Plant Circular RNA Database

Detail information of Solyc11g018670.1_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc11g018670.1_circ_g.1
					
						ID in PlantcircBase
						sly_circ_003332
					
						Alias
						11:8894849|8903158
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr11: 8894849-8903158  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc11g018670.1						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						7
					
						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
						Solyc11g018670.1.1:8

General Information
CircRNA Name	Solyc11g018670.1_circ_g.1
ID in PlantcircBase	sly_circ_003332
Alias	11:8894849\|8903158
Organism	Solanum lycopersicum
Position	chr11: 8894849-8903158 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc11g018670.1
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	NA
Support reads	7
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	Solyc11g018670.1.1:8

			
						 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  
						
							ATAGTCAGATTCAGAAAATGATTCAGATGAGGACGTGGCTGATTCTTCTTGTTTTCTTTTCTTC
CTTCTGCTCGAACTCTCTCCCATGGTGATCCTTGTTcttgcaaacgtctccactgggcagcttc
acgcatagcttgtaattctgcctacagaaccaaatcttgtgttaatagatccgtagtcaagagt
gttttgag

									
								

					

						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: 1328
Transcript exons: 8894849-8894897,8894985-8895038,8897090-8897201,8898482-
8898570,8899286-8899388,8900247-8900324,8900560-8900960,
8902717-8903158
CTTGCAAACGTCTCCACTGGGCAGCTTCACGCATAGCTTGTAATTCTGCCTTCATTTCCTCTTG
TTCTTCCTTGCGCTTTATTTTCTCATCCAACACATTCCTTTTATCTGGATCTTGCAAATCTTTA
AAGGCTTTGTTCAGCTTGATGAACGCTTGGTGAGCTTCAGGATGCGTGCACTTATCAGGATGCA
CCATAAGAGACAACTTCCAGTACCTTTTCTTCATGTTGTCACTCAACATATTTCTGTTCGCACC
CAAAACATCATATGAGTTGTCAGCATCTGCTACCATGATTCTTGTAACCTCTTCAAAACGTTCG
GCCTCGTTTGCTGATTCTACCTCAGTCACCAAAGCAGGAGGTGGGGGTCCTATAAACAATTCAG
TATCTTCTTCCAGCTCAACATCCCTCAGCTCCGCTTGTGCTTCAGTCAACTTAGCTGCGGCAGC
AAGTAGTTCTGCAGAAGGCATTGCAGGACCAATCACCCTCTTTTTTGGGCCAGTATCTTCTTCG
GCAGGCAAGCTTAAATTAGCATCGTAAGCGGTAGCACTATCGCTTGACAAACTCAAATTGGCAT
TATGACCACCAGCTGCTTCATTTGGCAAACTCAAATTGGCATTACAATGTTCCTGTCCAACTCC
CGAATCCAACGGCTTGGACTGCTCATCATTTTGATGCAACTCTTGACTTTGAAGTTGCATTTGG
GAGCGGATTAAGGGTCCTACAGTCTCCAAAGTAGGAAATGCTTTTGATGGTAATAGAAAAACAT
GATCACCCGTTTCCTTAAGGTTTAAGGAGAGGAACAGTTTTCGCAGACGCTTGACCAACAATTT
TTCAGATAAACCCCTTATATCTACAGCTTGTCCATCATCAATCATTTGAAGAAGCTGTTTCAAA
TCACCAGCTACAGTAGGGAACTCCTGCAATATGCCTTTGACCACATCCCCAGGACTATCCCTTC
GCCGCTCGGGCTGGAAGTCATCACAGTCTGACCCGGAACCGGTGTCCGATTCACTAGAATCTGA
ATACTTCCTCTTTCCCTCTGGTTTCGATCTCCTACTACTGCTGCTGCCTCTATGCTCCCGCTTC
TTCACAAGCTTCTTTTTTCTCTTCGCCCTCTCCCTATGCTTATCACTCCTTGAGGAGCTCCTTC
GACTCCTCTCCCCCTCGCGACGCCGTTTGTGCCGACGCTTTCGCCGTTTTTCATCTTCAGAGGA
GCTATCAACTTCATAGTCAGATTCAGAAAATGATTCAGATGAGGACGTGGCTGATTCTTCTTGT
TTTCTTTTCTTCCTTCTGCTCGAACTCTCTCCCATGGTGATCCTTGTT
						
					

						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.						
					

			
		

