Plant Circular RNA Database

Detail information of Solyc01g057780.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc01g057780.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_000135
					
						Alias
						1:56766363|56768149
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr1: 63865963-63867749  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc01g057780.2						
					
						Parent gene annotation
						
							Zinc finger protein VAR3, chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc01g057780.2_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
						Solyc01g057780.2.1:2

General Information
CircRNA Name	Solyc01g057780.2_circ_g.2
ID in PlantcircBase	sly_circ_000135
Alias	1:56766363\|56768149
Organism	Solanum lycopersicum
Position	chr1: 63865963-63867749 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc01g057780.2
Parent gene annotation	Zinc finger protein VAR3, chloroplastic
Parent gene strand	-
Alternative splicing	Solyc01g057780.2_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	Solyc01g057780.2.1:2

			
						 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  
						
							CAAGAATGCCCTCATTCTTCTTGCCGTTTCCAGAGCACCTTTGAACAAAAATGGTGTCCCATTT
GATACAACAGCCTCAATATCCCTCCTTGAAAGCAACttttgacatatccagtcgcctctcttca
ttacaatattttgtctaataggccttggtgtttgtccatatctacctgaaaaatcatattgctc
tgcaggag

									
								

					

						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: 402
Transcript exons: 63865963-63866246,63867632-63867749
TTTTGACATATCCAGTCGCCTCTCTTCATTACAATATTTTGTCTAATAGGCCTTGGTGTTTGTC
CATATCTACCTGAAAAATCATATTGCTCTGCAGGAGGCAGGTTGACTGCTGGAGCTCCGCAGCT
CACTTCAACCAACTCACGCAAAAGACTCCGGCAAGATGATTCTATAAGGTCCCTGCTATAGAGG
GAGTTTTTTTCTGAAGAAACAGAGGGTTTACTCGCGTAACATAATATGTATTTCATGAGATCAA
CCGTGTTAGCGTTGCCATGATCCAGCACAGTGCTCCCGTCAATACCCAAGAATGCCCTCATTCT
TCTTGCCGTTTCCAGAGCACCTTTGAACAAAAATGGTGTCCCATTTGATACAACAGCCTCAATA
TCCCTCCTTGAAAGCAAC
						
					

						Genomic sequence
						
							TTTTGACATATCCAGTCGCCTCTCTTCATTACAATATTTTGTCTAATAGGCCTTGGTGTTTGTC
CATATCTACCTGAAAAATCATATTGCTCTGCAGGAGGCAGGTTGACTGCTGGAGCTCCGCAGCT
CACTTCAACCAACTCACGCAAAAGACTCCGGCAAGATGATTCTATAAGGTCCCTGCTATAGAGG
GAGTTTTTTTCTGAAGAAACAGAGGGTTTACTCGCGTAACATAATATGTATTTCATGAGATCAA
CCGTGTTAGCGTTGCCATGATCCAGCACCTGATATTTCAATCAAGATAAAATTTCAAAAACAAA
CTAAAAGTAAGAGGAAAAAACAATGTTCAGCAACCCTATATCAGATGTGTACTTGAAAGTAAAG
CTATTTCAGTAACTCAACAAAAAAATGTAAAGAGAAAAATTGTTGATGCAAGCTCAGTATAGTA
TTTCCTTCAGTTTTCTCCAAGGGGTCAAGGAATAGTCAAGAGGTGTAAGAAGCAAATTACAAGA
CATAGGATAGCTTAGAGATTACTTTGGCCAGATGTATTACTTCCTAGAGGATTAATTCAAAGGA
AAAAAAACAAAGTCAATAAACAAAGCAGTTACATCATAAGACACCTATTTTTAAGTCTAAGTAG
TACCTAAAGCTCTTCAATTTTAAAAACAAAGACAACTTGGAAGTCATACCTAGGCGTTCACTTC
CATCTTAAAGAAGGAAACCAATCGGCAATGAAATATCACACAAACCCTTCGACAGATTACAACT
TTTTTTTAGATATCACAGAGCATTAGAGTTTATAGTGTAAACAGAGGATTAGAGTTTATAGTGA
AAACAGAGGATTTTCTGCAATCATTCTTGCAGGGGATTCATAGGCACCTGGACCGGATGGATTC
ACCATGGAATTTTTCACCAGTTGCTGGGAGATAGTTAGCAAAGAAGTAGTGGCAGCAGTTCAAA
ACTTTTGTAATCAGACAATTTTTTGAAAGGAGTTCAATGCCACCTTCATAACCTTGATCCCAAA
AGAATTGGGGGCCAATAGGTAGCATATTAGCTTAATAGGTAGCACATACAAGATCAACTCAAAA
TTGTTGACTCAAAGGCTGAAAAAGGTCTTCTCAAAACTGGTAGATGCACATTAGATGGTATTTA
TTGAAACTGGTACATGCACATCAGATGGCATTTTTTAAGGGCACGCAGATCATGGATGCTATTA
TGATTGCAGTAAACAGGATTGTAAGGCACCAAATGAAGCATTCCCTAGCCTCAACCAAAGTAAA
AATTGGGCATCAACTTAAGTTCTACCAACACTCACAAATAGAATTACCTTACTCTATCTTAATA
AGCTCAAGTATCAAAAATGTCTCATCAAGTTAAGTAGTTTAGCTTTGAGCTTAGTTGAGGTCAT
CAAAAGGAAGCTCAACCCTGAATCGATCCAACTTTGCTTAGTTTGTAATCAAAACGTAAAATTA
TTTTAAATAGATATAATGTCCACAAATGTAACTGAACCCTTAAGCTTATTTCCAAATTGATTGG
ACTAAGTAAGTCTTATAGTAATCCTTCTTCTAATATGTACAAATCCTTCAAATTAAATAATTTG
ATGAAGGAACCATTGTAACGACAACAGAATACTATATTATACTGTAAAATAAGAATAGATTGTG
CTTACAGTGCTCCCGTCAATACCCAAGAATGCCCTCATTCTTCTTGCCGTTTCCAGAGCACCTT
TGAACAAAAATGGTGTCCCATTTGATACAACAGCCTCAATATCCCTCCTTGAAAGCAAC
						
