Plant Circular RNA Database

Detail information of Solyc02g079000.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc02g079000.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_000702
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr2: 43618155-43620571  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc02g079000.2						
					
						Parent gene annotation
						
							ATP-dependent zinc metalloprotease FTSH 12, chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc02g079000.2_circ_g.2 						
					
						Support reads
						8
					
						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
						Solyc02g079000.2.1:6

General Information
CircRNA Name	Solyc02g079000.2_circ_g.3
ID in PlantcircBase	sly_circ_000702
Alias	NA
Organism	Solanum lycopersicum
Position	chr2: 43618155-43620571 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc02g079000.2
Parent gene annotation	ATP-dependent zinc metalloprotease FTSH 12, chloroplastic
Parent gene strand	+
Alternative splicing	Solyc02g079000.2_circ_g.2
Support reads	8
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	Solyc02g079000.2.1:6

			
						 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  
						
							TGAGACGGAAGAACTTGCAATGAGGGGGTTATTGGCCAACAGACATATACTGGACTTGATTTCC
AATGAGCTTCTTGAACACTCAAGAATAACTGGATTGgtaagaaaaggacattctaagatcaacc
agcaggatatcgtcgatgttttggacaagcaattgcttgagggtatgggtgttctactgacaga
ggaagagc

									
								

					

						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: 717
Transcript exons: 43618155-43618274,43618357-43618473,43618568-43618744,43
619484-43619603,43619712-43619786,43620464-43620571
GTAAGAAAAGGACATTCTAAGATCAACCAGCAGGATATCGTCGATGTTTTGGACAAGCAATTGC
TTGAGGGTATGGGTGTTCTACTGACAGAGGAAGAGCAGCAGAAGTGTGAGCAAAGTGTATCTCG
CGAAAAAAGACAACTGTTGGCAGTACATGAAGCTGGTCACATTGTGTTGGCGCACTTGTTCCCT
CAGTTTGATTGGCATGCTTTTTCTCAGCTTCTACCTGGGGGCAAGGAAACTGCTGTATCAGTTT
TCTACCCTAGAGAAGATGTGGTTGATCAAGGTTATACAACCTTTGGCTACATGAAAATGCAAAT
GGTAGTAGCTCATGGCGGGCGCTGTGCCGAACGTATTGTATTTGGTGATGACATTACTGATGGA
GGAGTAGATGATCTAGAAAAGATTACCAAGATTGCTCGGGAAATGGTGATAAGTCCTAGAAACT
CTAGGTTGGGCCTCACTTCTTTGACAAAAAAAATAGGATTGGGTGATCGACCTGACAATCCTGA
TGGTGAGATTATAAAATATAAGTGGGATGATCCTCATATAGTTCCTGCTGATATGACAGTTGAA
GTTGCTGAGCTATTTACTCGTGAATTGACAAGGTATATTGATGAGACGGAAGAACTTGCAATGA
GGGGGTTATTGGCCAACAGACATATACTGGACTTGATTTCCAATGAGCTTCTTGAACACTCAAG
AATAACTGGATTG
						
					

