Plant Circular RNA Database

Detail information of Solyc01g097320.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc01g097320.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_000342
					
						Alias
						1:79978476|79981188
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr1: 88217676-88220388  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc01g097320.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc01g097320.2_circ_g.1 Solyc01g097320.2_circ_g.3 Solyc01g097320.2_circ_g.4 						
					
						Support reads
						10
					
						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
						Solyc01g097320.2.1:2

General Information
CircRNA Name	Solyc01g097320.2_circ_g.2
ID in PlantcircBase	sly_circ_000342
Alias	1:79978476\|79981188
Organism	Solanum lycopersicum
Position	chr1: 88217676-88220388 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc01g097320.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc01g097320.2_circ_g.1 Solyc01g097320.2_circ_g.3 Solyc01g097320.2_circ_g.4
Support reads	10
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	Solyc01g097320.2.1:2

			
						 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  
						
							CTTCATGCATAAAAAACAACGAGTCGGCAGCTTGGGTGAAACATGTATCATGACTAGATAAAGT
GGATGCAAGCTGCTGACTGTATTGTATCAACGGGACcttatgtttattgcaagggtgaagaacg
atgagccgaaggcacgtacacgcaggacttcttgaccttgatattccctgctgtcaaatttgtt
atccttct

									
								

					

						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: 1178
Transcript exons: 88217676-88217773,88219309-88220388
CTTATGTTTATTGCAAGGGTGAAGAACGATGAGCCGAAGGCACGTACACGCAGGACTTCTTGAC
CTTGATATTCCCTGCTGTCAAATTTGTTATCCTTCTTGCGAGAATCGCCAAGCATTTCTTCTAC
ATGGCATTGAAGCTGAATATCGCTGGGAACTCTGCAGATCTGACTATTTTTCTCAAGTTCTTTA
AGAATCTCTAGCAAACGAGTATAGCGATTACAGCATATCACCCTTAGCAGCAACTTCTCAATGT
CAATACAACTCTGGTCAAGGGAAAATTCTGCTTCTTTTCCCGTTAGAGGATCAATAACAAATGT
GCTATGAAGACACTTAATTCGCAGATCTGGTCCAGGTTCAATTTTTATAAATGGGCATGTTCCA
ATTTCGGATGTTCCAGAGTTCTTATCCAAATCCAACCAATACAAAATCTTCAGCCCAGGAGTAC
GCAAACTAGCAGAGTCAGACTCCCCGTCTTGTGATGTTTGTGTGGAGCCAGCACTGCCAGCCTG
TCCAGTACTGACATCAGTTATGAGCTCAAAACGAATAGCATCTTTCCACCTTCCTTGACGAAGT
GTTTGCACTTGCCTTATGACTGTGTCCATAACAAGTGCCACACAAAGCTCATGCAAGATAGAGT
ATAAGGTCATAAATGGATGGTCTGCAGCAGCCATTCTTCGTTCTAAATCATCACCAAGAGCATG
CCGCCGAAAGTCATCCAGCTTCATAGGACCACTTCTCTCACCAACAAGCAGCTCCATATGTAAT
ATCCTCCACATTGACAAGTGTCCTCTGTAACCGAGGGTAACTAGAACTTTAAATTCTCCTTCCA
CACGAAGCAGAACAGTACCATCAGAAACTTTGACTTCAGTAATGTCCTTAGGAAGCGAAACTTC
AAGGAGTTTCGACCTAACCAGTGTGTCTAATTTCTTTAATGCTGGTTTTTGCTGGTCATCATTT
AATGTGCTCTGCAAGCCTACATCTTCTATACATTTTGGCAAACGATCATAACTTCCGGTAAGAA
GAACTTCAACAGCTGAAGGAACATCATAGATGGGAGCACGGGCTTGTTGTAGTCCTTCATGCAT
AAAAAACAACGAGTCGGCAGCTTGGGTGAAACATGTATCATGACTAGATAAAGTGGATGCAAGC
TGCTGACTGTATTGTATCAACGGGAC
						
					

