Plant Circular RNA Database

Detail information of Solyc07g065980.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc07g065980.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_002438
					
						Alias
						7:64769687|64770759
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr7: 67546087-67547159  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc07g065980.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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
						Solyc07g065980.2.1:4

General Information
CircRNA Name	Solyc07g065980.2_circ_g.1
ID in PlantcircBase	sly_circ_002438
Alias	7:64769687\|64770759
Organism	Solanum lycopersicum
Position	chr7: 67546087-67547159 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc07g065980.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	NA
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	Solyc07g065980.2.1:4

			
						 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  
						
							AGAAGCTTGTACTTCCAGATGGTTCCATATTACGCGCCAAACTTCCAGGAAGGCCAACTAGAGA
CTGCTTGTTTTCTGATCCAGCAAGAGACGGGATAAGgtatgtgtacatgtggcatgcacttgct
ggttactggggcggtgtgagacccggggtccctgggatggaacactatgaatccaagttatctt
tcccagtt

									
								

					

						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: 756
Transcript exons: 67546087-67546497,67546629-67546770,67546864-67546931,67
547025-67547159
GTATGTGTACATGTGGCATGCACTTGCTGGTTACTGGGGCGGTGTGAGACCCGGGGTCCCTGGG
ATGGAACACTATGAATCCAAGTTATCTTTCCCAGTTTCATCTCCCGGGACTGAGTCACAGGAAC
CTGATGATGCTTTGAGCAGCTTGATAAAGAACGGTCTTGGTCTAGTGAACCCTGAGAAAGTTTT
ATACTTCTATAATGAACTGCACTCATACCTTGCTTCTGCGGGTATAGATGGGGTTAAAGTAGAT
GTTCAGAACATCCTTGAAACACTTGGAGCTGGTCATGGTGGAAGGGTAAAACTCGCAAGGAAGT
ATCATCAAGCATTAGAGGCATCTATTGCTCGAAATTTTCCTGATAATGGAATTATTTCATGCAT
GAGCCATAGTAATGATAGTTTGTTCAGTGCAAAGCGTTCAGCTGTAATTAGAGCATCGGATGAT
TTCTGGCCACGAGACCCTGCATCACACACAATTCACATAGCATCAGTGGCGTACAACACCATTT
TCCTTGGTGAATTCATGCAGCCTGATTGGGATATGTTTCACAGTGTGCATCCCATGGCTGAATA
CCACGGAGCTGCACGAGCTGTTGGAGGCTGTGCTATTTACGTTAGTGACAAGCCTGGACAGCAC
GACTTTAATCTTCTGAAGAAGCTTGTACTTCCAGATGGTTCCATATTACGCGCCAAACTTCCAG
GAAGGCCAACTAGAGACTGCTTGTTTTCTGATCCAGCAAGAGACGGGATAAG
						
					