						Genomic sequence
						
							GTAAGAAAAGGACATTCTAAGATCAACCAGCAGGATATCGTCGATGTTTTGGACAAGCAATTGC
TTGAGGGTATGGGTGTTCTACTGACAGAGGAAGAGCAGCAGAAGTGTGAGCAAAGTGTATGCAA
TCTTACCCTGTTGCTCCTAAAAAGAACAAGATGTATTGGTTTATTGTTTTGATCGATTTGAAAA
TTTGTAATAGGTATCTCGCGAAAAAAGACAACTGTTGGCAGTACATGAAGCTGGTCACATTGTG
TTGGCGCACTTGTTCCCTCAGTTTGATTGGCATGCTTTTTCTCAGCTTCTACCTGGGGGCAAGG
TGTATTATGTTTTCTGTGAACATAAGTTGTGTCATATTCATTCCAAGCTTTTGTTGACTCCAGT
ACTCAACTGTTGCTCGTTTGTCTGACCAGGAAACTGCTGTATCAGTTTTCTACCCTAGAGAAGA
TGTGGTTGATCAAGGTTATACAACCTTTGGCTACATGAAAATGCAAATGGTAGTAGCTCATGGC
GGGCGCTGTGCCGAACGTATTGTATTTGGTGATGACATTACTGATGGAGGAGTAGATGATCTAG
AAAAGATTACCAAGGTAGACACCATTTCTTCAAATGTTGCAACATCCAGTAGTGACCGATGAAG
TACTCTTGATTTTACCCTTTGTTGTGTTGGTTGTGCTGGTAGCAAAACTATAGGGTGGTGGGGT
AGTACATTTTATTGGCACATGAATGTTGTTGAATCTCACGTCAATGGTGGGATTGGGTACTTGG
CCTCCTTATATGGTCTTGCAATCCACACCTCTTGAACTAGCTTATTGTGTTGAGTTAGGCCTAA
GGTCAATTTCTTATCTTGGTATCAAATTCAGACCTATCCAAATTCTTGGTTTACATGATGTCGA
GCACCCATTTATATTGTTTACGCTCCAGTTGGCAGGTCTGAGCATCGCAGTGGGTGGGGGGTGG
GGATGTTGAATCCCACATAGGCGGTGGGATGGGGACTTGATCTACTTATATGGTCTTGGGAAAT
TCTCAGATCTTTAGCTAGTTTTTCGGGGTTGAATCACGCCGAAAGTCCATTTTGTACAAATGTT
CTTGAGGTGTGGAGGAAGATAAAATTTAAGGTATTGAGGAAATTACAACATCATGAATGTGGAT
TATTATTAACAAAATCTTTGCTGGCCTTTTACATACCTACATATCTGTATGTTAGTACAAATGT
GTGTATATATGCTAACTTTGCCTTGGCTGGCGTTAGTAGTGGGGAGGTGAAGAAGGGACAATTT
TTGAGTATGTGATTGCTGTGAACTCAAATTTTTACTACTTCTATGCCAGATTGCTCGGGAAATG
GTGATAAGTCCTAGAAACTCTAGGTTGGGCCTCACTTCTTTGACAAAAAAAATAGGATTGGGTG
ATCGACCTGACAATCCTGATGGTGAGATTATAAAATATAAGGTATGATTCCTTTGTGAAGCATG
AACTGGCTTGGTTTAATGCTTTATATTTATTTTTCACAACATATTCTCGATTCACTAACTTGTT
CACCTCCTTGGATGAATTCAGTGGGATGATCCTCATATAGTTCCTGCTGATATGACAGTTGAAG
TTGCTGAGCTATTTACTCGTGAATTGACAAGGGTAACTCAAATGTCTTCTCTTATGGTTATATT
TGGTTATTCCGGACAACAGATTTTGTTTCTACATTTGTAATCTTTCAAAGCATGAATTTTGCTT
GCGGATATACTACTTGTACCACTTGTTAAATACATCAACAATTTACAGCTGTCTAGGTGTATGC
AACCAGCCACCACCCTAGCCTCTCCGCACCATTTTTTAATTAACCAGAGTGTCTGGCCCAGCTA
ACTCTCCACTCCGACCTAAATAGGAAAGAAATAGAATCAAACCAGGCTTCTTGATTATACAATG
CAAGTTTTGAAATTTCAAGTGCCATTGGCCTTCTTCCTATGTTCTTTGGTAATAACTTGTGGAA
AGGTCATCTCAAATGGTTAATGATTGCGGTACTTCTTTTACATTAATCTAGTTTTCCTTTTTCT
TTTTCTTTTTGCTTTATGGCTGATTTAAATCACACAATCTAAAGCTGTAGGTCTAACTTCAGTT
TCATTCTATTGCCATCAAAATACTATTAACTGCCACAAAAAAAATTGAAAACTGGAGAGCACTA
CAAATTCAGAAGGAAGATAGCTGCTAGCTTATTTAGTTCCATGATGCAACTTTGAGTCATCAAT
CTGTTACAAGTAGTTCATCTTCTACTCTTTTGCAATATAAAAGATAATCTAACTTAATTTATAT
CACAGTATATTGATGAGACGGAAGAACTTGCAATGAGGGGGTTATTGGCCAACAGACATATACT
GGACTTGATTTCCAATGAGCTTCTTGAACACTCAAGAATAACTGGATTG
						
