Plant Circular RNA Database

Detail information of Solyc04g076140.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc04g076140.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_001510
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 61089087-61092433  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc04g076140.2						
					
						Parent gene annotation
						
							Rho GTPase-activating protein REN1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						2
					
						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
						Solyc04g076140.2.1:5

General Information
CircRNA Name	Solyc04g076140.2_circ_g.1
ID in PlantcircBase	sly_circ_001510
Alias	NA
Organism	Solanum lycopersicum
Position	chr4: 61089087-61092433 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc04g076140.2
Parent gene annotation	Rho GTPase-activating protein REN1
Parent gene strand	+
Alternative splicing	NA
Support reads	2
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	Solyc04g076140.2.1:5

			
						 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  
						
							TGTAATTGTTGATAGAAACTGAGCGGAGCATTAGAGTCAATGCTATGCATACAGCTATATTGGA
GACATTTCCAGAACCAAATCGTCGTTTGCTGCAGAGctaatgatagacagcctgtgaagtccat
ggtaattggtaggccagttttacttgctctggaagatattgatggaactccatcttttttggag
aaagccct

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							CTAATGATAGACAGCCTGTGAAGTCCATGGTAATTGGTAGGCCAGTTTTACTTGCTCTGGAAGA
TATTGATGGAACTCCATCTTTTTTGGAGAAAGCCCTGAGATTTGTAGAAGAGCATGGTAAGCTT
CTTTTACTGTGTCAAATAACTATGGGATGGCCGCTTCTGTAATATGTTACTTTCTTATGCGTCC
AGCTTCAAATTTCAAATATTTCTTTCATCTGTAAAGGATCAATTGTCAGTGGGGCTTATTCCCA
AGTGCATATTCTTGCTTAAAAGACGAGGAGATCCAGTATCTATTTTTCATCAAATCAGATGCAT
TGTTTGTTTTCAGTATCTAATTTTGCCACATGGGTGTGTTTGAGATTGTCCAATTAGAGGATTT
TTAGGGGTTATACTCTATAAGAAATGAAAGACCAATATAGGTGGACCCCAGCTGCACAATTCCA
TTCACTGCAGAAGTCTATTTTGCTATGAATTTGCCTATTGTCCCATTGCTTTGTTTTGACTTTT
GAGCCAAGGGTCTATCAAAAACGGTCGCTCTACTCCACAAAGGTGGGGGTAAGGTCTCCCCAAA
CTAACACCTGTGGGATTACTCTCTGCATGTTGTTGTTGTTGTTATTTATATGTTGTCCCATGTT
ACTAGGTAGTTGTGATATCTGTATTGATTACTCCTGTAGGTTGTTTTTCAAACTGATTCTAGGC
TTCAACATTGATATAAATGTCAAAACTTAAAAATTAGTACTCCCTCTTTCTTGAAGTTTCACTT
TCTAAGAGTTGAAGAATGGAATCTTGGAATAAGATTTTCGAAGAGGTAGTAGTTTTCATCACCG
CCAACTGGTAAGTTGGAGGTCGAGTCATGTGGAGGATAAGTTGGAGGTTTGAGTCGTTTGGAGG
GTAAGTAGGAATATGATTTATCCTCCTCGAGGGTGGGGAAATACGAAAAAGAATGAAAAAGGTT
GGAAATGTTTGTAACTTGTATACTTTTTGTGTTATATCTAAATTGCTATTCAGATTTTGGTTAG
