Plant Circular RNA Database

Detail information of Solyc02g020980.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc02g020980.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_000592
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr2: 20822830-20825544  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc02g020980.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc02g020980.2_circ_g.1 						
					
						Support reads
						3
					
						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
						Solyc02g020980.2.1:6

General Information
CircRNA Name	Solyc02g020980.2_circ_g.2
ID in PlantcircBase	sly_circ_000592
Alias	NA
Organism	Solanum lycopersicum
Position	chr2: 20822830-20825544 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc02g020980.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc02g020980.2_circ_g.1
Support reads	3
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	Solyc02g020980.2.1:6

			
						 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  
						
							TTCGTCGTAGTTTCACTTCACTCTCTAAAAACATGGATGTTTCCAAGACTGACTTCAGCGCAGA
TGCAATTTTCTTCTCAGTATTGCATTTGTCCTTGAAgatatcgccaataatgttttgggtttgt
tggatcattgatagtctcttccactgcaggccgtgtcgtgtaatcttctttaagtgctagcaaa
tcctgtat

									
								

					

						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: 769
Transcript exons: 20822830-20822923,20823787-20823984,20824603-20824701,20
824797-20824956,20825168-20825265,20825425-20825544
GATATCGCCAATAATGTTTTGGGTTTGTTGGATCATTGATAGTCTCTTCCACTGCAGGCCGTGT
CGTGTAATCTTCTTTAAGTGCTAGCAAATCCTGGAGGGGAAATATTGACCACATTGATGGGGCT
TCAACATGCTGTCGCAAGACAAAGTGCACAATTTCAGGAGTGCATTGATCAGGTGGCAACTCAT
CAGATCCCATCACTGCTTGAAAAAAGCGGTGCCTTCTCTCTTCATCTTCCTCCCACCAAGCACG
TAGAGTAGAACAGTCATGGCATGATGGAGCACAAACCGTCATGTAGTTGTATTGAGAAGGAATA
TCAAATTCTAGATCAGGTTCACTTGGCATGCGTTGAATGCGTAGGCCTACTAAGCCCAGTTCTT
GCATAACAGGATGAACACAGGAGGGAATTAGGCCTAGGTCTTCCCCACAAGCGAGCATGTCTGA
TGAGTTCAAAAGAACAGGCAGAGTCTTAAAGGCATTGTCACGCCAAAGACCTTCTTGTCGATGG
AAGTAGTAATCATAGTATAATCTTTTTAGGACATTTTGACTGTGCTGATCCAAATCCATAAAGC
TTGTTGTGTCTTCAACATTGAAGCGAGGGTAAAACTTTCTTGGATCTTCTGGATCGTTAATAAG
CGCCACATTCTGCAGAAGATCAAAGAGTTTTCGTCGTAGTTTCACTTCACTCTCTAAAAACATG
GATGTTTCCAAGACTGACTTCAGCGCAGATGCAATTTTCTTCTCAGTATTGCATTTGTCCTTGA
A
						
					

