Plant Circular RNA Database

Detail information of Solyc04g015970.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc04g015970.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_001332
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 6532541-6534728  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc04g015970.2						
					
						Parent gene annotation
						
							ABC transporter A family member 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc04g015970.2_circ_g.1 Solyc04g015970.2_circ_g.2 						
					
						Support reads
						NA
					
						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
						Solyc04g015970.2.1:3

General Information
CircRNA Name	Solyc04g015970.2_circ_g.3
ID in PlantcircBase	sly_circ_001332
Alias	NA
Organism	Solanum lycopersicum
Position	chr4: 6532541-6534728 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc04g015970.2
Parent gene annotation	ABC transporter A family member 1
Parent gene strand	+
Alternative splicing	Solyc04g015970.2_circ_g.1 Solyc04g015970.2_circ_g.2
Support reads	NA
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	Solyc04g015970.2.1:3

			
						 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  
						
							GCTGTCCATTCACTGACTTTCTCTGTCCAAGAAGGAGAGTGTTTTGGGTTCTTAGGAACTAATG
GAGCAGGAAAGACAACAACACTGTCAATGCTATCTGaacttctttagactgtcaccaggatttt
gctttgctgatggattagcttcattggcgcttttaagacaagggatgaagaatggatctagaga
taacatac

									
								

					

						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: 547
Transcript exons: 6532541-6532687,6533535-6533798,6534593-6534728
AACTTCTTTAGACTGTCACCAGGATTTTGCTTTGCTGATGGATTAGCTTCATTGGCGCTTTTAA
GACAAGGGATGAAGAATGGATCTAGAGATAACATACTTGACTGGAATGTGACTGGTGCTTCCTT
ATCATACTTGGCTGCTGAGGCCATTGTGTATTTCCTTATAACTCTGGGGCTTGAATTCCTGCCT
CAACAAAAAAGAAATCTTTCCAGAATTCATGAGTGGTGGAAAATCTTGGGAAAATCTAGGCGTG
CTAATTCCTTTGGGTTTTCGGAACCTCTTCTGAGATCATCCTCAGGGAATGTTGCTTCTGAACC
CGACGAGGACATAGATGTTAAAGCAGAGAGAGACAGGGTTTTGTCTGGCTCAACTGATAATGCA
GTTATCCACCTCCGTAATCTTCGGAAGGTCTATCCCGGAGGGAAGTCCCATGTTCCAAAAGCTG
CTGTCCATTCACTGACTTTCTCTGTCCAAGAAGGAGAGTGTTTTGGGTTCTTAGGAACTAATGG
AGCAGGAAAGACAACAACACTGTCAATGCTATCTG
						
					