					

			
		

Sequences
Splice junction sequence	TGAGACGGAAGAACTTGCAATGAGGGGGTTATTGGCCAACAGACATATACTGGACTTGATTTCC AATGAGCTTCTTGAACACTCAAGAATAACTGGATTGgtaagaaaaggacattctaagatcaacc agcaggatatcgtcgatgttttggacaagcaattgcttgagggtatgggtgttctactgacaga ggaagagc
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: 717 Transcript exons: 43618155-43618274,43618357-43618473,43618568-43618744,43 619484-43619603,43619712-43619786,43620464-43620571 GTAAGAAAAGGACATTCTAAGATCAACCAGCAGGATATCGTCGATGTTTTGGACAAGCAATTGC TTGAGGGTATGGGTGTTCTACTGACAGAGGAAGAGCAGCAGAAGTGTGAGCAAAGTGTATCTCG CGAAAAAAGACAACTGTTGGCAGTACATGAAGCTGGTCACATTGTGTTGGCGCACTTGTTCCCT CAGTTTGATTGGCATGCTTTTTCTCAGCTTCTACCTGGGGGCAAGGAAACTGCTGTATCAGTTT TCTACCCTAGAGAAGATGTGGTTGATCAAGGTTATACAACCTTTGGCTACATGAAAATGCAAAT GGTAGTAGCTCATGGCGGGCGCTGTGCCGAACGTATTGTATTTGGTGATGACATTACTGATGGA GGAGTAGATGATCTAGAAAAGATTACCAAGATTGCTCGGGAAATGGTGATAAGTCCTAGAAACT CTAGGTTGGGCCTCACTTCTTTGACAAAAAAAATAGGATTGGGTGATCGACCTGACAATCCTGA TGGTGAGATTATAAAATATAAGTGGGATGATCCTCATATAGTTCCTGCTGATATGACAGTTGAA GTTGCTGAGCTATTTACTCGTGAATTGACAAGGTATATTGATGAGACGGAAGAACTTGCAATGA GGGGGTTATTGGCCAACAGACATATACTGGACTTGATTTCCAATGAGCTTCTTGAACACTCAAG AATAACTGGATTG
Genomic sequence	GTAAGAAAAGGACATTCTAAGATCAACCAGCAGGATATCGTCGATGTTTTGGACAAGCAATTGC TTGAGGGTATGGGTGTTCTACTGACAGAGGAAGAGCAGCAGAAGTGTGAGCAAAGTGTATGCAA TCTTACCCTGTTGCTCCTAAAAAGAACAAGATGTATTGGTTTATTGTTTTGATCGATTTGAAAA TTTGTAATAGGTATCTCGCGAAAAAAGACAACTGTTGGCAGTACATGAAGCTGGTCACATTGTG TTGGCGCACTTGTTCCCTCAGTTTGATTGGCATGCTTTTTCTCAGCTTCTACCTGGGGGCAAGG TGTATTATGTTTTCTGTGAACATAAGTTGTGTCATATTCATTCCAAGCTTTTGTTGACTCCAGT ACTCAACTGTTGCTCGTTTGTCTGACCAGGAAACTGCTGTATCAGTTTTCTACCCTAGAGAAGA TGTGGTTGATCAAGGTTATACAACCTTTGGCTACATGAAAATGCAAATGGTAGTAGCTCATGGC GGGCGCTGTGCCGAACGTATTGTATTTGGTGATGACATTACTGATGGAGGAGTAGATGATCTAG AAAAGATTACCAAGGTAGACACCATTTCTTCAAATGTTGCAACATCCAGTAGTGACCGATGAAG