GGAGAAATAGTTTCAGAGTTGGGTTTTGGAAAAGTATGTGTCTGGATTTGATTCAGGTTAGCAG
TTTTATCGATTAAATCATTAAAAGTCTAAAGTATTAGGTTAGAACTAAGTAACAGTTTCTTTCT
GCTATTAAATGCTTTCAGCACTAAAGGGGCCAAAATACAGTTTGTAAAATGGAAAAGCTGTTGG
GCTGTTTCTGAAAAAATCTTTTGGTTTCCAACGCCAATTTCAGTAAGGGGATTTTTTTATGTCC
TATTTAGGGCTGAGAATCAGCAAGTTGCGTAAATAGACGTCTGAGAATCAGTCAAGTTGAGTGT
GTAGAAGTAAAATGGACCAAATATTGGGATAGAAGAGATTTATAGTCAAATTGTTTTTTTACGG
TTTCAATATGAACACCATGCTTCCCTATTCTTCTTATATAAAAAAAAATGAACATCATTTACTT
GTAAGGACAGTGCTTCTTCCTACTGTACTTCTTCATTTGCTTTGATGTGGTTACAAGTGATCTT
TGATACTGAATAAGTTTAGCTAGACGATAAATTGCCTACAAACTACTCTCTACTTTCATGCTCT
AATTGATTTTTATAAAAATATGCTTTTGGAGAACGTCTATTTATCTCTAACCTTCTTTCAGTTG
ATACTTCTCATTTTTTTGTCTAAGAAATTTAATACTTCTCGTTTTGTGGGCTGTTCATTTATTT
ATTTATTGATGTCTTGCATTCTCATCAAATGGTACTGATCTTCTACAATTTCTTCCAGGGATTA
GAACTGAAGGCATCCTGCGGCAAGCAGCAGATGTTGATGATGTTGAGCAACGAATACGGGAATA
TGAACAGGGTCTGTTACCTTTAAATTGAGAGGATTTCACTTTTGTTATTTTTTACTAGGTGCTG
ATACCCCAAGTATCTGCTGAAAAAGTTTACATTTTGCCACTGGCGACTAGACTTCATTACTCAT
CAAAAAGTTGCAATAATAAGCTTACTCCTTTCTCTCTCTCTATATAATAAGCTTACTCCTAGTG
GTGCACAACAATGTTGTTAAGTCTCACAGTGAACTTTATAGAGCTGCAGATTTTGCTGAGTTGC
TTTTTCTATGTGTGTTTAACTGGTTTCCTCTTCTCAGATGCTACTGAATTATGATAGATGAGAT
GCAATTCTCAAATGACATCAGATTGTTATTAGCTAAGTAAATAATATGTTCTGATATAATGGCT
GTGGAAGATCATTTACCTGTCAAAAATCTTTTACTAATTTTCTTCATTTGAGGGGTAGCTTGTA
CAAGTGCCTCTTGTGTAGTTCACTTGCCTCACAATATGTAATAAAATTTTGTTCTCTTATTCCA
GGTAAAACTGACTTTTCTACAGATGAGGATGCACATGTTATTGCTGACTGTGTGAAGGTATATC
CTTCAAAACTGAAGTTTAGGGTTTCTATAAGATTGTTTGTATGAAATTACTTTCAGAACTTGCT
ATTCATCTTTATTCTGCAGTATATTCTGCGGGAGTTGCCATCATCTCCAGTTCCTGCATCTTGC
TGCAATGCCCTTTTGGAAGCATTTAGTAAGTTTATTGTCTTAATGTTGGGTCCTTTTAGATTGC
CTCTTTTCATTACATGATTTAAGCTAGTTCTTATAGAAGAAAGAAGGATACATTTAGTAACACT
ACTCCAAGATTTGTAGAGTTGTATAGATATACTTTATACATTCAATAGCATTACATGCATGGTC
CATTTCTCTTGATGAAATATTTGCTAGAGCCCCTTTGATAGTAATGACCACTCACCATGAGATT
CTCAACTCTTTTCTATGATTCACGAGTCCTGTGATCCATGTCATTAGTGCCACCCTTCCATATG
AAGCTACTATCTATTATAATTTACTAAAGTGAATTCCTAGTCATGCTTATCCAATTACTTTTCA
ACAGGCACAAAATAAAATATACATATTTATGCATAGAGTTTGTTTGAAATCTATGACTTTATGA
AAGCTGCTTGTCAATTTGGTCTTTAACTTTATTGTGAGCCAGGTGAAGTGAATAAAAAAAAATG
TTTGGAAACTATGATCATATAAGTTTTATCCTAGCTTGAATGTTGGTCAACAAGAATCTCGGAC
TACCTGAAGTGTTTCTGTGTCTTTCATCACAAGATTGGATATTTATACATTTCCATTAAAGATA
AAAGTTGGAAGATTTGTCAGCTTGTATTATATCTGTTAAAATACTTTTGTAATTGTTGATAGAA
ACTGAGCGGAGCATTAGAGTCAATGCTATGCATACAGCTATATTGGAGACATTTCCAGAACCAA
ATCGTCGTTTGCTGCAGAG
						
					

			
		

