Plant Circular RNA Database

Detail information of Solyc03g063560.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc03g063560.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_001002
					
						Alias
						3:32293540|32295326
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr3: 34916981-34918767  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc03g063560.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc03g063560.2_circ_g.1 						
					
						Support reads
						6
					
						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
						Solyc03g063560.2.1:4

General Information
CircRNA Name	Solyc03g063560.2_circ_g.2
ID in PlantcircBase	sly_circ_001002
Alias	3:32293540\|32295326
Organism	Solanum lycopersicum
Position	chr3: 34916981-34918767 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc03g063560.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc03g063560.2_circ_g.1
Support reads	6
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	Solyc03g063560.2.1:4

			
						 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  
						
							TAGCCACGGCACCCGCAATGCGACCACATACAGCACGGTCAATATTATATATTTCAACTGTCTT
GTTGACCACCTTTTCATTCTCAATTGCATCAGATATcttaggtacaaatgtttcgtcctcatct
agaatgtatgccaaacctccagtcataccagcagctacatttctaccaaccctgttgtaagcaa
gaaaacat

									
								

					

						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: 555
Transcript exons: 34916981-34917059,34917176-34917414,34918433-34918526,34
918625-34918767
CTTAGGTACAAATGTTTCGTCCTCATCTAGAATGTATGCCAAACCTCCAGTCATACCAGCAGCT
ACATTTCTACCAACCTTTCCAAGCACAACAACACATCCTCCTGTCATGTACTCACAACAGTGGT
CCCCAGTGCCTTCTACAACAGCTTGAGCAAGAGAATTCCTCACAGCAAAACGCTCTCCTGCTTT
ACCTCTGACAAATACTTGACCACCTGTTGCTCCATATAAGCAGGTGTTCCCTACTATGGTAGCA
TCCTCTGGAACAAATCCAGTATTTTCAACGGGAGTTACAACCAACTCTCCTCCAGCCATGCCCT
TTCCTACATAGTCATTAGCTTCTCCAATAAGTCTGATGTTCATTCCAGGTGTCAGAAAACAAGC
AAAAGATTGGCCAGCACTCCCGGTAAATGTTATGTTCAGCTGTCCGGCAAAACCAGTATCACCA
TATTTCTTAGCCACGGCACCCGCAATGCGACCACATACAGCACGGTCAATATTATATATTTCAA
CTGTCTTGTTGACCACCTTTTCATTCTCAATTGCATCAGATAT
						
					