						Genomic sequence
						
							CTTATGTTTATTGCAAGGGTGAAGAACGATGAGCCGAAGGCACGTACACGCAGGACTTCTTGAC
CTTGATATTCCCTGCTGTCAAATTTGTTATCCTTCTGCAAAGAGGCAACAGTTAAAGAAGGAAA
AAGTTTGTCATGCAGATATAGTACCAGAGAGTCTAGACTAGATTAGAGAACTTCAGAAAAGATC
ATATGTGAACTTCATCACTTACAAATAGCATCAGGATTCAAGATCTCAGCTTGGCTGCCTTAAG
ACAACGTACAACTATATTATATGCAGAAAGGATCTACCAAAGTTGGGGCAAGAAGCAAACACAG
CACTTCAACATGCAACGATAAAGAGCTCTGGAACTCAGTCACCTAATATCTCCTCCGTCTTTTG
GTTTTCGGTAGAGATGATAGTTCGAGTACTGCTTCACTGTTGCATTTTTATTAACTATGTATGC
TCTTAGAGAATAAACTAAATTAACGACAAAGGGGACTGCTAATCAATTATATCATGTGCAACAA
TGCACAAATTACTATTCGCTAGTCTATATAGTATGCCATACCATGGAATTATTCTGTTAGTGGA
AAATCACGAAACTTACATTTGTGTATGCATTGCCTACAGTGGCCAATAAATAGAACTTCTTCTA
CACAGATGTATTCCTTACCTAAAGATTGTAAATAAGTAGACTGCACTTATCCAAAATAAATGTC
AACAAGTTGACCTTAACACCCTTGTCTGCATGGACAAAAATAATGCATACCCCTCACATCTCCT
AAACCTTATTGTTAGGCCTCGCAACACATTGCTTGGTATAGAAATGACCTCAGTAGCTGGAGTC
GTGTGTAATATTGATTTAGCACACATTTTTTTCCTTCTATCTTTTTCCTATGATTGGTAAGTTA
GCACACAGTTCTGAGCTGTTTTGGTGACTAACAATATATTTGGTAAGCCGGTATTGGTTGTTAC
CAGCCTCTAAACGCCATATCTCAACTATATGTGTAGTTATTCACAGTTAGCCCCTAGCTTTTAA
ACAGCAAATACTACATAGAACAGTAATTTAGATACTTGATCCTCCACCCAAAAGCAACCAAACA
AGCTAGTGCCCCCTACTTGATTTTTATGAACACGTTCTGTTTCTAACATTTAGATCACATGTGC
AATGGTATAGACATAAAGCAGCCTAAATTAAACAGAACTCCCTCCAAATTTTCTAAGCATTTGG
ACAGCTGGCAAGTTCTTTCCTACATAACTGCTACTGGAAACTTCTAACTTAGATTCTTCCACTC
TTTCTTCCTTGAATATCATTGTAATGCTACTTCTCTGACATCCTTAATTCTATATATCATTTAT
GAAGAGTCCATCGGTTATCACAACTCTACCCTATCATACTTGTGATGCAAAAGACAGACAACAT
AATGACAAAAATAGCTATTTGTGGGAGAAGGCAGAGATTGACTTGATCGGTTTTATCCTTGCTA
AACCATACATCAATTTCTTTTTAACGTAGTGGTTAAGAGAGGCAGATCTTTAAAACAACACGAC
ATGGATGATGCATACAACCATGTATAATAAACCAATATGGAACTTATGATTTGCATGAGCTCTC
AAAAATTCCAAGAGATGTATTAAAATAACTAACCTTGCGAGAATCGCCAAGCATTTCTTCTACA
TGGCATTGAAGCTGAATATCGCTGGGAACTCTGCAGATCTGACTATTTTTCTCAAGTTCTTTAA
GAATCTCTAGCAAACGAGTATAGCGATTACAGCATATCACCCTTAGCAGCAACTTCTCAATGTC
AATACAACTCTGGTCAAGGGAAAATTCTGCTTCTTTTCCCGTTAGAGGATCAATAACAAATGTG
CTATGAAGACACTTAATTCGCAGATCTGGTCCAGGTTCAATTTTTATAAATGGGCATGTTCCAA
TTTCGGATGTTCCAGAGTTCTTATCCAAATCCAACCAATACAAAATCTTCAGCCCAGGAGTACG
CAAACTAGCAGAGTCAGACTCCCCGTCTTGTGATGTTTGTGTGGAGCCAGCACTGCCAGCCTGT
CCAGTACTGACATCAGTTATGAGCTCAAAACGAATAGCATCTTTCCACCTTCCTTGACGAAGTG
TTTGCACTTGCCTTATGACTGTGTCCATAACAAGTGCCACACAAAGCTCATGCAAGATAGAGTA
TAAGGTCATAAATGGATGGTCTGCAGCAGCCATTCTTCGTTCTAAATCATCACCAAGAGCATGC
CGCCGAAAGTCATCCAGCTTCATAGGACCACTTCTCTCACCAACAAGCAGCTCCATATGTAATA
TCCTCCACATTGACAAGTGTCCTCTGTAACCGAGGGTAACTAGAACTTTAAATTCTCCTTCCAC
ACGAAGCAGAACAGTACCATCAGAAACTTTGACTTCAGTAATGTCCTTAGGAAGCGAAACTTCA
AGGAGTTTCGACCTAACCAGTGTGTCTAATTTCTTTAATGCTGGTTTTTGCTGGTCATCATTTA
ATGTGCTCTGCAAGCCTACATCTTCTATACATTTTGGCAAACGATCATAACTTCCGGTAAGAAG
AACTTCAACAGCTGAAGGAACATCATAGATGGGAGCACGGGCTTGTTGTAGTCCTTCATGCATA
AAAAACAACGAGTCGGCAGCTTGGGTGAAACATGTATCATGACTAGATAAAGTGGATGCAAGCT
GCTGACTGTATTGTATCAACGGGAC
						