						Genomic sequence
						
							GATATCGCCAATAATGTTTTGGGTTTGTTGGATCATTGATAGTCTCTTCCACTGCAGGCCGTGT
CGTGTAATCTTCTTTAAGTGCTAGCAAATCCTGTATATTATTTAGCAATGGTGTCAGTGCCGTG
GAAGAAAATCCTGAATGCTGAGATGAGCATTGAGACATTAATCTCGCTGGGAAGCTCACTTGCA
TCAGAAATAAATTGCACAATGTAGCATAATGTCAAGATTATGTTCTTCAAAGTTCAAACTGAAT
GATACCATGAAAAACAACCACCTAAATTTTTTCTCATGAATGGTTCAGAGTAGGGCAAAAAAGA
TGCTTATTAGTGGCATATTTAGTCATGAAGGAGGTTTAGTAAGCCTGACTGAACCATAGTGCTA
ACAAATTACCATGTGTCCTTAAATAAGTACAAAGTCCAAATTTTCGGACACTAGGAGACAAAAC
ATAATTAATCGACCATTTCTACAGAGCTACCAAATCCATATATCTCCGTATTGTTTGAAAACAT
CTATTCCGAGATACAAAATCACAATCTCTTTGATAGAACTTAGAATTCATACAATGTCAATATG
GTGAATAATCAAAAGAATTTGTTTATGGAATTCTTTCTTTTGGGAGAAGAGGGAGGTCATAAGT
AATTATTAATATCTTTGGACAGCAGCCCTTTTCAAATTGAATTTGATTGGCTCAAACCTCCCCA
AGAAAAGGAATTCTGACTTTTTTTCTTGCACTTTGGACAAAAACATTATACTTTAGAAGCCTAG
AGAGCTGACGCCTTTAGAAGGACTTAAGTAATTATTTGAAGGACATAGAACTCACTAATCACCC
TGGCCAGTAGTTCAGCACTATGAAGCTTTGAGGCAAATATGGAGCGAATCAATTTAGCAAAGAC
TACTACTAAAGAATTAATTACATGCTACAAAAGAAGTAGGATCCTTATATCAATTAAGTACCTG
GAGGGGAAATATTGACCACATTGATGGGGCTTCAACATGCTGTCGCAAGACAAAGTGCACAATT
TCAGGAGTGCATTGATCAGGTGGCAACTCATCAGATCCCATCACTGCTTGAAAAAAGCGGTGCC
TTCTCTCTTCATCTTCCTCCCACCAAGCACGTAGAGTAGAACAGTCATGGCATGATGGAGCACA
AACCTAAGTTTGAAGTACTAACATTATTGTCCAGTCTTTGATCAACAAGGACTAATATGCATTG
AAAACAGATAAATACTTGAGTGTAAAAGCACTCTTAAAAATCATTTACAAGATATACGGAGGAA
AAGGGAGGCATACTCAAAGGTGTCTTGACAGCCTCTATCTTTAATATATTCCCGGGGGGGCAGC
TTTATAACAAGAATTAACTAATAAAACATTAAAAGCAGCACAACAGTTGGTTGATGCAATTTTT
TTTTCATGCTAAGCAAAATTAGAGTTTGCATTCTAGTTTCCACTATCCAATGACTTTTAGCAGA
TTTCCAGTACATCAATATGTTTTCACTTAAAAGGTTATATCATAAACAACAAGCATAACAATAA
AGCATTTTGTCATGCCTCCAGGTGCTTTTTCTTATAGCCAAAGGGAGCACTTGAACAAATGTTA
AAGTAAATCGATGTATGATCATATGAATAAAATTTCTCTATTAGGTAAAGTATATTTTAAATTT
CACGGGAAAAGGTTTTTATAGTAGATTATCATAGAAGCTGCAGTAACTAAGACCATCTTTCATA
TCAAATAAGTTGGGATGTAGTAGAAGAGATCTCAGAGAATTTTACCGTCATGTAGTTGTATTGA
GAAGGAATATCAAATTCTAGATCAGGTTCACTTGGCATGCGTTGAATGCGTAGGCCTACTAAGC
CCAGTTCTTGCATAACCTGCATCAAAGTGGTCATAACTCAAATCATACATTGAGATGCAAGAAG
TGATGTGACATAATGATTCACAAGGATGATAGTTCTGAGTGGCATACAGGATGAACACAGGAGG
GAATTAGGCCTAGGTCTTCCCCACAAGCGAGCATGTCTGATGAGTTCAAAAGAACAGGCAGAGT
CTTAAAGGCATTGTCACGCCAAAGACCTTCTTGTCGATGGAAGTAGTAATCATAGTATAATCTT
TTTAGGACATTTTGACTGCACCAGCAAACAGATCATAAGATAACCATAAAAATTAGCATAACTG
CCTTAAATTAGAGGCTAAAACCCTAGTATTCTATACATGCACAGCAAATGTGTAGACATCTAAA
AGGATGAAAGATAAACACTGGTGTTTACTTTAAAAATGTCACTGCAATTTATCAAATCCGACAT
CAGATAATGTGAACTAGAAAAACGCATGAGGTACCTGTGCTGATCCAAATCCATAAAGCTTGTT
GTGTCTTCAACATTGAAGCGAGGGTAAAACTTTCTTGGATCTTCTGGATCGTTAATAAGCGCCA
CATTCTGTGATAAAGATTGGATCATGAACATAACAGTCAAGTGTAGAATAATAAGCATCGGTGC
AGAAAAAGCATAATATTTTTTAAAAAAGGATTAAAAGCATAGTTTTAAAATAGGAGAAGAATAC
ACAAAATTAGACTTCTGGACATCAAAGCAATGTACCTGCAGAAGATCAAAGAGTTTTCGTCGTA
GTTTCACTTCACTCTCTAAAAACATGGATGTTTCCAAGACTGACTTCAGCGCAGATGCAATTTT
CTTCTCAGTATTGCATTTGTCCTTGAA
						