						Genomic sequence
						
							CTTAGGTACAAATGTTTCGTCCTCATCTAGAATGTATGCCAAACCTCCAGTCATACCAGCAGCT
ACATTTCTACCAACCCTGTTGTAAGCAAGAAAACATAGCTCAAATCCATGTCCCGAATTCTGCA
CTGTCCAAATTGTACCTTCAAATCTCTTATGACAATGAGTAGAGCATGAACAAGAAGTAATACT
TACTTTCCAAGCACAACAACACATCCTCCTGTCATGTACTCACAACAGTGGTCCCCAGTGCCTT
CTACAACAGCTTGAGCAAGAGAATTCCTCACAGCAAAACGCTCTCCTGCTTTACCTCTGACAAA
TACTTGACCACCTGTTGCTCCATATAAGCAGGTGTTCCCTACTATGGTAGCATCCTCTGGAACA
AATCCAGTATTTTCAACGGGAGTTACAACCAACTCTCCTCCAGCCATGCCCTTTTGAAATTTCA
TTCAGTAACATCATTTAGTATGGATGAATTATTCAAGTAAACTACTTCTCAATCCCAAAATAGT
TGGGGTCAAACTAAATGAATCCTGATTTCTCATTTAAACTCATATCATATTATCATGACAAATA
AGATAGAATTGAAAAATATGTTTAAAATATATAATAATAACAACAACAACAACAATAATAATAA
TAATAATAATAACTTTAAAAGCATGGTCAAGAAATGTTGATTAAGCTTTTGTGCCATTCATTAA
AAGACACAACAATAGACAAAATTGTCATTTGCTTATTTCATCAAATCATTGTCATTTAATTGTT
ATCCTAATATTCAGGACTTTGAAGTTAATCAAAGTTAAAGCTATTAAATCTTTACTTATTTGTA
ATAAATAAGAACTCTTATCATTTAATACTTTTGACTAAAATTTTAGTTCCTAAATCTTTCTTTA
ATTGCACCATATGTCCTTACATTTAAGACTTTCAAAAACTAATATTTCTCCTTTATACAAAATC
TTAAATTATGTTTATAAAATTAATTAAATAAATAAAAGAATTAAAAATACCAAAGAATGAGGTT
CATCTTTTAAAATAACTTCTTCACAAAGTTCCTGTACTATTATTTTATCATTGAGATAGATTTA
ACATTTATTTTAGCGTCAATTGCTATTTTTTTTAAGAAAAAAACTGTTCCTCTTGTATATATTT
TTGTTGGTGTTAGCGAGATTCACAAACACTAATCTAATTATAATAATAATAATAATTATAATAA
TAAGAATAATAATAGAAGTTCCATACAAGCCTAAAACCTATTATATTCATAAACTTCATATAGT
AAGCTCTACCCAGCCTGGCAATATTACTTCGCAGTTTGCACATCAGAGAAATCACATGCAGCAT
GTGATCCAGAAATAAACTACACCAATTACCAATGCCCAGTTAGGGAACCATAACAGAGTTTCAT
ATCCACATGGAGCATATGGATAAGATATAGGTTGTCCAACAAACCTTTCCTACATAGTCATTAG
CTTCTCCAATAAGTCTGATGTTCATTCCAGGTGTCAGAAAACAAGCAAAAGATTGGCCAGCACT
CCCGGTAAATCTGCATAGTGGAGAAAGAGTTGACTTGTTCATGCTGATCTAGGACTCTAAATAT
AATAATTGCAAATACAAAAGACAAATCACAAAAGATAATCTTACGTTATGTTCAGCTGTCCGGC
AAAACCAGTATCACCATATTTCTTAGCCACGGCACCCGCAATGCGACCACATACAGCACGGTCA
ATATTATATATTTCAACTGTCTTGTTGACCACCTTTTCATTCTCAATTGCATCAGATAT
						
					

			
		