					

			
		

Sequences
Splice junction sequence	CAAGAATGCCCTCATTCTTCTTGCCGTTTCCAGAGCACCTTTGAACAAAAATGGTGTCCCATTT GATACAACAGCCTCAATATCCCTCCTTGAAAGCAACttttgacatatccagtcgcctctcttca ttacaatattttgtctaataggccttggtgtttgtccatatctacctgaaaaatcatattgctc tgcaggag
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: 402 Transcript exons: 63865963-63866246,63867632-63867749 TTTTGACATATCCAGTCGCCTCTCTTCATTACAATATTTTGTCTAATAGGCCTTGGTGTTTGTC CATATCTACCTGAAAAATCATATTGCTCTGCAGGAGGCAGGTTGACTGCTGGAGCTCCGCAGCT CACTTCAACCAACTCACGCAAAAGACTCCGGCAAGATGATTCTATAAGGTCCCTGCTATAGAGG GAGTTTTTTTCTGAAGAAACAGAGGGTTTACTCGCGTAACATAATATGTATTTCATGAGATCAA CCGTGTTAGCGTTGCCATGATCCAGCACAGTGCTCCCGTCAATACCCAAGAATGCCCTCATTCT TCTTGCCGTTTCCAGAGCACCTTTGAACAAAAATGGTGTCCCATTTGATACAACAGCCTCAATA TCCCTCCTTGAAAGCAAC
Genomic sequence	TTTTGACATATCCAGTCGCCTCTCTTCATTACAATATTTTGTCTAATAGGCCTTGGTGTTTGTC CATATCTACCTGAAAAATCATATTGCTCTGCAGGAGGCAGGTTGACTGCTGGAGCTCCGCAGCT CACTTCAACCAACTCACGCAAAAGACTCCGGCAAGATGATTCTATAAGGTCCCTGCTATAGAGG GAGTTTTTTTCTGAAGAAACAGAGGGTTTACTCGCGTAACATAATATGTATTTCATGAGATCAA CCGTGTTAGCGTTGCCATGATCCAGCACCTGATATTTCAATCAAGATAAAATTTCAAAAACAAA CTAAAAGTAAGAGGAAAAAACAATGTTCAGCAACCCTATATCAGATGTGTACTTGAAAGTAAAG CTATTTCAGTAACTCAACAAAAAAATGTAAAGAGAAAAATTGTTGATGCAAGCTCAGTATAGTA TTTCCTTCAGTTTTCTCCAAGGGGTCAAGGAATAGTCAAGAGGTGTAAGAAGCAAATTACAAGA CATAGGATAGCTTAGAGATTACTTTGGCCAGATGTATTACTTCCTAGAGGATTAATTCAAAGGA AAAAAAACAAAGTCAATAAACAAAGCAGTTACATCATAAGACACCTATTTTTAAGTCTAAGTAG TACCTAAAGCTCTTCAATTTTAAAAACAAAGACAACTTGGAAGTCATACCTAGGCGTTCACTTC CATCTTAAAGAAGGAAACCAATCGGCAATGAAATATCACACAAACCCTTCGACAGATTACAACT TTTTTTTAGATATCACAGAGCATTAGAGTTTATAGTGTAAACAGAGGATTAGAGTTTATAGTGA AAACAGAGGATTTTCTGCAATCATTCTTGCAGGGGATTCATAGGCACCTGGACCGGATGGATTC ACCATGGAATTTTTCACCAGTTGCTGGGAGATAGTTAGCAAAGAAGTAGTGGCAGCAGTTCAAA ACTTTTGTAATCAGACAATTTTTTGAAAGGAGTTCAATGCCACCTTCATAACCTTGATCCCAAA AGAATTGGGGGCCAATAGGTAGCATATTAGCTTAATAGGTAGCACATACAAGATCAACTCAAAA TTGTTGACTCAAAGGCTGAAAAAGGTCTTCTCAAAACTGGTAGATGCACATTAGATGGTATTTA TTGAAACTGGTACATGCACATCAGATGGCATTTTTTAAGGGCACGCAGATCATGGATGCTATTA TGATTGCAGTAAACAGGATTGTAAGGCACCAAATGAAGCATTCCCTAGCCTCAACCAAAGTAAA AATTGGGCATCAACTTAAGTTCTACCAACACTCACAAATAGAATTACCTTACTCTATCTTAATA AGCTCAAGTATCAAAAATGTCTCATCAAGTTAAGTAGTTTAGCTTTGAGCTTAGTTGAGGTCAT CAAAAGGAAGCTCAACCCTGAATCGATCCAACTTTGCTTAGTTTGTAATCAAAACGTAAAATTA TTTTAAATAGATATAATGTCCACAAATGTAACTGAACCCTTAAGCTTATTTCCAAATTGATTGG ACTAAGTAAGTCTTATAGTAATCCTTCTTCTAATATGTACAAATCCTTCAAATTAAATAATTTG ATGAAGGAACCATTGTAACGACAACAGAATACTATATTATACTGTAAAATAAGAATAGATTGTG CTTACAGTGCTCCCGTCAATACCCAAGAATGCCCTCATTCTTCTTGCCGTTTCCAGAGCACCTT TGAACAAAAATGGTGTCCCATTTGATACAACAGCCTCAATATCCCTCCTTGAAAGCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.498185022

