Plant Circular RNA Database

Detail information of Solyc07g008500.1_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc07g008500.1_circ_g.2
					
						ID in PlantcircBase
						sly_circ_002215
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr7: 3430852-3433035  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc07g008500.1						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc07g008500.1_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  
						
							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
						Solyc07g008500.1.1:6

General Information
CircRNA Name	Solyc07g008500.1_circ_g.2
ID in PlantcircBase	sly_circ_002215
Alias	NA
Organism	Solanum lycopersicum
Position	chr7: 3430852-3433035 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc07g008500.1
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc07g008500.1_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	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	Solyc07g008500.1.1:6

			
						 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  
						
							GCACACTAAGGTATTGAATGACAGTGAGGCGTCTACGTTCAAGGTGGAACCAACTAAGAGCAGA
ACCAAGAAGAAGTCTCAGCCCAAACCCAAGCTGAAGagattccagaaatgtgaatatgcaagaa
ctaagttgttcaggactgaagggcgtggctggggtcttttagctgatgagaatataaaggtaat
tctgttga

									
								

					

						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: 696
Transcript exons: 3430852-3430938,3431031-3431115,3431196-3431289,3431374-
3431572,3431752-3431795,3432849-3433035
AGATTCCAGAAATGTGAATATGCAAGAACTAAGTTGTTCAGGACTGAAGGGCGTGGCTGGGGTC
TTTTAGCTGATGAGAATATAAAGGCTGGACAGTTCATCATGGAATATTGTGGAGAAGTGTTATC
ATCTGAAGTAGCAAAGAAAAGGAGTCTGTCTTATGAAGCTCATAAGGTCAAGGACGCATACATC
ATGTCACTGAATGCGAATTATTTCATTGATGCTACCAAGAAGGGAAGTCTAGCAAGATTCATTA
ATCATTCCTGCCAACCAAATTGTGAAACAAGGAAATGGATAGTGTTAGGGAAAACAAGGGTAGG
AATATTTGCAAAGAAAGATATATCCGTTGGAATGGAGCTTTTATATAACTATAACTTTGAGTGG
TATGGTGGTGCACGTGTTCGTTGTCTGTGTGGAGCTGCAAACTGTTCTCTTTTTTTGGGTGCCG
AATCTCAAGGATTTAAGTTGGCTCAGGAGTGCAGCGATGTCTCGGAAGAAGAGGGTAACAGATA
TATCATGGATAATATTCTACTTTATGACACGACGGATGATGATGAATCTTCTCCAGTGATCTCT
GGAACTGGTGAAGGAAATAAGCACACTAAGGTATTGAATGACAGTGAGGCGTCTACGTTCAAGG
TGGAACCAACTAAGAGCAGAACCAAGAAGAAGTCTCAGCCCAAACCCAAGCTGAAG
						
					