Sequences
Splice junction sequence	TAGCCACGGCACCCGCAATGCGACCACATACAGCACGGTCAATATTATATATTTCAACTGTCTT GTTGACCACCTTTTCATTCTCAATTGCATCAGATATcttaggtacaaatgtttcgtcctcatct agaatgtatgccaaacctccagtcataccagcagctacatttctaccaaccctgttgtaagcaa gaaaacat
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: 555 Transcript exons: 34916981-34917059,34917176-34917414,34918433-34918526,34 918625-34918767 CTTAGGTACAAATGTTTCGTCCTCATCTAGAATGTATGCCAAACCTCCAGTCATACCAGCAGCT ACATTTCTACCAACCTTTCCAAGCACAACAACACATCCTCCTGTCATGTACTCACAACAGTGGT CCCCAGTGCCTTCTACAACAGCTTGAGCAAGAGAATTCCTCACAGCAAAACGCTCTCCTGCTTT ACCTCTGACAAATACTTGACCACCTGTTGCTCCATATAAGCAGGTGTTCCCTACTATGGTAGCA TCCTCTGGAACAAATCCAGTATTTTCAACGGGAGTTACAACCAACTCTCCTCCAGCCATGCCCT TTCCTACATAGTCATTAGCTTCTCCAATAAGTCTGATGTTCATTCCAGGTGTCAGAAAACAAGC AAAAGATTGGCCAGCACTCCCGGTAAATGTTATGTTCAGCTGTCCGGCAAAACCAGTATCACCA TATTTCTTAGCCACGGCACCCGCAATGCGACCACATACAGCACGGTCAATATTATATATTTCAA CTGTCTTGTTGACCACCTTTTCATTCTCAATTGCATCAGATAT
Genomic sequence	CTTAGGTACAAATGTTTCGTCCTCATCTAGAATGTATGCCAAACCTCCAGTCATACCAGCAGCT ACATTTCTACCAACCCTGTTGTAAGCAAGAAAACATAGCTCAAATCCATGTCCCGAATTCTGCA CTGTCCAAATTGTACCTTCAAATCTCTTATGACAATGAGTAGAGCATGAACAAGAAGTAATACT TACTTTCCAAGCACAACAACACATCCTCCTGTCATGTACTCACAACAGTGGTCCCCAGTGCCTT CTACAACAGCTTGAGCAAGAGAATTCCTCACAGCAAAACGCTCTCCTGCTTTACCTCTGACAAA TACTTGACCACCTGTTGCTCCATATAAGCAGGTGTTCCCTACTATGGTAGCATCCTCTGGAACA AATCCAGTATTTTCAACGGGAGTTACAACCAACTCTCCTCCAGCCATGCCCTTTTGAAATTTCA TTCAGTAACATCATTTAGTATGGATGAATTATTCAAGTAAACTACTTCTCAATCCCAAAATAGT TGGGGTCAAACTAAATGAATCCTGATTTCTCATTTAAACTCATATCATATTATCATGACAAATA AGATAGAATTGAAAAATATGTTTAAAATATATAATAATAACAACAACAACAACAATAATAATAA TAATAATAATAACTTTAAAAGCATGGTCAAGAAATGTTGATTAAGCTTTTGTGCCATTCATTAA AAGACACAACAATAGACAAAATTGTCATTTGCTTATTTCATCAAATCATTGTCATTTAATTGTT ATCCTAATATTCAGGACTTTGAAGTTAATCAAAGTTAAAGCTATTAAATCTTTACTTATTTGTA ATAAATAAGAACTCTTATCATTTAATACTTTTGACTAAAATTTTAGTTCCTAAATCTTTCTTTA ATTGCACCATATGTCCTTACATTTAAGACTTTCAAAAACTAATATTTCTCCTTTATACAAAATC TTAAATTATGTTTATAAAATTAATTAAATAAATAAAAGAATTAAAAATACCAAAGAATGAGGTT CATCTTTTAAAATAACTTCTTCACAAAGTTCCTGTACTATTATTTTATCATTGAGATAGATTTA ACATTTATTTTAGCGTCAATTGCTATTTTTTTTAAGAAAAAAACTGTTCCTCTTGTATATATTT TTGTTGGTGTTAGCGAGATTCACAAACACTAATCTAATTATAATAATAATAATAATTATAATAA TAAGAATAATAATAGAAGTTCCATACAAGCCTAAAACCTATTATATTCATAAACTTCATATAGT AAGCTCTACCCAGCCTGGCAATATTACTTCGCAGTTTGCACATCAGAGAAATCACATGCAGCAT GTGATCCAGAAATAAACTACACCAATTACCAATGCCCAGTTAGGGAACCATAACAGAGTTTCAT ATCCACATGGAGCATATGGATAAGATATAGGTTGTCCAACAAACCTTTCCTACATAGTCATTAG CTTCTCCAATAAGTCTGATGTTCATTCCAGGTGTCAGAAAACAAGCAAAAGATTGGCCAGCACT CCCGGTAAATCTGCATAGTGGAGAAAGAGTTGACTTGTTCATGCTGATCTAGGACTCTAAATAT AATAATTGCAAATACAAAAGACAAATCACAAAAGATAATCTTACGTTATGTTCAGCTGTCCGGC AAAACCAGTATCACCATATTTCTTAGCCACGGCACCCGCAATGCGACCACATACAGCACGGTCA ATATTATATATTTCAACTGTCTTGTTGACCACCTTTTCATTCTCAATTGCATCAGATAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.335152077

Conservation Information
Conserved circRNAs	NA
PMCS	0.335152077

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							34918471-34917247(+)
34918479-34916983(-)
34917008-34918634(-)
						