						Genomic sequence
						
							AACTTCTTTAGACTGTCACCAGGATTTTGCTTTGCTGATGGATTAGCTTCATTGGCGCTTTTAA
GACAAGGGATGAAGAATGGATCTAGAGATAACATACTTGACTGGAATGTGACTGGTGCTTCCTT
ATCATACTTGGCTGCTGAGGTAGTCATCTGGTCTGCTGACTAATAACTTCATTGCAGCTTGATC
ATTTTTTTTCTTTGGAAGAAGTATATCTTATTTCAGCTTGATCATCTCGTAGCTACTTCTTAAG
AAAAAAGTTCATGTGTGCTATATCTTCTGGTAGAGGTTTTGTTAAGTTATACCTCTGTTCTCTC
CTCGTGTGATGGAAAGAGACAATTCATTTGTTGAAAACAAGTGAGATTCATCTCCACCAGATTG
TATCATTTATGCTTAAATATGCTAAGATTAGGTGCATTTTTTACCTCTTCTGACATAAATAGTT
ACCTTGCTGTTTGCAAGTTCGAACCCAGCAGACCAAAGCCTAATATTTTGGAGACGGGAAGAGG
GACAGACCCATTATCACCGAATTTGGAACCCTGTTCTACTGGTCCTTGGGGATTTAGTTATCAC
CACATAAAAAAGAAAAAAAAGGGCTACTCTGTACAGCCAATCATTTCCACCATCTTCATGGACT
ACTTTATCACTACTACTCTGAGCTTGTACATGCTGACAATGGAATAATTCATTGACTGACCTCA
AATTTTGCACAAGCAGTTTTGTCGGTTGAGATCTTCATTTGGTAGTCATATTTCTTCTTGGTCT
TTTGTAGTCTTTGATCAGTTCATGCAAGTTTTGTGATTTATACATTCACATATATTATGTATTG
TAAGGAACAATAGTTTTTCTCTTAGCATTATTAACCCCCGTCGTGTCTTCGTTATTCATGATTT
TCTTCCTTGCTTTCTGTATGCCACCTCATTTATAGCCTTTGCTAAGATCTCTTAGGTTTTAAGA
GAACTTTTTGATTTTGGATAATCCATCAATGCAGGCCATTGTGTATTTCCTTATAACTCTGGGG
CTTGAATTCCTGCCTCAACAAAAAAGAAATCTTTCCAGAATTCATGAGTGGTGGAAAATCTTGG
GAAAATCTAGGCGTGCTAATTCCTTTGGGTTTTCGGAACCTCTTCTGAGATCATCCTCAGGGAA
TGTTGCTTCTGAACCCGACGAGGACATAGATGTTAAAGCAGAGAGAGACAGGGTTTTGTCTGGC
TCAACTGATAATGCAGTTATCCACCTCCGTAATCTTCGGAAGGTATGAATTTTCTCTTTCCTGT
TCCATCTCAAAAAGAAAATCTCTTTCCTGTAGATCAAAATATTTGTGTCTTTTTGTCAAAATGT
TAAAAATATTTGAGTGTTAATTCTGTTCAATTACACCCAAGGTTGTGGCCTAGTGGTCAATCAA
GTCGGTTGAGAACCATGAGGTCTCTAGTTCAAATCACCGTAGAGACGAAAGAAGAACACTAGGT
GATTTCTTCACATCTGTTCTAGCCTGAACATCCTTAGTGGACAGTGTAATGAGAGGTGGGCAGG
TATCCCGTGGAATTAGCTGAGGTTTGAAAGCGGGCCTTGACACCAATATATCAAAAAATATAAA
GGGAAACTTACATAAATATACTATATTAAAAAAATATTTACCATTTATAGCAATAACATTTGTT
TTTACTTGATCACTTTTAATACATTATAATAAAGTTCTAATACATATTACGGGGAACAATTTAT
TATTCACATATAAAATTGATGAATAATACATTTATCACTCATTTTAATACACTTGTAACACAAT
GTGTCATTTCTTACCAAACAAGCATAATATATTTTTAAAAAAAGTCATAATACATATATATTGC
ATACATATTCACTGTAAATGCATATTGCAGATTTAACATAGTATTGCTATGTATTGTTACAAAA
TGGTAATAAATAAAAAGTATCGCTAAAATCAGTAATTATTTATTAAAATGTATTCATCCAAGTA
ATTTCCCCCCACCCCCCCCCCCCCAAAAAAAAAAAAAAGAGTGTTAATTATGTATGCATCTTTT
TCAGGTCTATCCCGGAGGGAAGTCCCATGTTCCAAAAGCTGCTGTCCATTCACTGACTTTCTCT
GTCCAAGAAGGAGAGTGTTTTGGGTTCTTAGGAACTAATGGAGCAGGAAAGACAACAACACTGT
CAATGCTATCTG
						
					

			
		