					

			
		

Sequences
Splice junction sequence	TTCGTCGTAGTTTCACTTCACTCTCTAAAAACATGGATGTTTCCAAGACTGACTTCAGCGCAGA TGCAATTTTCTTCTCAGTATTGCATTTGTCCTTGAAgatatcgccaataatgttttgggtttgt tggatcattgatagtctcttccactgcaggccgtgtcgtgtaatcttctttaagtgctagcaaa tcctgtat
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: 769 Transcript exons: 20822830-20822923,20823787-20823984,20824603-20824701,20 824797-20824956,20825168-20825265,20825425-20825544 GATATCGCCAATAATGTTTTGGGTTTGTTGGATCATTGATAGTCTCTTCCACTGCAGGCCGTGT CGTGTAATCTTCTTTAAGTGCTAGCAAATCCTGGAGGGGAAATATTGACCACATTGATGGGGCT TCAACATGCTGTCGCAAGACAAAGTGCACAATTTCAGGAGTGCATTGATCAGGTGGCAACTCAT CAGATCCCATCACTGCTTGAAAAAAGCGGTGCCTTCTCTCTTCATCTTCCTCCCACCAAGCACG TAGAGTAGAACAGTCATGGCATGATGGAGCACAAACCGTCATGTAGTTGTATTGAGAAGGAATA TCAAATTCTAGATCAGGTTCACTTGGCATGCGTTGAATGCGTAGGCCTACTAAGCCCAGTTCTT GCATAACAGGATGAACACAGGAGGGAATTAGGCCTAGGTCTTCCCCACAAGCGAGCATGTCTGA TGAGTTCAAAAGAACAGGCAGAGTCTTAAAGGCATTGTCACGCCAAAGACCTTCTTGTCGATGG AAGTAGTAATCATAGTATAATCTTTTTAGGACATTTTGACTGTGCTGATCCAAATCCATAAAGC TTGTTGTGTCTTCAACATTGAAGCGAGGGTAAAACTTTCTTGGATCTTCTGGATCGTTAATAAG CGCCACATTCTGCAGAAGATCAAAGAGTTTTCGTCGTAGTTTCACTTCACTCTCTAAAAACATG GATGTTTCCAAGACTGACTTCAGCGCAGATGCAATTTTCTTCTCAGTATTGCATTTGTCCTTGA A
Genomic sequence	GATATCGCCAATAATGTTTTGGGTTTGTTGGATCATTGATAGTCTCTTCCACTGCAGGCCGTGT CGTGTAATCTTCTTTAAGTGCTAGCAAATCCTGTATATTATTTAGCAATGGTGTCAGTGCCGTG GAAGAAAATCCTGAATGCTGAGATGAGCATTGAGACATTAATCTCGCTGGGAAGCTCACTTGCA TCAGAAATAAATTGCACAATGTAGCATAATGTCAAGATTATGTTCTTCAAAGTTCAAACTGAAT GATACCATGAAAAACAACCACCTAAATTTTTTCTCATGAATGGTTCAGAGTAGGGCAAAAAAGA TGCTTATTAGTGGCATATTTAGTCATGAAGGAGGTTTAGTAAGCCTGACTGAACCATAGTGCTA ACAAATTACCATGTGTCCTTAAATAAGTACAAAGTCCAAATTTTCGGACACTAGGAGACAAAAC ATAATTAATCGACCATTTCTACAGAGCTACCAAATCCATATATCTCCGTATTGTTTGAAAACAT CTATTCCGAGATACAAAATCACAATCTCTTTGATAGAACTTAGAATTCATACAATGTCAATATG GTGAATAATCAAAAGAATTTGTTTATGGAATTCTTTCTTTTGGGAGAAGAGGGAGGTCATAAGT AATTATTAATATCTTTGGACAGCAGCCCTTTTCAAATTGAATTTGATTGGCTCAAACCTCCCCA AGAAAAGGAATTCTGACTTTTTTTCTTGCACTTTGGACAAAAACATTATACTTTAGAAGCCTAG