						Potential amino acid sequence
						
							MFIPGVRKQAKDWPALPVNVMFSCPAKPVSPYFLATAPAMRPHTARSILYISTVLLTTFSFSIA
SDILGTNVSSSSRMYAKPPVIPAATFLPTFPSTTTHPPVMYSQQWSPVPSTTA*(+)
MNIRLIGEANDYVGKGMAGGELVVTPVENTGFVPEDATIVGNTCLYGATGGQVFVRGKAGERFA
VRNSLAQAVVEGTGDHCCEYMTGGCVVVLGKVGRNVAAGMTGGLAYILDEDETFVPKISDAIEN
EKVVNKTVEIYNIDRAVCGRIAGAVAKKYGDTGFAGQLNITFTGSAGQSFACFLTPGMNIRLIG
EANDYVGKGMAGGELVVTPVENTGFVPEDATIVGNTCLYGATGGQVFVRGKAGERFAVRNSLAQ
AVVEGTGDHCCEYMTGGCVVVLGKVGRNVAAGMTGGLAYILDEDETFVPKISDAIENEKVVNKT
VEIYNIDRAVCGRIAGAVAKKYGDTGFAGQLNITFTGSAGQSFACFLTPGMNIRLIGEANDYVG
KGMAGGELVVTPVENTGFVPEDATIVGNTCLYGATGGQVFVRGKAGERFAVRNSLAQAVVEGTG
DHCCEYMTGGCVVVLGKVGRNVAAGMTGGLAYILDEDETFVPKISDAIENEKVVNKTVEIYNID
RAVCGRIAGAVAKKYGDTGFAGQLNITFTGSAGQSFACFLTPGMNIRLIGEANDYVGKGMAGGE
LVVTPVENTGFVPEDATIVGNTCLYGATGGQVFVRGKAGERFAVRNSLAQAVVEGTGDHCCEYM
TGGCVVVLGKVGRNVAAGMTGGLAYILDEDETFVPK(-)
MRTKHLYLRYLMQLRMKRWSTRQLKYIILTVLYVVALRVPWLRNMVILVLPDS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	34918471-34917247(+) 34918479-34916983(-) 34917008-34918634(-)
Potential amino acid sequence	MFIPGVRKQAKDWPALPVNVMFSCPAKPVSPYFLATAPAMRPHTARSILYISTVLLTTFSFSIA SDILGTNVSSSSRMYAKPPVIPAATFLPTFPSTTTHPPVMYSQQWSPVPSTTA(+) MNIRLIGEANDYVGKGMAGGELVVTPVENTGFVPEDATIVGNTCLYGATGGQVFVRGKAGERFA VRNSLAQAVVEGTGDHCCEYMTGGCVVVLGKVGRNVAAGMTGGLAYILDEDETFVPKISDAIEN EKVVNKTVEIYNIDRAVCGRIAGAVAKKYGDTGFAGQLNITFTGSAGQSFACFLTPGMNIRLIG EANDYVGKGMAGGELVVTPVENTGFVPEDATIVGNTCLYGATGGQVFVRGKAGERFAVRNSLAQ AVVEGTGDHCCEYMTGGCVVVLGKVGRNVAAGMTGGLAYILDEDETFVPKISDAIENEKVVNKT VEIYNIDRAVCGRIAGAVAKKYGDTGFAGQLNITFTGSAGQSFACFLTPGMNIRLIGEANDYVG KGMAGGELVVTPVENTGFVPEDATIVGNTCLYGATGGQVFVRGKAGERFAVRNSLAQAVVEGTG DHCCEYMTGGCVVVLGKVGRNVAAGMTGGLAYILDEDETFVPKISDAIENEKVVNKTVEIYNID RAVCGRIAGAVAKKYGDTGFAGQLNITFTGSAGQSFACFLTPGMNIRLIGEANDYVGKGMAGGE LVVTPVENTGFVPEDATIVGNTCLYGATGGQVFVRGKAGERFAVRNSLAQAVVEGTGDHCCEYM TGGCVVVLGKVGRNVAAGMTGGLAYILDEDETFVPK(-) MRTKHLYLRYLMQLRMKRWSTRQLKYIILTVLYVVALRVPWLRNMVILVLPDS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc03g063560.2_circ_g.2

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