVNPLENAVKQSMKNIGRAEAAQATVDQVKVEGIDTNVVVMKELL
FPLIKPMNQLQLLASWKDPWKSILFMVFVSYAIIRKVDIN*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4090965-4089489(+) 4089529-4089499(+)
Potential amino acid sequence	MERSVEVDFIYGVCKLCYNQEG(+) MGLYDKAVRYDLASDLKQIIKPELTGPLGARLFDKAVMYKSSSMMDPAYFEFPEFKGSSRRDYW LDICLEIFHAHNFARKYKLKEDQQSEALARAVLGIYRYKAVREAFKVIHPVSRVSLCRLGIISC KDVDIIGEATMLVGDVFVGEVNPLENAVKQSMKNIGRAEAAQATVDQVKVEGIDTNVVVMKELL FPLIKPMNQLQLLASWKDPWKSILFMVFVSYAIIRKVDIN(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yin et al., 2018; Wang et al., 2018b

circRNA

Detail information of Solyc02g050140.2_circ_g.2

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