						Genomic sequence
						
							AGATTCCAGAAATGTGAATATGCAAGAACTAAGTTGTTCAGGACTGAAGGGCGTGGCTGGGGTC
TTTTAGCTGATGAGAATATAAAGGTAATTCTGTTGAAGCAACTGTAGTTATGATGTAGTTACGG
GCCTATGGGTTATTTATAATTACTAATTAGCTTCTATCAACCGATTGTTAGGCTGGACAGTTCA
TCATGGAATATTGTGGAGAAGTGTTATCATCTGAAGTAGCAAAGAAAAGGAGTCTGTCTTATGA
AGCTCATAGTAAGTTATCGACAATAGAGATGGCTATCAATGCATCTACAGATCGATCACTACTA
TATAATTTCGTATGATTTTTGCAGAGGTCAAGGACGCATACATCATGTCACTGAATGCGAATTA
TTTCATTGATGCTACCAAGAAGGGAAGTCTAGCAAGATTCATTAATCATTCCTGGTAAGCACTG
AAACTTCAGTTATTGAAATTATGAAAAGTGAATTAAGTCCGTTAACTGATACTGTGTGTTCCTG
AATTTTCCAGCCAACCAAATTGTGAAACAAGGAAATGGATAGTGTTAGGGAAAACAAGGGTAGG
AATATTTGCAAAGAAAGATATATCCGTTGGAATGGAGCTTTTATATAACTATAACTTTGAGTGG
TATGGTGGTGCACGTGTTCGTTGTCTGTGTGGAGCTGCAAACTGTTCTCTTTTTTTGGGTGCCG
AATCTCAAGGATTTAAGGTAACTTAAGTTTCTTGTGAATTGTTATATCTAGAATGCCCTTTATA
CCGCCATTTCACTTATTCCTTATTTCCAGAATTAGACAACACAAATAATGTTTTATGATAGATG
CTTCTAAATTCGGTATGAGTCTGTCAATTCCATTTCTTATTCTTTCGTTCACTTTTTTATCTTG
GCAGTTGGCTCAGGAGTGCAGCGATGTCTCGGAAGAAGAGGGTAACAGGTAATCAATGTTCTGT
TAACTTGATTTATTTCAGGAGCTCATCTCTTTCCATTACGTCTGCGTCTTGATTCTCTATGTAA
AAGAGAAACATTAGTGATTCCATTAAAACCACACTGAGATATATAACTTTGATAGGCAACGGCT
TCATAAGAGATCTTACATGTTTTATTTGATGTGTTACGTCTTTCCATAAGCCGAAGTATGAGAA
GAGTTGCTCCTCCCATAATCTTAGGAATGGGAAAGCTCAAAAGCTATCATATGGAACTGGCTTG
CTCCTCACCGCTCTATAATATATCATAGTCATATTGTGTTTCATACCTAGTAGCTACCCTTTCA
TTTCCTCGTTGTAAGTATAAAAAAAAGAGATCGATTTTTCTCTCATTGATCCAATATTGTGTTT
ATATACAAGAATGGACTAAGTAATTGCCTAAACTAACTTCTCTGAAAGTGAAGTGCTAAACTAC
GTGAAGAGATATAGGAGTGCTAGACTACTAGCTGAAGAATATGTCAGACAATAATCAACTAAAT
ATAATAATTAGCATGTGCTTGAATAGTAAGATACATGTAATAGTCAATGAAGTGAGGAATAGCC
CTGATGTCTCGAGTTCATATCAGAGTGGAGACAAAAAAAATAGGTGATTTTTTTTCATGTGTCC
TAACTTTAGTGACAAACTTAGCCAATACATGGGTTGGTGGGAGGTAGCAAGTAAGGGGCAGAAT
TAGTTGAGATACAGGTAAAAAGAAAATATACTATTTTCTGAAGTATTACATGCTTAGGTAATAA
GGGATGATGAAATAATATTAAAGGCAAAGACGAAGCTTGTTTCATTTTGGTTCACTGTTGGATT
ACTTGAACTTTACTTTGGAACTAAATGATATAATTAAGGTAGTTCACTTATGTGTCAACAGTAA
TATAAGAGTAAAATGTCAGGTAGTTATTTATGAGTTCCATTGGAGCAAATTGCCTATGATAATA
TAGTTTGGATGTTACAACATCAACTCATTTCCTTGTAATGTTTGGATATTTATTTCAATTTGGC
TTTCATACTGCAGATATATCATGGATAATATTCTACTTTATGACACGACGGATGATGATGAATC
TTCTCCAGTGATCTCTGGAACTGGTGAAGGAAATAAGCACACTAAGGTATTGAATGACAGTGAG
GCGTCTACGTTCAAGGTGGAACCAACTAAGAGCAGAACCAAGAAGAAGTCTCAGCCCAAACCCA
AGCTGAAG
						
					

			
		