Sequences
Splice junction sequence	ATAGTCAGATTCAGAAAATGATTCAGATGAGGACGTGGCTGATTCTTCTTGTTTTCTTTTCTTC CTTCTGCTCGAACTCTCTCCCATGGTGATCCTTGTTcttgcaaacgtctccactgggcagcttc acgcatagcttgtaattctgcctacagaaccaaatcttgtgttaatagatccgtagtcaagagt gttttgag
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: 1328 Transcript exons: 8894849-8894897,8894985-8895038,8897090-8897201,8898482- 8898570,8899286-8899388,8900247-8900324,8900560-8900960, 8902717-8903158 CTTGCAAACGTCTCCACTGGGCAGCTTCACGCATAGCTTGTAATTCTGCCTTCATTTCCTCTTG TTCTTCCTTGCGCTTTATTTTCTCATCCAACACATTCCTTTTATCTGGATCTTGCAAATCTTTA AAGGCTTTGTTCAGCTTGATGAACGCTTGGTGAGCTTCAGGATGCGTGCACTTATCAGGATGCA CCATAAGAGACAACTTCCAGTACCTTTTCTTCATGTTGTCACTCAACATATTTCTGTTCGCACC CAAAACATCATATGAGTTGTCAGCATCTGCTACCATGATTCTTGTAACCTCTTCAAAACGTTCG GCCTCGTTTGCTGATTCTACCTCAGTCACCAAAGCAGGAGGTGGGGGTCCTATAAACAATTCAG TATCTTCTTCCAGCTCAACATCCCTCAGCTCCGCTTGTGCTTCAGTCAACTTAGCTGCGGCAGC AAGTAGTTCTGCAGAAGGCATTGCAGGACCAATCACCCTCTTTTTTGGGCCAGTATCTTCTTCG GCAGGCAAGCTTAAATTAGCATCGTAAGCGGTAGCACTATCGCTTGACAAACTCAAATTGGCAT TATGACCACCAGCTGCTTCATTTGGCAAACTCAAATTGGCATTACAATGTTCCTGTCCAACTCC CGAATCCAACGGCTTGGACTGCTCATCATTTTGATGCAACTCTTGACTTTGAAGTTGCATTTGG GAGCGGATTAAGGGTCCTACAGTCTCCAAAGTAGGAAATGCTTTTGATGGTAATAGAAAAACAT GATCACCCGTTTCCTTAAGGTTTAAGGAGAGGAACAGTTTTCGCAGACGCTTGACCAACAATTT TTCAGATAAACCCCTTATATCTACAGCTTGTCCATCATCAATCATTTGAAGAAGCTGTTTCAAA TCACCAGCTACAGTAGGGAACTCCTGCAATATGCCTTTGACCACATCCCCAGGACTATCCCTTC GCCGCTCGGGCTGGAAGTCATCACAGTCTGACCCGGAACCGGTGTCCGATTCACTAGAATCTGA ATACTTCCTCTTTCCCTCTGGTTTCGATCTCCTACTACTGCTGCTGCCTCTATGCTCCCGCTTC TTCACAAGCTTCTTTTTTCTCTTCGCCCTCTCCCTATGCTTATCACTCCTTGAGGAGCTCCTTC GACTCCTCTCCCCCTCGCGACGCCGTTTGTGCCGACGCTTTCGCCGTTTTTCATCTTCAGAGGA GCTATCAACTTCATAGTCAGATTCAGAAAATGATTCAGATGAGGACGTGGCTGATTCTTCTTGT TTTCTTTTCTTCCTTCTGCTCGAACTCTCTCCCATGGTGATCCTTGTT
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.300556834

Conservation Information
Conserved circRNAs	NA
PMCS	0.300556834

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8903147-8902922(-)
						
						Potential amino acid sequence
						
							MGESSSRRKKRKQEESATSSSESFSESDYEVDSSSEDEKRRKRRHKRRREGERSRRSSSRSDKH
RERAKRKKKLVKKREHRGSSSSRRSKPEGKRKYSDSSESDTGSGSDCDDFQPERRRDSPGDVVK
GILQEFPTVAGDLKQLLQMIDDGQAVDIRGLSEKLLVKRLRKLFLSLNLKETGDHVFLLPSKAF
PTLETVGPLIRSQMQLQSQELHQNDEQSKPLDSGVGQEHCNANLSLPNEAAGGHNANLSLSSDS
ATAYDANLSLPAEEDTGPKKRVIGPAMPSAELLAAAAKLTEAQAELRDVELEEDTELFIGPPPP
ALVTEVESANEAERFEEVTRIMVADADNSYDVLGANRNMLSDNMKKRYWKLSLMVHPDKCTHPE
AHQAFIKLNKAFKDLQDPDKRNVLDEKIKRKEEQEEMKAELQAMREAAQWRRLQEQGSPWERVR
AEGRKENKKNQPRPHLNHFLNLTMKLIAPLKMKNGESVGTNGVARGRGVEGAPQGVISIGRGRR
EKRSL*(-)
						
						Sponge-miRNAs
						
							sly-miR9476-5p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	8903147-8902922(-)
Potential amino acid sequence	MGESSSRRKKRKQEESATSSSESFSESDYEVDSSSEDEKRRKRRHKRRREGERSRRSSSRSDKH RERAKRKKKLVKKREHRGSSSSRRSKPEGKRKYSDSSESDTGSGSDCDDFQPERRRDSPGDVVK GILQEFPTVAGDLKQLLQMIDDGQAVDIRGLSEKLLVKRLRKLFLSLNLKETGDHVFLLPSKAF PTLETVGPLIRSQMQLQSQELHQNDEQSKPLDSGVGQEHCNANLSLPNEAAGGHNANLSLSSDS ATAYDANLSLPAEEDTGPKKRVIGPAMPSAELLAAAAKLTEAQAELRDVELEEDTELFIGPPPP ALVTEVESANEAERFEEVTRIMVADADNSYDVLGANRNMLSDNMKKRYWKLSLMVHPDKCTHPE AHQAFIKLNKAFKDLQDPDKRNVLDEKIKRKEEQEEMKAELQAMREAAQWRRLQEQGSPWERVR AEGRKENKKNQPRPHLNHFLNLTMKLIAPLKMKNGESVGTNGVARGRGVEGAPQGVISIGRGRR EKRSL*(-)
Sponge-miRNAs	sly-miR9476-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc11g018670.1_circ_g.1

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