					

			
		

Sequences
Splice junction sequence	CTTCATGCATAAAAAACAACGAGTCGGCAGCTTGGGTGAAACATGTATCATGACTAGATAAAGT GGATGCAAGCTGCTGACTGTATTGTATCAACGGGACcttatgtttattgcaagggtgaagaacg atgagccgaaggcacgtacacgcaggacttcttgaccttgatattccctgctgtcaaatttgtt atccttct
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: 1178 Transcript exons: 88217676-88217773,88219309-88220388 CTTATGTTTATTGCAAGGGTGAAGAACGATGAGCCGAAGGCACGTACACGCAGGACTTCTTGAC CTTGATATTCCCTGCTGTCAAATTTGTTATCCTTCTTGCGAGAATCGCCAAGCATTTCTTCTAC ATGGCATTGAAGCTGAATATCGCTGGGAACTCTGCAGATCTGACTATTTTTCTCAAGTTCTTTA AGAATCTCTAGCAAACGAGTATAGCGATTACAGCATATCACCCTTAGCAGCAACTTCTCAATGT CAATACAACTCTGGTCAAGGGAAAATTCTGCTTCTTTTCCCGTTAGAGGATCAATAACAAATGT GCTATGAAGACACTTAATTCGCAGATCTGGTCCAGGTTCAATTTTTATAAATGGGCATGTTCCA ATTTCGGATGTTCCAGAGTTCTTATCCAAATCCAACCAATACAAAATCTTCAGCCCAGGAGTAC GCAAACTAGCAGAGTCAGACTCCCCGTCTTGTGATGTTTGTGTGGAGCCAGCACTGCCAGCCTG TCCAGTACTGACATCAGTTATGAGCTCAAAACGAATAGCATCTTTCCACCTTCCTTGACGAAGT GTTTGCACTTGCCTTATGACTGTGTCCATAACAAGTGCCACACAAAGCTCATGCAAGATAGAGT ATAAGGTCATAAATGGATGGTCTGCAGCAGCCATTCTTCGTTCTAAATCATCACCAAGAGCATG CCGCCGAAAGTCATCCAGCTTCATAGGACCACTTCTCTCACCAACAAGCAGCTCCATATGTAAT ATCCTCCACATTGACAAGTGTCCTCTGTAACCGAGGGTAACTAGAACTTTAAATTCTCCTTCCA CACGAAGCAGAACAGTACCATCAGAAACTTTGACTTCAGTAATGTCCTTAGGAAGCGAAACTTC AAGGAGTTTCGACCTAACCAGTGTGTCTAATTTCTTTAATGCTGGTTTTTGCTGGTCATCATTT AATGTGCTCTGCAAGCCTACATCTTCTATACATTTTGGCAAACGATCATAACTTCCGGTAAGAA GAACTTCAACAGCTGAAGGAACATCATAGATGGGAGCACGGGCTTGTTGTAGTCCTTCATGCAT AAAAAACAACGAGTCGGCAGCTTGGGTGAAACATGTATCATGACTAGATAAAGTGGATGCAAGC TGCTGACTGTATTGTATCAACGGGAC
Genomic sequence	CTTATGTTTATTGCAAGGGTGAAGAACGATGAGCCGAAGGCACGTACACGCAGGACTTCTTGAC CTTGATATTCCCTGCTGTCAAATTTGTTATCCTTCTGCAAAGAGGCAACAGTTAAAGAAGGAAA AAGTTTGTCATGCAGATATAGTACCAGAGAGTCTAGACTAGATTAGAGAACTTCAGAAAAGATC ATATGTGAACTTCATCACTTACAAATAGCATCAGGATTCAAGATCTCAGCTTGGCTGCCTTAAG ACAACGTACAACTATATTATATGCAGAAAGGATCTACCAAAGTTGGGGCAAGAAGCAAACACAG CACTTCAACATGCAACGATAAAGAGCTCTGGAACTCAGTCACCTAATATCTCCTCCGTCTTTTG GTTTTCGGTAGAGATGATAGTTCGAGTACTGCTTCACTGTTGCATTTTTATTAACTATGTATGC TCTTAGAGAATAAACTAAATTAACGACAAAGGGGACTGCTAATCAATTATATCATGTGCAACAA TGCACAAATTACTATTCGCTAGTCTATATAGTATGCCATACCATGGAATTATTCTGTTAGTGGA AAATCACGAAACTTACATTTGTGTATGCATTGCCTACAGTGGCCAATAAATAGAACTTCTTCTA