Sequences
Splice junction sequence	GCACACTAAGGTATTGAATGACAGTGAGGCGTCTACGTTCAAGGTGGAACCAACTAAGAGCAGA ACCAAGAAGAAGTCTCAGCCCAAACCCAAGCTGAAGagattccagaaatgtgaatatgcaagaa ctaagttgttcaggactgaagggcgtggctggggtcttttagctgatgagaatataaaggtaat tctgttga
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: 696 Transcript exons: 3430852-3430938,3431031-3431115,3431196-3431289,3431374- 3431572,3431752-3431795,3432849-3433035 AGATTCCAGAAATGTGAATATGCAAGAACTAAGTTGTTCAGGACTGAAGGGCGTGGCTGGGGTC TTTTAGCTGATGAGAATATAAAGGCTGGACAGTTCATCATGGAATATTGTGGAGAAGTGTTATC ATCTGAAGTAGCAAAGAAAAGGAGTCTGTCTTATGAAGCTCATAAGGTCAAGGACGCATACATC ATGTCACTGAATGCGAATTATTTCATTGATGCTACCAAGAAGGGAAGTCTAGCAAGATTCATTA ATCATTCCTGCCAACCAAATTGTGAAACAAGGAAATGGATAGTGTTAGGGAAAACAAGGGTAGG AATATTTGCAAAGAAAGATATATCCGTTGGAATGGAGCTTTTATATAACTATAACTTTGAGTGG TATGGTGGTGCACGTGTTCGTTGTCTGTGTGGAGCTGCAAACTGTTCTCTTTTTTTGGGTGCCG AATCTCAAGGATTTAAGTTGGCTCAGGAGTGCAGCGATGTCTCGGAAGAAGAGGGTAACAGATA TATCATGGATAATATTCTACTTTATGACACGACGGATGATGATGAATCTTCTCCAGTGATCTCT GGAACTGGTGAAGGAAATAAGCACACTAAGGTATTGAATGACAGTGAGGCGTCTACGTTCAAGG TGGAACCAACTAAGAGCAGAACCAAGAAGAAGTCTCAGCCCAAACCCAAGCTGAAG
Genomic sequence	AGATTCCAGAAATGTGAATATGCAAGAACTAAGTTGTTCAGGACTGAAGGGCGTGGCTGGGGTC TTTTAGCTGATGAGAATATAAAGGTAATTCTGTTGAAGCAACTGTAGTTATGATGTAGTTACGG GCCTATGGGTTATTTATAATTACTAATTAGCTTCTATCAACCGATTGTTAGGCTGGACAGTTCA TCATGGAATATTGTGGAGAAGTGTTATCATCTGAAGTAGCAAAGAAAAGGAGTCTGTCTTATGA AGCTCATAGTAAGTTATCGACAATAGAGATGGCTATCAATGCATCTACAGATCGATCACTACTA TATAATTTCGTATGATTTTTGCAGAGGTCAAGGACGCATACATCATGTCACTGAATGCGAATTA TTTCATTGATGCTACCAAGAAGGGAAGTCTAGCAAGATTCATTAATCATTCCTGGTAAGCACTG AAACTTCAGTTATTGAAATTATGAAAAGTGAATTAAGTCCGTTAACTGATACTGTGTGTTCCTG AATTTTCCAGCCAACCAAATTGTGAAACAAGGAAATGGATAGTGTTAGGGAAAACAAGGGTAGG