AGAGCTGACGCCTTTAGAAGGACTTAAGTAATTATTTGAAGGACATAGAACTCACTAATCACCC TGGCCAGTAGTTCAGCACTATGAAGCTTTGAGGCAAATATGGAGCGAATCAATTTAGCAAAGAC TACTACTAAAGAATTAATTACATGCTACAAAAGAAGTAGGATCCTTATATCAATTAAGTACCTG GAGGGGAAATATTGACCACATTGATGGGGCTTCAACATGCTGTCGCAAGACAAAGTGCACAATT TCAGGAGTGCATTGATCAGGTGGCAACTCATCAGATCCCATCACTGCTTGAAAAAAGCGGTGCC TTCTCTCTTCATCTTCCTCCCACCAAGCACGTAGAGTAGAACAGTCATGGCATGATGGAGCACA AACCTAAGTTTGAAGTACTAACATTATTGTCCAGTCTTTGATCAACAAGGACTAATATGCATTG AAAACAGATAAATACTTGAGTGTAAAAGCACTCTTAAAAATCATTTACAAGATATACGGAGGAA AAGGGAGGCATACTCAAAGGTGTCTTGACAGCCTCTATCTTTAATATATTCCCGGGGGGGCAGC TTTATAACAAGAATTAACTAATAAAACATTAAAAGCAGCACAACAGTTGGTTGATGCAATTTTT TTTTCATGCTAAGCAAAATTAGAGTTTGCATTCTAGTTTCCACTATCCAATGACTTTTAGCAGA TTTCCAGTACATCAATATGTTTTCACTTAAAAGGTTATATCATAAACAACAAGCATAACAATAA AGCATTTTGTCATGCCTCCAGGTGCTTTTTCTTATAGCCAAAGGGAGCACTTGAACAAATGTTA AAGTAAATCGATGTATGATCATATGAATAAAATTTCTCTATTAGGTAAAGTATATTTTAAATTT CACGGGAAAAGGTTTTTATAGTAGATTATCATAGAAGCTGCAGTAACTAAGACCATCTTTCATA TCAAATAAGTTGGGATGTAGTAGAAGAGATCTCAGAGAATTTTACCGTCATGTAGTTGTATTGA GAAGGAATATCAAATTCTAGATCAGGTTCACTTGGCATGCGTTGAATGCGTAGGCCTACTAAGC CCAGTTCTTGCATAACCTGCATCAAAGTGGTCATAACTCAAATCATACATTGAGATGCAAGAAG TGATGTGACATAATGATTCACAAGGATGATAGTTCTGAGTGGCATACAGGATGAACACAGGAGG GAATTAGGCCTAGGTCTTCCCCACAAGCGAGCATGTCTGATGAGTTCAAAAGAACAGGCAGAGT CTTAAAGGCATTGTCACGCCAAAGACCTTCTTGTCGATGGAAGTAGTAATCATAGTATAATCTT TTTAGGACATTTTGACTGCACCAGCAAACAGATCATAAGATAACCATAAAAATTAGCATAACTG CCTTAAATTAGAGGCTAAAACCCTAGTATTCTATACATGCACAGCAAATGTGTAGACATCTAAA AGGATGAAAGATAAACACTGGTGTTTACTTTAAAAATGTCACTGCAATTTATCAAATCCGACAT CAGATAATGTGAACTAGAAAAACGCATGAGGTACCTGTGCTGATCCAAATCCATAAAGCTTGTT GTGTCTTCAACATTGAAGCGAGGGTAAAACTTTCTTGGATCTTCTGGATCGTTAATAAGCGCCA CATTCTGTGATAAAGATTGGATCATGAACATAACAGTCAAGTGTAGAATAATAAGCATCGGTGC AGAAAAAGCATAATATTTTTTAAAAAAGGATTAAAAGCATAGTTTTAAAATAGGAGAAGAATAC ACAAAATTAGACTTCTGGACATCAAAGCAATGTACCTGCAGAAGATCAAAGAGTTTTCGTCGTA GTTTCACTTCACTCTCTAAAAACATGGATGTTTCCAAGACTGACTTCAGCGCAGATGCAATTTT CTTCTCAGTATTGCATTTGTCCTTGAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.352086763