CACAGATGTATTCCTTACCTAAAGATTGTAAATAAGTAGACTGCACTTATCCAAAATAAATGTC AACAAGTTGACCTTAACACCCTTGTCTGCATGGACAAAAATAATGCATACCCCTCACATCTCCT AAACCTTATTGTTAGGCCTCGCAACACATTGCTTGGTATAGAAATGACCTCAGTAGCTGGAGTC GTGTGTAATATTGATTTAGCACACATTTTTTTCCTTCTATCTTTTTCCTATGATTGGTAAGTTA GCACACAGTTCTGAGCTGTTTTGGTGACTAACAATATATTTGGTAAGCCGGTATTGGTTGTTAC CAGCCTCTAAACGCCATATCTCAACTATATGTGTAGTTATTCACAGTTAGCCCCTAGCTTTTAA ACAGCAAATACTACATAGAACAGTAATTTAGATACTTGATCCTCCACCCAAAAGCAACCAAACA AGCTAGTGCCCCCTACTTGATTTTTATGAACACGTTCTGTTTCTAACATTTAGATCACATGTGC AATGGTATAGACATAAAGCAGCCTAAATTAAACAGAACTCCCTCCAAATTTTCTAAGCATTTGG ACAGCTGGCAAGTTCTTTCCTACATAACTGCTACTGGAAACTTCTAACTTAGATTCTTCCACTC TTTCTTCCTTGAATATCATTGTAATGCTACTTCTCTGACATCCTTAATTCTATATATCATTTAT GAAGAGTCCATCGGTTATCACAACTCTACCCTATCATACTTGTGATGCAAAAGACAGACAACAT AATGACAAAAATAGCTATTTGTGGGAGAAGGCAGAGATTGACTTGATCGGTTTTATCCTTGCTA AACCATACATCAATTTCTTTTTAACGTAGTGGTTAAGAGAGGCAGATCTTTAAAACAACACGAC ATGGATGATGCATACAACCATGTATAATAAACCAATATGGAACTTATGATTTGCATGAGCTCTC AAAAATTCCAAGAGATGTATTAAAATAACTAACCTTGCGAGAATCGCCAAGCATTTCTTCTACA TGGCATTGAAGCTGAATATCGCTGGGAACTCTGCAGATCTGACTATTTTTCTCAAGTTCTTTAA GAATCTCTAGCAAACGAGTATAGCGATTACAGCATATCACCCTTAGCAGCAACTTCTCAATGTC AATACAACTCTGGTCAAGGGAAAATTCTGCTTCTTTTCCCGTTAGAGGATCAATAACAAATGTG CTATGAAGACACTTAATTCGCAGATCTGGTCCAGGTTCAATTTTTATAAATGGGCATGTTCCAA TTTCGGATGTTCCAGAGTTCTTATCCAAATCCAACCAATACAAAATCTTCAGCCCAGGAGTACG CAAACTAGCAGAGTCAGACTCCCCGTCTTGTGATGTTTGTGTGGAGCCAGCACTGCCAGCCTGT CCAGTACTGACATCAGTTATGAGCTCAAAACGAATAGCATCTTTCCACCTTCCTTGACGAAGTG TTTGCACTTGCCTTATGACTGTGTCCATAACAAGTGCCACACAAAGCTCATGCAAGATAGAGTA TAAGGTCATAAATGGATGGTCTGCAGCAGCCATTCTTCGTTCTAAATCATCACCAAGAGCATGC CGCCGAAAGTCATCCAGCTTCATAGGACCACTTCTCTCACCAACAAGCAGCTCCATATGTAATA TCCTCCACATTGACAAGTGTCCTCTGTAACCGAGGGTAACTAGAACTTTAAATTCTCCTTCCAC ACGAAGCAGAACAGTACCATCAGAAACTTTGACTTCAGTAATGTCCTTAGGAAGCGAAACTTCA AGGAGTTTCGACCTAACCAGTGTGTCTAATTTCTTTAATGCTGGTTTTTGCTGGTCATCATTTA ATGTGCTCTGCAAGCCTACATCTTCTATACATTTTGGCAAACGATCATAACTTCCGGTAAGAAG AACTTCAACAGCTGAAGGAACATCATAGATGGGAGCACGGGCTTGTTGTAGTCCTTCATGCATA AAAAACAACGAGTCGGCAGCTTGGGTGAAACATGTATCATGACTAGATAAAGTGGATGCAAGCT GCTGACTGTATTGTATCAACGGGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.767212651