Sequences
Splice junction sequence	GCTGTCCATTCACTGACTTTCTCTGTCCAAGAAGGAGAGTGTTTTGGGTTCTTAGGAACTAATG GAGCAGGAAAGACAACAACACTGTCAATGCTATCTGaacttctttagactgtcaccaggatttt gctttgctgatggattagcttcattggcgcttttaagacaagggatgaagaatggatctagaga taacatac
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: 547 Transcript exons: 6532541-6532687,6533535-6533798,6534593-6534728 AACTTCTTTAGACTGTCACCAGGATTTTGCTTTGCTGATGGATTAGCTTCATTGGCGCTTTTAA GACAAGGGATGAAGAATGGATCTAGAGATAACATACTTGACTGGAATGTGACTGGTGCTTCCTT ATCATACTTGGCTGCTGAGGCCATTGTGTATTTCCTTATAACTCTGGGGCTTGAATTCCTGCCT CAACAAAAAAGAAATCTTTCCAGAATTCATGAGTGGTGGAAAATCTTGGGAAAATCTAGGCGTG CTAATTCCTTTGGGTTTTCGGAACCTCTTCTGAGATCATCCTCAGGGAATGTTGCTTCTGAACC CGACGAGGACATAGATGTTAAAGCAGAGAGAGACAGGGTTTTGTCTGGCTCAACTGATAATGCA GTTATCCACCTCCGTAATCTTCGGAAGGTCTATCCCGGAGGGAAGTCCCATGTTCCAAAAGCTG CTGTCCATTCACTGACTTTCTCTGTCCAAGAAGGAGAGTGTTTTGGGTTCTTAGGAACTAATGG AGCAGGAAAGACAACAACACTGTCAATGCTATCTG
Genomic sequence	AACTTCTTTAGACTGTCACCAGGATTTTGCTTTGCTGATGGATTAGCTTCATTGGCGCTTTTAA GACAAGGGATGAAGAATGGATCTAGAGATAACATACTTGACTGGAATGTGACTGGTGCTTCCTT ATCATACTTGGCTGCTGAGGTAGTCATCTGGTCTGCTGACTAATAACTTCATTGCAGCTTGATC ATTTTTTTTCTTTGGAAGAAGTATATCTTATTTCAGCTTGATCATCTCGTAGCTACTTCTTAAG AAAAAAGTTCATGTGTGCTATATCTTCTGGTAGAGGTTTTGTTAAGTTATACCTCTGTTCTCTC CTCGTGTGATGGAAAGAGACAATTCATTTGTTGAAAACAAGTGAGATTCATCTCCACCAGATTG TATCATTTATGCTTAAATATGCTAAGATTAGGTGCATTTTTTACCTCTTCTGACATAAATAGTT ACCTTGCTGTTTGCAAGTTCGAACCCAGCAGACCAAAGCCTAATATTTTGGAGACGGGAAGAGG GACAGACCCATTATCACCGAATTTGGAACCCTGTTCTACTGGTCCTTGGGGATTTAGTTATCAC CACATAAAAAAGAAAAAAAAGGGCTACTCTGTACAGCCAATCATTTCCACCATCTTCATGGACT ACTTTATCACTACTACTCTGAGCTTGTACATGCTGACAATGGAATAATTCATTGACTGACCTCA AATTTTGCACAAGCAGTTTTGTCGGTTGAGATCTTCATTTGGTAGTCATATTTCTTCTTGGTCT TTTGTAGTCTTTGATCAGTTCATGCAAGTTTTGTGATTTATACATTCACATATATTATGTATTG TAAGGAACAATAGTTTTTCTCTTAGCATTATTAACCCCCGTCGTGTCTTCGTTATTCATGATTT TCTTCCTTGCTTTCTGTATGCCACCTCATTTATAGCCTTTGCTAAGATCTCTTAGGTTTTAAGA GAACTTTTTGATTTTGGATAATCCATCAATGCAGGCCATTGTGTATTTCCTTATAACTCTGGGG CTTGAATTCCTGCCTCAACAAAAAAGAAATCTTTCCAGAATTCATGAGTGGTGGAAAATCTTGG GAAAATCTAGGCGTGCTAATTCCTTTGGGTTTTCGGAACCTCTTCTGAGATCATCCTCAGGGAA TGTTGCTTCTGAACCCGACGAGGACATAGATGTTAAAGCAGAGAGAGACAGGGTTTTGTCTGGC TCAACTGATAATGCAGTTATCCACCTCCGTAATCTTCGGAAGGTATGAATTTTCTCTTTCCTGT TCCATCTCAAAAAGAAAATCTCTTTCCTGTAGATCAAAATATTTGTGTCTTTTTGTCAAAATGT TAAAAATATTTGAGTGTTAATTCTGTTCAATTACACCCAAGGTTGTGGCCTAGTGGTCAATCAA GTCGGTTGAGAACCATGAGGTCTCTAGTTCAAATCACCGTAGAGACGAAAGAAGAACACTAGGT GATTTCTTCACATCTGTTCTAGCCTGAACATCCTTAGTGGACAGTGTAATGAGAGGTGGGCAGG TATCCCGTGGAATTAGCTGAGGTTTGAAAGCGGGCCTTGACACCAATATATCAAAAAATATAAA GGGAAACTTACATAAATATACTATATTAAAAAAATATTTACCATTTATAGCAATAACATTTGTT TTTACTTGATCACTTTTAATACATTATAATAAAGTTCTAATACATATTACGGGGAACAATTTAT TATTCACATATAAAATTGATGAATAATACATTTATCACTCATTTTAATACACTTGTAACACAAT GTGTCATTTCTTACCAAACAAGCATAATATATTTTTAAAAAAAGTCATAATACATATATATTGC ATACATATTCACTGTAAATGCATATTGCAGATTTAACATAGTATTGCTATGTATTGTTACAAAA TGGTAATAAATAAAAAGTATCGCTAAAATCAGTAATTATTTATTAAAATGTATTCATCCAAGTA ATTTCCCCCCACCCCCCCCCCCCCAAAAAAAAAAAAAAGAGTGTTAATTATGTATGCATCTTTT TCAGGTCTATCCCGGAGGGAAGTCCCATGTTCCAAAAGCTGCTGTCCATTCACTGACTTTCTCT GTCCAAGAAGGAGAGTGTTTTGGGTTCTTAGGAACTAATGGAGCAGGAAAGACAACAACACTGT CAATGCTATCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.335951797