TACTCTTGATTTTACCCTTTGTTGTGTTGGTTGTGCTGGTAGCAAAACTATAGGGTGGTGGGGT AGTACATTTTATTGGCACATGAATGTTGTTGAATCTCACGTCAATGGTGGGATTGGGTACTTGG CCTCCTTATATGGTCTTGCAATCCACACCTCTTGAACTAGCTTATTGTGTTGAGTTAGGCCTAA GGTCAATTTCTTATCTTGGTATCAAATTCAGACCTATCCAAATTCTTGGTTTACATGATGTCGA GCACCCATTTATATTGTTTACGCTCCAGTTGGCAGGTCTGAGCATCGCAGTGGGTGGGGGGTGG GGATGTTGAATCCCACATAGGCGGTGGGATGGGGACTTGATCTACTTATATGGTCTTGGGAAAT TCTCAGATCTTTAGCTAGTTTTTCGGGGTTGAATCACGCCGAAAGTCCATTTTGTACAAATGTT CTTGAGGTGTGGAGGAAGATAAAATTTAAGGTATTGAGGAAATTACAACATCATGAATGTGGAT TATTATTAACAAAATCTTTGCTGGCCTTTTACATACCTACATATCTGTATGTTAGTACAAATGT GTGTATATATGCTAACTTTGCCTTGGCTGGCGTTAGTAGTGGGGAGGTGAAGAAGGGACAATTT TTGAGTATGTGATTGCTGTGAACTCAAATTTTTACTACTTCTATGCCAGATTGCTCGGGAAATG GTGATAAGTCCTAGAAACTCTAGGTTGGGCCTCACTTCTTTGACAAAAAAAATAGGATTGGGTG ATCGACCTGACAATCCTGATGGTGAGATTATAAAATATAAGGTATGATTCCTTTGTGAAGCATG AACTGGCTTGGTTTAATGCTTTATATTTATTTTTCACAACATATTCTCGATTCACTAACTTGTT CACCTCCTTGGATGAATTCAGTGGGATGATCCTCATATAGTTCCTGCTGATATGACAGTTGAAG TTGCTGAGCTATTTACTCGTGAATTGACAAGGGTAACTCAAATGTCTTCTCTTATGGTTATATT TGGTTATTCCGGACAACAGATTTTGTTTCTACATTTGTAATCTTTCAAAGCATGAATTTTGCTT GCGGATATACTACTTGTACCACTTGTTAAATACATCAACAATTTACAGCTGTCTAGGTGTATGC AACCAGCCACCACCCTAGCCTCTCCGCACCATTTTTTAATTAACCAGAGTGTCTGGCCCAGCTA ACTCTCCACTCCGACCTAAATAGGAAAGAAATAGAATCAAACCAGGCTTCTTGATTATACAATG CAAGTTTTGAAATTTCAAGTGCCATTGGCCTTCTTCCTATGTTCTTTGGTAATAACTTGTGGAA AGGTCATCTCAAATGGTTAATGATTGCGGTACTTCTTTTACATTAATCTAGTTTTCCTTTTTCT TTTTCTTTTTGCTTTATGGCTGATTTAAATCACACAATCTAAAGCTGTAGGTCTAACTTCAGTT TCATTCTATTGCCATCAAAATACTATTAACTGCCACAAAAAAAATTGAAAACTGGAGAGCACTA CAAATTCAGAAGGAAGATAGCTGCTAGCTTATTTAGTTCCATGATGCAACTTTGAGTCATCAAT CTGTTACAAGTAGTTCATCTTCTACTCTTTTGCAATATAAAAGATAATCTAACTTAATTTATAT CACAGTATATTGATGAGACGGAAGAACTTGCAATGAGGGGGTTATTGGCCAACAGACATATACT GGACTTGATTTCCAATGAGCTTCTTGAACACTCAAGAATAACTGGATTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.815942652