AATATTTGCAAAGAAAGATATATCCGTTGGAATGGAGCTTTTATATAACTATAACTTTGAGTGG TATGGTGGTGCACGTGTTCGTTGTCTGTGTGGAGCTGCAAACTGTTCTCTTTTTTTGGGTGCCG AATCTCAAGGATTTAAGGTAACTTAAGTTTCTTGTGAATTGTTATATCTAGAATGCCCTTTATA CCGCCATTTCACTTATTCCTTATTTCCAGAATTAGACAACACAAATAATGTTTTATGATAGATG CTTCTAAATTCGGTATGAGTCTGTCAATTCCATTTCTTATTCTTTCGTTCACTTTTTTATCTTG GCAGTTGGCTCAGGAGTGCAGCGATGTCTCGGAAGAAGAGGGTAACAGGTAATCAATGTTCTGT TAACTTGATTTATTTCAGGAGCTCATCTCTTTCCATTACGTCTGCGTCTTGATTCTCTATGTAA AAGAGAAACATTAGTGATTCCATTAAAACCACACTGAGATATATAACTTTGATAGGCAACGGCT TCATAAGAGATCTTACATGTTTTATTTGATGTGTTACGTCTTTCCATAAGCCGAAGTATGAGAA GAGTTGCTCCTCCCATAATCTTAGGAATGGGAAAGCTCAAAAGCTATCATATGGAACTGGCTTG CTCCTCACCGCTCTATAATATATCATAGTCATATTGTGTTTCATACCTAGTAGCTACCCTTTCA TTTCCTCGTTGTAAGTATAAAAAAAAGAGATCGATTTTTCTCTCATTGATCCAATATTGTGTTT ATATACAAGAATGGACTAAGTAATTGCCTAAACTAACTTCTCTGAAAGTGAAGTGCTAAACTAC GTGAAGAGATATAGGAGTGCTAGACTACTAGCTGAAGAATATGTCAGACAATAATCAACTAAAT ATAATAATTAGCATGTGCTTGAATAGTAAGATACATGTAATAGTCAATGAAGTGAGGAATAGCC CTGATGTCTCGAGTTCATATCAGAGTGGAGACAAAAAAAATAGGTGATTTTTTTTCATGTGTCC TAACTTTAGTGACAAACTTAGCCAATACATGGGTTGGTGGGAGGTAGCAAGTAAGGGGCAGAAT TAGTTGAGATACAGGTAAAAAGAAAATATACTATTTTCTGAAGTATTACATGCTTAGGTAATAA GGGATGATGAAATAATATTAAAGGCAAAGACGAAGCTTGTTTCATTTTGGTTCACTGTTGGATT ACTTGAACTTTACTTTGGAACTAAATGATATAATTAAGGTAGTTCACTTATGTGTCAACAGTAA TATAAGAGTAAAATGTCAGGTAGTTATTTATGAGTTCCATTGGAGCAAATTGCCTATGATAATA TAGTTTGGATGTTACAACATCAACTCATTTCCTTGTAATGTTTGGATATTTATTTCAATTTGGC TTTCATACTGCAGATATATCATGGATAATATTCTACTTTATGACACGACGGATGATGATGAATC TTCTCCAGTGATCTCTGGAACTGGTGAAGGAAATAAGCACACTAAGGTATTGAATGACAGTGAG GCGTCTACGTTCAAGGTGGAACCAACTAAGAGCAGAACCAAGAAGAAGTCTCAGCCCAAACCCA AGCTGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.324955846