						Genomic sequence
						
							GTATGTGTACATGTGGCATGCACTTGCTGGTTACTGGGGCGGTGTGAGACCCGGGGTCCCTGGG
ATGGAACACTATGAATCCAAGTTATCTTTCCCAGTTTCATCTCCCGGGACTGAGTCACAGGAAC
CTGATGATGCTTTGAGCAGCTTGATAAAGAACGGTCTTGGTCTAGTGAACCCTGAGAAAGTTTT
ATACTTCTATAATGAACTGCACTCATACCTTGCTTCTGCGGGTATAGATGGGGTTAAAGTAGAT
GTTCAGAACATCCTTGAAACACTTGGAGCTGGTCATGGTGGAAGGGTAAAACTCGCAAGGAAGT
ATCATCAAGCATTAGAGGCATCTATTGCTCGAAATTTTCCTGATAATGGAATTATTTCATGCAT
GAGCCATAGTAATGATAGTTTGTTCAGGTAATTTTTTCTTGCTTGTAATTGTTATAAACTGAAT
TAGTTCTAAGAAATGGAGAATCGTCGTAAAGAGATGCTAGATACTCTTACCATATATGTTCTGA
TCCAGTTTTTATTTCCCTTGCTTTGTGTAGTGCAAAGCGTTCAGCTGTAATTAGAGCATCGGAT
GATTTCTGGCCACGAGACCCTGCATCACACACAATTCACATAGCATCAGTGGCGTACAACACCA
TTTTCCTTGGTGAATTCATGCAGCCTGATTGGGATATGTTTCACGTGAGTTGATGATATGAATC
TCAGTTTCTTAGTATACTTTCCAACTTATCAAAAAAAAGGTTGAACTCACTAAAATGCTTGTAA
TATGTTAAGAGTGTGCATCCCATGGCTGAATACCACGGAGCTGCACGAGCTGTTGGAGGCTGTG
CTATTTACGTTAGGTACTGCTTATATATACCTTAAGAACAGCTAGTTATTTGGTGTATGATCCG
ATTTTCATTAATATTTTCTCAATACTGCCTATTTCCATGTAGTGACAAGCCTGGACAGCACGAC
TTTAATCTTCTGAAGAAGCTTGTACTTCCAGATGGTTCCATATTACGCGCCAAACTTCCAGGAA
GGCCAACTAGAGACTGCTTGTTTTCTGATCCAGCAAGAGACGGGATAAG
						
					

			
		

Sequences
Splice junction sequence	AGAAGCTTGTACTTCCAGATGGTTCCATATTACGCGCCAAACTTCCAGGAAGGCCAACTAGAGA CTGCTTGTTTTCTGATCCAGCAAGAGACGGGATAAGgtatgtgtacatgtggcatgcacttgct ggttactggggcggtgtgagacccggggtccctgggatggaacactatgaatccaagttatctt tcccagtt
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: 756 Transcript exons: 67546087-67546497,67546629-67546770,67546864-67546931,67 547025-67547159 GTATGTGTACATGTGGCATGCACTTGCTGGTTACTGGGGCGGTGTGAGACCCGGGGTCCCTGGG ATGGAACACTATGAATCCAAGTTATCTTTCCCAGTTTCATCTCCCGGGACTGAGTCACAGGAAC CTGATGATGCTTTGAGCAGCTTGATAAAGAACGGTCTTGGTCTAGTGAACCCTGAGAAAGTTTT ATACTTCTATAATGAACTGCACTCATACCTTGCTTCTGCGGGTATAGATGGGGTTAAAGTAGAT GTTCAGAACATCCTTGAAACACTTGGAGCTGGTCATGGTGGAAGGGTAAAACTCGCAAGGAAGT ATCATCAAGCATTAGAGGCATCTATTGCTCGAAATTTTCCTGATAATGGAATTATTTCATGCAT GAGCCATAGTAATGATAGTTTGTTCAGTGCAAAGCGTTCAGCTGTAATTAGAGCATCGGATGAT TTCTGGCCACGAGACCCTGCATCACACACAATTCACATAGCATCAGTGGCGTACAACACCATTT TCCTTGGTGAATTCATGCAGCCTGATTGGGATATGTTTCACAGTGTGCATCCCATGGCTGAATA CCACGGAGCTGCACGAGCTGTTGGAGGCTGTGCTATTTACGTTAGTGACAAGCCTGGACAGCAC GACTTTAATCTTCTGAAGAAGCTTGTACTTCCAGATGGTTCCATATTACGCGCCAAACTTCCAG GAAGGCCAACTAGAGACTGCTTGTTTTCTGATCCAGCAAGAGACGGGATAAG
Genomic sequence	GTATGTGTACATGTGGCATGCACTTGCTGGTTACTGGGGCGGTGTGAGACCCGGGGTCCCTGGG ATGGAACACTATGAATCCAAGTTATCTTTCCCAGTTTCATCTCCCGGGACTGAGTCACAGGAAC CTGATGATGCTTTGAGCAGCTTGATAAAGAACGGTCTTGGTCTAGTGAACCCTGAGAAAGTTTT ATACTTCTATAATGAACTGCACTCATACCTTGCTTCTGCGGGTATAGATGGGGTTAAAGTAGAT GTTCAGAACATCCTTGAAACACTTGGAGCTGGTCATGGTGGAAGGGTAAAACTCGCAAGGAAGT ATCATCAAGCATTAGAGGCATCTATTGCTCGAAATTTTCCTGATAATGGAATTATTTCATGCAT GAGCCATAGTAATGATAGTTTGTTCAGGTAATTTTTTCTTGCTTGTAATTGTTATAAACTGAAT TAGTTCTAAGAAATGGAGAATCGTCGTAAAGAGATGCTAGATACTCTTACCATATATGTTCTGA TCCAGTTTTTATTTCCCTTGCTTTGTGTAGTGCAAAGCGTTCAGCTGTAATTAGAGCATCGGAT GATTTCTGGCCACGAGACCCTGCATCACACACAATTCACATAGCATCAGTGGCGTACAACACCA TTTTCCTTGGTGAATTCATGCAGCCTGATTGGGATATGTTTCACGTGAGTTGATGATATGAATC TCAGTTTCTTAGTATACTTTCCAACTTATCAAAAAAAAGGTTGAACTCACTAAAATGCTTGTAA TATGTTAAGAGTGTGCATCCCATGGCTGAATACCACGGAGCTGCACGAGCTGTTGGAGGCTGTG CTATTTACGTTAGGTACTGCTTATATATACCTTAAGAACAGCTAGTTATTTGGTGTATGATCCG ATTTTCATTAATATTTTCTCAATACTGCCTATTTCCATGTAGTGACAAGCCTGGACAGCACGAC TTTAATCTTCTGAAGAAGCTTGTACTTCCAGATGGTTCCATATTACGCGCCAAACTTCCAGGAA GGCCAACTAGAGACTGCTTGTTTTCTGATCCAGCAAGAGACGGGATAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.584726453