Conservation Information
Conserved circRNAs	NA
PMCS	0.815942652

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							43618228-43620568(+)
						
						Potential amino acid sequence
						
							MGVLLTEEEQQKCEQSVSREKRQLLAVHEAGHIVLAHLFPQFDWHAFSQLLPGGKETAVSVFYP
REDVVDQGYTTFGYMKMQMVVAHGGRCAERIVFGDDITDGGVDDLEKITKIAREMVISPRNSRL
GLTSLTKKIGLGDRPDNPDGEIIKYKWDDPHIVPADMTVEVAELFTRELTRYIDETEELAMRGL
LANRHILDLISNELLEHSRITGLVRKGHSKINQQDIVDVLDKQLLEGMGVLLTEEEQQKCEQSV
SREKRQLLAVHEAGHIVLAHLFPQFDWHAFSQLLPGGKETAVSVFYPREDVVDQGYTTFGYMKM
QMVVAHGGRCAERIVFGDDITDGGVDDLEKITKIAREMVISPRNSRLGLTSLTKKIGLGDRPDN
PDGEIIKYKWDDPHIVPADMTVEVAELFTRELTRYIDETEELAMRGLLANRHILDLISNELLEH
SRITGLVRKGHSKINQQDIVDVLDKQLLEGMGVLLTEEEQQKCEQSVSREKRQLLAVHEAGHIV
LAHLFPQFDWHAFSQLLPGGKETAVSVFYPREDVVDQGYTTFGYMKMQMVVAHGGRCAERIVFG
DDITDGGVDDLEKITKIAREMVISPRNSRLGLTSLTKKIGLGDRPDNPDGEIIKYKWDDPHIVP
ADMTVEVAELFTRELTRYIDETEELAMRGLLANRHILDLISNELLEHSRITGLVRKGHSKINQQ
DIVDVLDKQLLEGMGVLLTEEEQQKCEQSVSREKRQLLAVHEAGHIVLAHLFPQFDWHAFSQLL
PGGKETAVSVFYPREDVVDQGYTTFGYMKMQMVVAHGGRCAERIVFGDDITDGGVDDLEKITKI
AREMVISPRNSRLGLTSLTKKIGLGDRPDNPDGEIIKYKWDDPHIVPADMTVEVAELFTRELTR
YIDETEELAMRGLLANRHILDLISNELLEHSRITGL(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	43618228-43620568(+)
Potential amino acid sequence	MGVLLTEEEQQKCEQSVSREKRQLLAVHEAGHIVLAHLFPQFDWHAFSQLLPGGKETAVSVFYP REDVVDQGYTTFGYMKMQMVVAHGGRCAERIVFGDDITDGGVDDLEKITKIAREMVISPRNSRL GLTSLTKKIGLGDRPDNPDGEIIKYKWDDPHIVPADMTVEVAELFTRELTRYIDETEELAMRGL LANRHILDLISNELLEHSRITGLVRKGHSKINQQDIVDVLDKQLLEGMGVLLTEEEQQKCEQSV SREKRQLLAVHEAGHIVLAHLFPQFDWHAFSQLLPGGKETAVSVFYPREDVVDQGYTTFGYMKM QMVVAHGGRCAERIVFGDDITDGGVDDLEKITKIAREMVISPRNSRLGLTSLTKKIGLGDRPDN PDGEIIKYKWDDPHIVPADMTVEVAELFTRELTRYIDETEELAMRGLLANRHILDLISNELLEH SRITGLVRKGHSKINQQDIVDVLDKQLLEGMGVLLTEEEQQKCEQSVSREKRQLLAVHEAGHIV LAHLFPQFDWHAFSQLLPGGKETAVSVFYPREDVVDQGYTTFGYMKMQMVVAHGGRCAERIVFG DDITDGGVDDLEKITKIAREMVISPRNSRLGLTSLTKKIGLGDRPDNPDGEIIKYKWDDPHIVP ADMTVEVAELFTRELTRYIDETEELAMRGLLANRHILDLISNELLEHSRITGLVRKGHSKINQQ DIVDVLDKQLLEGMGVLLTEEEQQKCEQSVSREKRQLLAVHEAGHIVLAHLFPQFDWHAFSQLL PGGKETAVSVFYPREDVVDQGYTTFGYMKMQMVVAHGGRCAERIVFGDDITDGGVDDLEKITKI AREMVISPRNSRLGLTSLTKKIGLGDRPDNPDGEIIKYKWDDPHIVPADMTVEVAELFTRELTR YIDETEELAMRGLLANRHILDLISNELLEHSRITGL(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc02g079000.2_circ_g.3

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