Conservation Information
Conserved circRNAs	NA
PMCS	0.352086763

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20825478-20822914(+)
20825480-20825524(-)
20822867-20825524(-)
						
						Potential amino acid sequence
						
							MDVSKTDFSADAIFFSVLHLSLKISPIMFWVCWIIDSLFHCRPCRVIFFKC*(+)
MFLESEVKLRRKLFDLLQNVALINDPEDPRKFYPRFNVEDTTSFMDLDQHSQNVLKRLYYDYYF
HRQEGLWRDNAFKTLPVLLNSSDMLACGEDLGLIPSCVHPVMQELGLVGLRIQRMPSEPDLEFD
IPSQYNYMTVCAPSCHDCSTLRAWWEEDEERRHRFFQAVMGSDELPPDQCTPEIVHFVLRQHVE
APSMWSIFPLQDLLALKEDYTTRPAVEETINDPTNPKHYWRYLQGQMQY*(-)
MIQQTQNIIGDIFKDKCNTEKKIASALKSVLETSMFLESEVKLRRKLFDLLQNVALINDPEDPR
KFYPRFNVEDTTSFMDLDQHSQNVLKRLYYDYYFHRQEGLWRDNAFKTLPVLLNSSDMLACGED
LGLIPSCVHPVMQELGLVGLRIQRMPSEPDLEFDIPSQYNYMTVCAPSCHDCSTLRAWWEEDEE
RRHRFFQAVMGSDELPPDQCTPEIVHFVLRQHVEAPSMWSIFPLQDLLALKEDYTTRPAVEETI
NDPTNPKHYWRYLQGQMQY*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	20825478-20822914(+) 20825480-20825524(-) 20822867-20825524(-)
Potential amino acid sequence	MDVSKTDFSADAIFFSVLHLSLKISPIMFWVCWIIDSLFHCRPCRVIFFKC(+) MFLESEVKLRRKLFDLLQNVALINDPEDPRKFYPRFNVEDTTSFMDLDQHSQNVLKRLYYDYYF HRQEGLWRDNAFKTLPVLLNSSDMLACGEDLGLIPSCVHPVMQELGLVGLRIQRMPSEPDLEFD IPSQYNYMTVCAPSCHDCSTLRAWWEEDEERRHRFFQAVMGSDELPPDQCTPEIVHFVLRQHVE APSMWSIFPLQDLLALKEDYTTRPAVEETINDPTNPKHYWRYLQGQMQY(-) MIQQTQNIIGDIFKDKCNTEKKIASALKSVLETSMFLESEVKLRRKLFDLLQNVALINDPEDPR KFYPRFNVEDTTSFMDLDQHSQNVLKRLYYDYYFHRQEGLWRDNAFKTLPVLLNSSDMLACGED LGLIPSCVHPVMQELGLVGLRIQRMPSEPDLEFDIPSQYNYMTVCAPSCHDCSTLRAWWEEDEE RRHRFFQAVMGSDELPPDQCTPEIVHFVLRQHVEAPSMWSIFPLQDLLALKEDYTTRPAVEETI NDPTNPKHYWRYLQGQMQY*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc02g020980.2_circ_g.2

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