Plant Circular RNA Database

Detail information of Solyc11g067200.1_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc11g067200.1_circ_g.1
					
						ID in PlantcircBase
						sly_circ_003443
					
						Alias
						11:50042623|50043676
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr11: 52959123-52960176  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc11g067200.1						
					
						Parent gene annotation
						
							Protein HIRA
							
						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  
						
							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
						Solyc11g067200.1.1:3

General Information
CircRNA Name	Solyc11g067200.1_circ_g.1
ID in PlantcircBase	sly_circ_003443
Alias	11:50042623\|50043676
Organism	Solanum lycopersicum
Position	chr11: 52959123-52960176 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc11g067200.1
Parent gene annotation	Protein HIRA
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	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	Solyc11g067200.1.1:3

			
						 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  
						
							TGACGAGCAAAAAGTTCCAAGATTCATCACAATCAACAAATACTGCAGCAGATCCCATCATCAT
GGTCGGCATGGCACGTCGGCCACATTTTGTATAAATcttgctaaaaaccgaacgtaggataaaa
ggcattgacgatattcactaggagacttcaaagcaagagcagacgccaattgagactccaaatg
agcacgtg

									
								

					

						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: 566
Transcript exons: 52959123-52959245,52959418-52959658,52959975-52960176
CTTGCTAAAAACCGAACGTAGGATAAAAGGCATTGACGATATTCACTAGGAGACTTCAAAGCAA
GAGCAGACGCCAATTGAGACTCCAAATGAGCACGTGTTTGTACCCCATCATCAGTGACTCTGCT
CCAGCCAGGTCTTCTAGCCAGGAACTTCTTAACATCCACCTGCAGTGCCGCTAGTTCACCACCA
TGCAATGAGCCCGAACTCCAGGAGCTTGAAAAATTTGAAGCCGGAAAACAATCATCTGCAACCC
TCAGCCAGCACATGAGGCTCATATCAAAGAGGTATGCATGCCGTGTGGCCAGGACAACAAGAGG
AAAACCAGATTTTGATAATTTTGCTGTTATCACTTTGATTGTGCCTGCATTTGCCTTGGGATCT
GAGTTCATAAGGGACGCCAACGAGTCTTGAAGGAGACACTTCCGGTTGAATAGATCCCAAAGAT
GTAATGAACCTTTCCTTGTGACGAGCAAAAAGTTCCAAGATTCATCACAATCAACAAATACTGC
AGCAGATCCCATCATCATGGTCGGCATGGCACGTCGGCCACATTTTGTATAAAT
						
					

						Genomic sequence
						
							CTTGCTAAAAACCGAACGTAGGATAAAAGGCATTGACGATATTCACTAGGAGACTTCAAAGCAA
GAGCAGACGCCAATTGAGACTCCAAATGAGCACGTGTTTGTACCCCATCATCAGTGACTCTGCA
GATGCACAAACTTTAGTAAGAGAGATGAGCCGCCAAAACAAAATTAGGCAAGAAACTTACACAT
AAATGCCAACTGTACAGTTATTCAAACAGCAAAAGTCACACTGTAACTGATAACATTTCAACAT
GCTAATATAGTAAGATACAGACTAAACATGGACATTGACCTGCTCCAGCCAGGTCTTCTAGCCA
GGAACTTCTTAACATCCACCTGCAGTGCCGCTAGTTCACCACCATGCAATGAGCCCGAACTCCA
GGAGCTTGAAAAATTTGAAGCCGGAAAACAATCATCTGCAACCCTCAGCCAGCACATGAGGCTC
ATATCAAAGAGGTATGCATGCCGTGTGGCCAGGACAACAAGAGGAAAACCAGATTTTGATAATT
TTGCTGTTATCACTTTGATTGTGCCTGTTAACAAATCAAGAAAAAGTTAAAAGATATGAAATGC
AGCTAAGACGATGCAATATGTTGGTCCAATTTTGGATTTAATGAATCAACAAAGAAACAAATGA
CTGCAGCTCTTGTGCAGCGAAATACTAGAAAATGTTACTTCCAGCAGTACACTTAACAGGACAA
CGGTCAGCTTGTAAGCGAAGTAATATCCCCTTGAGGACAAGGCATAAAAGAGGAAAAACACAGT
TCTCAGTCGCAATGCTTAAAAAGAAGGAGCACAATTCTCTGCCAGAAGACACATGAATTAAATC
TTGGGACTTTTATTACTCACCTGCATTTGCCTTGGGATCTGAGTTCATAAGGGACGCCAACGAG
TCTTGAAGGAGACACTTCCGGTTGAATAGATCCCAAAGATGTAATGAACCTTTCCTTGTGACGA
GCAAAAAGTTCCAAGATTCATCACAATCAACAAATACTGCAGCAGATCCCATCATCATGGTCGG
CATGGCACGTCGGCCACATTTTGTATAAAT
						
					

			
		