Conservation Information
Conserved circRNAs	NA
PMCS	0.767212651

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							88220356-88217704(+)
88220300-88220381(-)
						
						Potential amino acid sequence
						
							MQAADCIVSTGPYVYCKGEER*(+)
MHEGLQQARAPIYDVPSAVEVLLTGSYDRLPKCIEDVGLQSTLNDDQQKPALKKLDTLVRSKLL
EVSLPKDITEVKVSDGTVLLRVEGEFKVLVTLGYRGHLSMWRILHMELLVGERSGPMKLDDFRR
HALGDDLERRMAAADHPFMTLYSILHELCVALVMDTVIRQVQTLRQGRWKDAIRFELITDVSTG
QAGSAGSTQTSQDGESDSASLRTPGLKILYWLDLDKNSGTSEIGTCPFIKIEPGPDLRIKCLHS
TFVIDPLTGKEAEFSLDQSCIDIEKLLLRVICCNRYTRLLEILKELEKNSQICRVPSDIQLQCH
VEEMLGDSRKKDNKFDSREYQGQEVLRVRAFGSSFFTLAINIRSR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	88220356-88217704(+) 88220300-88220381(-)
Potential amino acid sequence	MQAADCIVSTGPYVYCKGEER(+) MHEGLQQARAPIYDVPSAVEVLLTGSYDRLPKCIEDVGLQSTLNDDQQKPALKKLDTLVRSKLL EVSLPKDITEVKVSDGTVLLRVEGEFKVLVTLGYRGHLSMWRILHMELLVGERSGPMKLDDFRR HALGDDLERRMAAADHPFMTLYSILHELCVALVMDTVIRQVQTLRQGRWKDAIRFELITDVSTG QAGSAGSTQTSQDGESDSASLRTPGLKILYWLDLDKNSGTSEIGTCPFIKIEPGPDLRIKCLHS TFVIDPLTGKEAEFSLDQSCIDIEKLLLRVICCNRYTRLLEILKELEKNSQICRVPSDIQLQCH VEEMLGDSRKKDNKFDSREYQGQEVLRVRAFGSSFFTLAINIRSR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc01g097320.2_circ_g.2

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