Conservation Information
Conserved circRNAs	NA
PMCS	0.584726453

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							67546098-67547156(+)
67546100-67546925(-)
67546306-67547119(-)
67546107-67547091(-)
						
					

						Potential amino acid sequence
						
							MWHALAGYWGGVRPGVPGMEHYESKLSFPVSSPGTESQEPDDALSSLIKNGLGLVNPEKVLYFY
NELHSYLASAGIDGVKVDVQNILETLGAGHGGRVKLARKYHQALEASIARNFPDNGIISCMSHS
NDSLFSAKRSAVIRASDDFWPRDPASHTIHIASVAYNTIFLGEFMQPDWDMFHSVHPMAEYHGA
ARAVGGCAIYVSDKPGQHDFNLLKKLVLPDGSILRAKLPGRPTRDCLFSDPARDGIRYVYMWHA
LAGYWGGVRPGVPGMEHYESKLSFPVSSPGTESQEPDDALSSLIKNGLGLVNPEKVLYFYNELH
SYLASAGIDGVKVDVQNILETLGAGHGGRVKLARKYHQALEASIARNFPDNGIISCMSHSNDSL
FSAKRSAVIRASDDFWPRDPASHTIHIASVAYNTIFLGEFMQPDWDMFHSVHPMAEYHGAARAV
GGCAIYVSDKPGQHDFNLLKKLVLPDGSILRAKLPGRPTRDCLFSDPARDGIRYVYMWHALAGY
WGGVRPGVPGMEHYESKLSFPVSSPGTESQEPDDALSSLIKNGLGLVNPEKVLYFYNELHSYLA
SAGIDGVKVDVQNILETLGAGHGGRVKLARKYHQALEASIARNFPDNGIISCMSHSNDSLFSAK
RSAVIRASDDFWPRDPASHTIHIASVAYNTIFLGEFMQPDWDMFHSVHPMAEYHGAARAVGGCA
IYVSDKPGQHDFNLLKKLVLPDGSILRAKLPGRPTRDCLFSDPARDGIRYVYMWHALAGYWGGV
RPGVPGMEHYESKLSFPVSSPGTESQEPDDALSSLIKNGLGLVNPEKVLYFYNELHSYLASAGI
DGVKVDVQNILETLGAGHGGRVKLARKYHQALEASIARNFPDNGIISCMSHSNDSLFSAKRSAV
IRASDDFWPRDPASHTIHIASVAYNTIFLGEFMQPDWDMFHSVHPMAEYHGAARAVGGCAIYVS
DKPGQHDFNLLKKLVLPDGSILRAKLPGRPTRDCLFSDPARDGI(+)
MYTYLIPSLAGSENKQSLVGLPGSLARNMEPSGSTSFFRRLKSCCPGLSLT*(-)
MSAVHYRSIKLSQGSLDQDRSLSSCSKHHQVPVTQSREMKLGKITWIHSVPSQGPRVSHRPSNQ
QVHATCTHTLSRLLLDQKTSSL*(-)
MPHVHIPYPVSCWIRKQAVSSWPSWKFGA*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						fruit ripening
					