Conservation Information
Conserved circRNAs	NA
PMCS	0.335951797

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6532614-6532548(+)
6534691-6532548(+)
6533541-6534724(-)
						
						Potential amino acid sequence
						
							MKNGSRDNILDWNVTGASLSYLAAEAIVYFLITLGLEFLPQQKRNLSRIHEWWKILGKSRRANS
FGFSEPLLRSSSGNVASEPDEDIDVKAERDRVLSGSTDNAVIHLRNLRKVYPGGKSHVPKAAVH
SLTFSVQEGECFGFLGTNGAGKTTTLSMLSELL*(+)
MEQERQQHCQCYLNFFRLSPGFCFADGLASLALLRQGMKNGSRDNILDWNVTGASLSYLAAEAI
VYFLITLGLEFLPQQKRNLSRIHEWWKILGKSRRANSFGFSEPLLRSSSGNVASEPDEDIDVKA
ERDRVLSGSTDNAVIHLRNLRKVYPGGKSHVPKAAVHSLTFSVQEGECFGFLGTNGAGKTTTLS
MLSELL*(+)
MASAAKYDKEAPVTFQSSMLSLDPFFIPCLKSANEANPSAKQNPGDSLKKFR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6532614-6532548(+) 6534691-6532548(+) 6533541-6534724(-)
Potential amino acid sequence	MKNGSRDNILDWNVTGASLSYLAAEAIVYFLITLGLEFLPQQKRNLSRIHEWWKILGKSRRANS FGFSEPLLRSSSGNVASEPDEDIDVKAERDRVLSGSTDNAVIHLRNLRKVYPGGKSHVPKAAVH SLTFSVQEGECFGFLGTNGAGKTTTLSMLSELL(+) MEQERQQHCQCYLNFFRLSPGFCFADGLASLALLRQGMKNGSRDNILDWNVTGASLSYLAAEAI VYFLITLGLEFLPQQKRNLSRIHEWWKILGKSRRANSFGFSEPLLRSSSGNVASEPDEDIDVKA ERDRVLSGSTDNAVIHLRNLRKVYPGGKSHVPKAAVHSLTFSVQEGECFGFLGTNGAGKTTTLS MLSELL(+) MASAAKYDKEAPVTFQSSMLSLDPFFIPCLKSANEANPSAKQNPGDSLKKFR*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Tan et al., 2017

circRNA

Detail information of Solyc04g015970.2_circ_g.3

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