Sequences
Splice junction sequence	TGACGAGCAAAAAGTTCCAAGATTCATCACAATCAACAAATACTGCAGCAGATCCCATCATCAT GGTCGGCATGGCACGTCGGCCACATTTTGTATAAATcttgctaaaaaccgaacgtaggataaaa ggcattgacgatattcactaggagacttcaaagcaagagcagacgccaattgagactccaaatg agcacgtg
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: 566 Transcript exons: 52959123-52959245,52959418-52959658,52959975-52960176 CTTGCTAAAAACCGAACGTAGGATAAAAGGCATTGACGATATTCACTAGGAGACTTCAAAGCAA GAGCAGACGCCAATTGAGACTCCAAATGAGCACGTGTTTGTACCCCATCATCAGTGACTCTGCT CCAGCCAGGTCTTCTAGCCAGGAACTTCTTAACATCCACCTGCAGTGCCGCTAGTTCACCACCA TGCAATGAGCCCGAACTCCAGGAGCTTGAAAAATTTGAAGCCGGAAAACAATCATCTGCAACCC TCAGCCAGCACATGAGGCTCATATCAAAGAGGTATGCATGCCGTGTGGCCAGGACAACAAGAGG AAAACCAGATTTTGATAATTTTGCTGTTATCACTTTGATTGTGCCTGCATTTGCCTTGGGATCT GAGTTCATAAGGGACGCCAACGAGTCTTGAAGGAGACACTTCCGGTTGAATAGATCCCAAAGAT GTAATGAACCTTTCCTTGTGACGAGCAAAAAGTTCCAAGATTCATCACAATCAACAAATACTGC AGCAGATCCCATCATCATGGTCGGCATGGCACGTCGGCCACATTTTGTATAAAT
Genomic sequence	CTTGCTAAAAACCGAACGTAGGATAAAAGGCATTGACGATATTCACTAGGAGACTTCAAAGCAA GAGCAGACGCCAATTGAGACTCCAAATGAGCACGTGTTTGTACCCCATCATCAGTGACTCTGCA GATGCACAAACTTTAGTAAGAGAGATGAGCCGCCAAAACAAAATTAGGCAAGAAACTTACACAT AAATGCCAACTGTACAGTTATTCAAACAGCAAAAGTCACACTGTAACTGATAACATTTCAACAT GCTAATATAGTAAGATACAGACTAAACATGGACATTGACCTGCTCCAGCCAGGTCTTCTAGCCA GGAACTTCTTAACATCCACCTGCAGTGCCGCTAGTTCACCACCATGCAATGAGCCCGAACTCCA GGAGCTTGAAAAATTTGAAGCCGGAAAACAATCATCTGCAACCCTCAGCCAGCACATGAGGCTC ATATCAAAGAGGTATGCATGCCGTGTGGCCAGGACAACAAGAGGAAAACCAGATTTTGATAATT TTGCTGTTATCACTTTGATTGTGCCTGTTAACAAATCAAGAAAAAGTTAAAAGATATGAAATGC AGCTAAGACGATGCAATATGTTGGTCCAATTTTGGATTTAATGAATCAACAAAGAAACAAATGA CTGCAGCTCTTGTGCAGCGAAATACTAGAAAATGTTACTTCCAGCAGTACACTTAACAGGACAA CGGTCAGCTTGTAAGCGAAGTAATATCCCCTTGAGGACAAGGCATAAAAGAGGAAAAACACAGT TCTCAGTCGCAATGCTTAAAAAGAAGGAGCACAATTCTCTGCCAGAAGACACATGAATTAAATC TTGGGACTTTTATTACTCACCTGCATTTGCCTTGGGATCTGAGTTCATAAGGGACGCCAACGAG TCTTGAAGGAGACACTTCCGGTTGAATAGATCCCAAAGATGTAATGAACCTTTCCTTGTGACGA GCAAAAAGTTCCAAGATTCATCACAATCAACAAATACTGCAGCAGATCCCATCATCATGGTCGG CATGGCACGTCGGCCACATTTTGTATAAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.563121869

Conservation Information
Conserved circRNAs	NA
PMCS	0.563121869

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							52960151-52960139(-)
52959157-52960139(-)
						
						Potential amino acid sequence
						
							MPTMMMGSAAVFVDCDESWNFLLVTRKGSLHLWDLFNRKCLLQDSLASLMNSDPKANAGTIKVI
TAKLSKSGFPLVVLATRHAYLFDMSLMCWLRVADDCFPASNFSSSWSSGSLHGGELAALQVDVK
KFLARRPGWSRVTDDGVQTRAHLESQLASALALKSPSEYRQCLLSYVRFLARFIQNVADVPCRP
*(-)
MPFILRSVFSKIYTKCGRRAMPTMMMGSAAVFVDCDESWNFLLVTRKGSLHLWDLFNRKCLLQD
SLASLMNSDPKANAGTIKVITAKLSKSGFPLVVLATRHAYLFDMSLMCWLRVADDCFPASNFSS
SWSSGSLHGGELAALQVDVKKFLARRPGWSRVTDDGVQTRAHLESQLASALALKSPSEYRQCLL
SYVRFLARFIQNVADVPCRP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	52960151-52960139(-) 52959157-52960139(-)
Potential amino acid sequence	MPTMMMGSAAVFVDCDESWNFLLVTRKGSLHLWDLFNRKCLLQDSLASLMNSDPKANAGTIKVI TAKLSKSGFPLVVLATRHAYLFDMSLMCWLRVADDCFPASNFSSSWSSGSLHGGELAALQVDVK KFLARRPGWSRVTDDGVQTRAHLESQLASALALKSPSEYRQCLLSYVRFLARFIQNVADVPCRP (-) MPFILRSVFSKIYTKCGRRAMPTMMMGSAAVFVDCDESWNFLLVTRKGSLHLWDLFNRKCLLQD SLASLMNSDPKANAGTIKVITAKLSKSGFPLVVLATRHAYLFDMSLMCWLRVADDCFPASNFSS SWSSGSLHGGELAALQVDVKKFLARRPGWSRVTDDGVQTRAHLESQLASALALKSPSEYRQCLL SYVRFLARFIQNVADVPCRP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc11g067200.1_circ_g.1

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