Sequences
Splice junction sequence	TGTAATTGTTGATAGAAACTGAGCGGAGCATTAGAGTCAATGCTATGCATACAGCTATATTGGA GACATTTCCAGAACCAAATCGTCGTTTGCTGCAGAGctaatgatagacagcctgtgaagtccat ggtaattggtaggccagttttacttgctctggaagatattgatggaactccatcttttttggag aaagccct
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CTAATGATAGACAGCCTGTGAAGTCCATGGTAATTGGTAGGCCAGTTTTACTTGCTCTGGAAGA TATTGATGGAACTCCATCTTTTTTGGAGAAAGCCCTGAGATTTGTAGAAGAGCATGGTAAGCTT CTTTTACTGTGTCAAATAACTATGGGATGGCCGCTTCTGTAATATGTTACTTTCTTATGCGTCC AGCTTCAAATTTCAAATATTTCTTTCATCTGTAAAGGATCAATTGTCAGTGGGGCTTATTCCCA AGTGCATATTCTTGCTTAAAAGACGAGGAGATCCAGTATCTATTTTTCATCAAATCAGATGCAT TGTTTGTTTTCAGTATCTAATTTTGCCACATGGGTGTGTTTGAGATTGTCCAATTAGAGGATTT TTAGGGGTTATACTCTATAAGAAATGAAAGACCAATATAGGTGGACCCCAGCTGCACAATTCCA TTCACTGCAGAAGTCTATTTTGCTATGAATTTGCCTATTGTCCCATTGCTTTGTTTTGACTTTT GAGCCAAGGGTCTATCAAAAACGGTCGCTCTACTCCACAAAGGTGGGGGTAAGGTCTCCCCAAA CTAACACCTGTGGGATTACTCTCTGCATGTTGTTGTTGTTGTTATTTATATGTTGTCCCATGTT ACTAGGTAGTTGTGATATCTGTATTGATTACTCCTGTAGGTTGTTTTTCAAACTGATTCTAGGC TTCAACATTGATATAAATGTCAAAACTTAAAAATTAGTACTCCCTCTTTCTTGAAGTTTCACTT TCTAAGAGTTGAAGAATGGAATCTTGGAATAAGATTTTCGAAGAGGTAGTAGTTTTCATCACCG CCAACTGGTAAGTTGGAGGTCGAGTCATGTGGAGGATAAGTTGGAGGTTTGAGTCGTTTGGAGG GTAAGTAGGAATATGATTTATCCTCCTCGAGGGTGGGGAAATACGAAAAAGAATGAAAAAGGTT GGAAATGTTTGTAACTTGTATACTTTTTGTGTTATATCTAAATTGCTATTCAGATTTTGGTTAG GGAGAAATAGTTTCAGAGTTGGGTTTTGGAAAAGTATGTGTCTGGATTTGATTCAGGTTAGCAG TTTTATCGATTAAATCATTAAAAGTCTAAAGTATTAGGTTAGAACTAAGTAACAGTTTCTTTCT GCTATTAAATGCTTTCAGCACTAAAGGGGCCAAAATACAGTTTGTAAAATGGAAAAGCTGTTGG GCTGTTTCTGAAAAAATCTTTTGGTTTCCAACGCCAATTTCAGTAAGGGGATTTTTTTATGTCC TATTTAGGGCTGAGAATCAGCAAGTTGCGTAAATAGACGTCTGAGAATCAGTCAAGTTGAGTGT GTAGAAGTAAAATGGACCAAATATTGGGATAGAAGAGATTTATAGTCAAATTGTTTTTTTACGG TTTCAATATGAACACCATGCTTCCCTATTCTTCTTATATAAAAAAAAATGAACATCATTTACTT GTAAGGACAGTGCTTCTTCCTACTGTACTTCTTCATTTGCTTTGATGTGGTTACAAGTGATCTT TGATACTGAATAAGTTTAGCTAGACGATAAATTGCCTACAAACTACTCTCTACTTTCATGCTCT AATTGATTTTTATAAAAATATGCTTTTGGAGAACGTCTATTTATCTCTAACCTTCTTTCAGTTG ATACTTCTCATTTTTTTGTCTAAGAAATTTAATACTTCTCGTTTTGTGGGCTGTTCATTTATTT ATTTATTGATGTCTTGCATTCTCATCAAATGGTACTGATCTTCTACAATTTCTTCCAGGGATTA GAACTGAAGGCATCCTGCGGCAAGCAGCAGATGTTGATGATGTTGAGCAACGAATACGGGAATA TGAACAGGGTCTGTTACCTTTAAATTGAGAGGATTTCACTTTTGTTATTTTTTACTAGGTGCTG ATACCCCAAGTATCTGCTGAAAAAGTTTACATTTTGCCACTGGCGACTAGACTTCATTACTCAT CAAAAAGTTGCAATAATAAGCTTACTCCTTTCTCTCTCTCTATATAATAAGCTTACTCCTAGTG GTGCACAACAATGTTGTTAAGTCTCACAGTGAACTTTATAGAGCTGCAGATTTTGCTGAGTTGC TTTTTCTATGTGTGTTTAACTGGTTTCCTCTTCTCAGATGCTACTGAATTATGATAGATGAGAT GCAATTCTCAAATGACATCAGATTGTTATTAGCTAAGTAAATAATATGTTCTGATATAATGGCT GTGGAAGATCATTTACCTGTCAAAAATCTTTTACTAATTTTCTTCATTTGAGGGGTAGCTTGTA CAAGTGCCTCTTGTGTAGTTCACTTGCCTCACAATATGTAATAAAATTTTGTTCTCTTATTCCA GGTAAAACTGACTTTTCTACAGATGAGGATGCACATGTTATTGCTGACTGTGTGAAGGTATATC CTTCAAAACTGAAGTTTAGGGTTTCTATAAGATTGTTTGTATGAAATTACTTTCAGAACTTGCT ATTCATCTTTATTCTGCAGTATATTCTGCGGGAGTTGCCATCATCTCCAGTTCCTGCATCTTGC TGCAATGCCCTTTTGGAAGCATTTAGTAAGTTTATTGTCTTAATGTTGGGTCCTTTTAGATTGC CTCTTTTCATTACATGATTTAAGCTAGTTCTTATAGAAGAAAGAAGGATACATTTAGTAACACT ACTCCAAGATTTGTAGAGTTGTATAGATATACTTTATACATTCAATAGCATTACATGCATGGTC CATTTCTCTTGATGAAATATTTGCTAGAGCCCCTTTGATAGTAATGACCACTCACCATGAGATT CTCAACTCTTTTCTATGATTCACGAGTCCTGTGATCCATGTCATTAGTGCCACCCTTCCATATG AAGCTACTATCTATTATAATTTACTAAAGTGAATTCCTAGTCATGCTTATCCAATTACTTTTCA ACAGGCACAAAATAAAATATACATATTTATGCATAGAGTTTGTTTGAAATCTATGACTTTATGA AAGCTGCTTGTCAATTTGGTCTTTAACTTTATTGTGAGCCAGGTGAAGTGAATAAAAAAAAATG TTTGGAAACTATGATCATATAAGTTTTATCCTAGCTTGAATGTTGGTCAACAAGAATCTCGGAC TACCTGAAGTGTTTCTGTGTCTTTCATCACAAGATTGGATATTTATACATTTCCATTAAAGATA AAAGTTGGAAGATTTGTCAGCTTGTATTATATCTGTTAAAATACTTTTGTAATTGTTGATAGAA ACTGAGCGGAGCATTAGAGTCAATGCTATGCATACAGCTATATTGGAGACATTTCCAGAACCAA ATCGTCGTTTGCTGCAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.171275573