Conservation Information
Conserved circRNAs	NA
PMCS	0.324955846

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3431047-3433032(+)
3431049-3433016(-)
						
						Potential amino acid sequence
						
							MEYCGEVLSSEVAKKRSLSYEAHKVKDAYIMSLNANYFIDATKKGSLARFINHSCQPNCETRKW
IVLGKTRVGIFAKKDISVGMELLYNYNFEWYGGARVRCLCGAANCSLFLGAESQGFKLAQECSD
VSEEEGNRYIMDNILLYDTTDDDESSPVISGTGEGNKHTKVLNDSEASTFKVEPTKSRTKKKSQ
PKPKLKRFQKCEYARTKLFRTEGRGWGLLADENIKAGQFIMEYCGEVLSSEVAKKRSLSYEAHK
VKDAYIMSLNANYFIDATKKGSLARFINHSCQPNCETRKWIVLGKTRVGIFAKKDISVGMELLY
NYNFEWYGGARVRCLCGAANCSLFLGAESQGFKLAQECSDVSEEEGNRYIMDNILLYDTTDDDE
SSPVISGTGEGNKHTKVLNDSEASTFKVEPTKSRTKKKSQPKPKLKRFQKCEYARTKLFRTEGR
GWGLLADENIKAGQFIMEYCGEVLSSEVAKKRSLSYEAHKVKDAYIMSLNANYFIDATKKGSLA
RFINHSCQPNCETRKWIVLGKTRVGIFAKKDISVGMELLYNYNFEWYGGARVRCLCGAANCSLF
LGAESQGFKLAQECSDVSEEEGNRYIMDNILLYDTTDDDESSPVISGTGEGNKHTKVLNDSEAS
TFKVEPTKSRTKKKSQPKPKLKRFQKCEYARTKLFRTEGRGWGLLADENIKAGQFIMEYCGEVL
SSEVAKKRSLSYEAHKVKDAYIMSLNANYFIDATKKGSLARFINHSCQPNCETRKWIVLGKTRV
GIFAKKDISVGMELLYNYNFEWYGGARVRCLCGAANCSLFLGAESQGFKLAQECSDVSEEEGNR
YIMDNILLYDTTDDDESSPVISGTGEGNKHTKVLNDSEASTFKVEPTKSRTKKKSQPKPKLK(+
)
MMNCPAFIFSSAKRPQPRPSVLNNLVLAYSHFWNLFSLGLG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3431047-3433032(+) 3431049-3433016(-)
Potential amino acid sequence	MEYCGEVLSSEVAKKRSLSYEAHKVKDAYIMSLNANYFIDATKKGSLARFINHSCQPNCETRKW IVLGKTRVGIFAKKDISVGMELLYNYNFEWYGGARVRCLCGAANCSLFLGAESQGFKLAQECSD VSEEEGNRYIMDNILLYDTTDDDESSPVISGTGEGNKHTKVLNDSEASTFKVEPTKSRTKKKSQ PKPKLKRFQKCEYARTKLFRTEGRGWGLLADENIKAGQFIMEYCGEVLSSEVAKKRSLSYEAHK VKDAYIMSLNANYFIDATKKGSLARFINHSCQPNCETRKWIVLGKTRVGIFAKKDISVGMELLY NYNFEWYGGARVRCLCGAANCSLFLGAESQGFKLAQECSDVSEEEGNRYIMDNILLYDTTDDDE SSPVISGTGEGNKHTKVLNDSEASTFKVEPTKSRTKKKSQPKPKLKRFQKCEYARTKLFRTEGR GWGLLADENIKAGQFIMEYCGEVLSSEVAKKRSLSYEAHKVKDAYIMSLNANYFIDATKKGSLA RFINHSCQPNCETRKWIVLGKTRVGIFAKKDISVGMELLYNYNFEWYGGARVRCLCGAANCSLF LGAESQGFKLAQECSDVSEEEGNRYIMDNILLYDTTDDDESSPVISGTGEGNKHTKVLNDSEAS TFKVEPTKSRTKKKSQPKPKLKRFQKCEYARTKLFRTEGRGWGLLADENIKAGQFIMEYCGEVL SSEVAKKRSLSYEAHKVKDAYIMSLNANYFIDATKKGSLARFINHSCQPNCETRKWIVLGKTRV GIFAKKDISVGMELLYNYNFEWYGGARVRCLCGAANCSLFLGAESQGFKLAQECSDVSEEEGNR YIMDNILLYDTTDDDESSPVISGTGEGNKHTKVLNDSEASTFKVEPTKSRTKKKSQPKPKLK(+ ) MMNCPAFIFSSAKRPQPRPSVLNNLVLAYSHFWNLFSLGLG*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc07g008500.1_circ_g.2

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