			
		

Functional Information
Coding potential	Y
Potential coding position	67546098-67547156(+) 67546100-67546925(-) 67546306-67547119(-) 67546107-67547091(-)
Potential amino acid sequence	MWHALAGYWGGVRPGVPGMEHYESKLSFPVSSPGTESQEPDDALSSLIKNGLGLVNPEKVLYFY NELHSYLASAGIDGVKVDVQNILETLGAGHGGRVKLARKYHQALEASIARNFPDNGIISCMSHS NDSLFSAKRSAVIRASDDFWPRDPASHTIHIASVAYNTIFLGEFMQPDWDMFHSVHPMAEYHGA ARAVGGCAIYVSDKPGQHDFNLLKKLVLPDGSILRAKLPGRPTRDCLFSDPARDGIRYVYMWHA LAGYWGGVRPGVPGMEHYESKLSFPVSSPGTESQEPDDALSSLIKNGLGLVNPEKVLYFYNELH SYLASAGIDGVKVDVQNILETLGAGHGGRVKLARKYHQALEASIARNFPDNGIISCMSHSNDSL FSAKRSAVIRASDDFWPRDPASHTIHIASVAYNTIFLGEFMQPDWDMFHSVHPMAEYHGAARAV GGCAIYVSDKPGQHDFNLLKKLVLPDGSILRAKLPGRPTRDCLFSDPARDGIRYVYMWHALAGY WGGVRPGVPGMEHYESKLSFPVSSPGTESQEPDDALSSLIKNGLGLVNPEKVLYFYNELHSYLA SAGIDGVKVDVQNILETLGAGHGGRVKLARKYHQALEASIARNFPDNGIISCMSHSNDSLFSAK RSAVIRASDDFWPRDPASHTIHIASVAYNTIFLGEFMQPDWDMFHSVHPMAEYHGAARAVGGCA IYVSDKPGQHDFNLLKKLVLPDGSILRAKLPGRPTRDCLFSDPARDGIRYVYMWHALAGYWGGV RPGVPGMEHYESKLSFPVSSPGTESQEPDDALSSLIKNGLGLVNPEKVLYFYNELHSYLASAGI DGVKVDVQNILETLGAGHGGRVKLARKYHQALEASIARNFPDNGIISCMSHSNDSLFSAKRSAV IRASDDFWPRDPASHTIHIASVAYNTIFLGEFMQPDWDMFHSVHPMAEYHGAARAVGGCAIYVS DKPGQHDFNLLKKLVLPDGSILRAKLPGRPTRDCLFSDPARDGI(+) MYTYLIPSLAGSENKQSLVGLPGSLARNMEPSGSTSFFRRLKSCCPGLSLT(-) MSAVHYRSIKLSQGSLDQDRSLSSCSKHHQVPVTQSREMKLGKITWIHSVPSQGPRVSHRPSNQ QVHATCTHTLSRLLLDQKTSSL(-) MPHVHIPYPVSCWIRKQAVSSWPSWKFGA*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc07g065980.2_circ_g.1

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