Conservation Information
Conserved circRNAs	NA
PMCS	0.171275573

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							61091652-61089087(+)
61089114-61089087(+)
61092366-61091625(-)
						
						Potential amino acid sequence
						
							MPFWKHLKLSGALESMLCIQLYWRHFQNQIVVCCRANDRQPVKSMVIGRPVLLALEDIDGTPSF
LEKALRFVEEHGIRTEGILRQAADVDDVEQRIREYEQGKTDFSTDEDAHVIADCVKYILRELPS
SPVPASCCNALLEAFKTERSIRVNAMHTAILETFPEPNRRLLQS*(+)
MVIGRPVLLALEDIDGTPSFLEKALRFVEEHGIRTEGILRQAADVDDVEQRIREYEQGKTDFST
DEDAHVIADCVKYILRELPSSPVPASCCNALLEAFKTERSIRVNAMHTAILETFPEPNRRLLQS
*(+)
MLRSVLNASKRALQQDAGTGDDGNSRRIYFTQSAITCASSSVEKSVLPCSYSRIRCSTSSTSAA
CRRMPSVLIPCSSTNLRAFSKKDGVPSISSRASKTGLPITMDFTGCLSLALQQTTIWFWKCLQY
SCMHSIDSNAPLSFKCFQKGIAARCRNWR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	61091652-61089087(+) 61089114-61089087(+) 61092366-61091625(-)
Potential amino acid sequence	MPFWKHLKLSGALESMLCIQLYWRHFQNQIVVCCRANDRQPVKSMVIGRPVLLALEDIDGTPSF LEKALRFVEEHGIRTEGILRQAADVDDVEQRIREYEQGKTDFSTDEDAHVIADCVKYILRELPS SPVPASCCNALLEAFKTERSIRVNAMHTAILETFPEPNRRLLQS(+) MVIGRPVLLALEDIDGTPSFLEKALRFVEEHGIRTEGILRQAADVDDVEQRIREYEQGKTDFST DEDAHVIADCVKYILRELPSSPVPASCCNALLEAFKTERSIRVNAMHTAILETFPEPNRRLLQS (+) MLRSVLNASKRALQQDAGTGDDGNSRRIYFTQSAITCASSSVEKSVLPCSYSRIRCSTSSTSAA CRRMPSVLIPCSSTNLRAFSKKDGVPSISSRASKTGLPITMDFTGCLSLALQQTTIWFWKCLQY SCMHSIDSNAPLSFKCFQKGIAARCRNWR*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc04g076140.2_circ_g.1

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