Conservation Information
Conserved circRNAs	NA
PMCS	0.498185022

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							63867701-63866005(+)
63867666-63865965(-)
						
						Potential amino acid sequence
						
							MVSHLIQQPQYPSLKATFDISSRLSSLQYFV*(+)
MRAFLGIDGSTVLDHGNANTVDLMKYILCYASKPSVSSEKNSLYSRDLIESSCRSLLRELVEVS
CGAPAVNLPPAEQYDFSGRYGQTPRPIRQNIVMKRGDWICQKLLSRRDIEAVVSNGTPFLFKGA
LETARRMRAFLGIDGSTVLDHGNANTVDLMKYILCYASKPSVSSEKNSLYSRDLIESSCRSLLR
ELVEVSCGAPAVNLPPAEQYDFSGRYGQTPRPIRQNIVMKRGDWICQKLLSRRDIEAVVSNGTP
FLFKGALETARRMRAFLGIDGSTVLDHGNANTVDLMKYILCYASKPSVSSEKNSLYSRDLIESS
CRSLLRELVEVSCGAPAVNLPPAEQYDFSGRYGQTPRPIRQNIVMKRGDWICQKLLSRRDIEAV
VSNGTPFLFKGALETARRMRAFLGIDGSTVLDHGNANTVDLMKYILCYASKPSVSSEKNSLYSR
DLIESSCRSLLRELVEVSCGAPAVNLPPAEQYDFSGRYGQTPRPIRQNIVMKRGDWICQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	63867701-63866005(+) 63867666-63865965(-)
Potential amino acid sequence	MVSHLIQQPQYPSLKATFDISSRLSSLQYFV*(+) MRAFLGIDGSTVLDHGNANTVDLMKYILCYASKPSVSSEKNSLYSRDLIESSCRSLLRELVEVS CGAPAVNLPPAEQYDFSGRYGQTPRPIRQNIVMKRGDWICQKLLSRRDIEAVVSNGTPFLFKGA LETARRMRAFLGIDGSTVLDHGNANTVDLMKYILCYASKPSVSSEKNSLYSRDLIESSCRSLLR ELVEVSCGAPAVNLPPAEQYDFSGRYGQTPRPIRQNIVMKRGDWICQKLLSRRDIEAVVSNGTP FLFKGALETARRMRAFLGIDGSTVLDHGNANTVDLMKYILCYASKPSVSSEKNSLYSRDLIESS CRSLLRELVEVSCGAPAVNLPPAEQYDFSGRYGQTPRPIRQNIVMKRGDWICQKLLSRRDIEAV VSNGTPFLFKGALETARRMRAFLGIDGSTVLDHGNANTVDLMKYILCYASKPSVSSEKNSLYSR DLIESSCRSLLRELVEVSCGAPAVNLPPAEQYDFSGRYGQTPRPIRQNIVMKRGDWICQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc01g057780.2_circ_g.2

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