Plant Circular RNA Database

Detail information of Solyc06g009220.2_circ_g.4

			
						 General Information
					
						CircRNA Name
						Solyc06g009220.2_circ_g.4
					
						ID in PlantcircBase
						sly_circ_001883
					
						Alias
						6:3159038|3162413
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr6: 3159038-3162413  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc06g009220.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc06g009220.2_circ_g.1 Solyc06g009220.2_circ_g.2 Solyc06g009220.2_circ_g.3 Solyc06g009220.2_circ_g.5 Solyc06g009220.2_circ_g.6 						
					
						Support reads
						9
					
						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
						Solyc06g009220.2.1:4

General Information
CircRNA Name	Solyc06g009220.2_circ_g.4
ID in PlantcircBase	sly_circ_001883
Alias	6:3159038\|3162413
Organism	Solanum lycopersicum
Position	chr6: 3159038-3162413 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc06g009220.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc06g009220.2_circ_g.1 Solyc06g009220.2_circ_g.2 Solyc06g009220.2_circ_g.3 Solyc06g009220.2_circ_g.5 Solyc06g009220.2_circ_g.6
Support reads	9
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	Solyc06g009220.2.1:4

			
						 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  
						
							ACATCTTCTCGAGCTTGGTGTCAATACAGTAGAATTATTGCCTGTTTTTGAGTTTGATGAACTG
GAATTACAAAGGCGACCTAATCCGAGAGATCACATGtgttcatgatggaatgattgaattagca
ttggatccacagaagaaccgcaccggagacatatggcacatatgcattaaggtagtaatttaac
tattttat

									
								

					

						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: 526
Transcript exons: 3159038-3159116,3160960-3161196,3161905-3162009,3162309-
3162413
TGTTCATGATGGAATGATTGAATTAGCATTGGATCCACAGAAGAACCGCACCGGAGACATATGG
CACATATGCATTAAGGAGTTGCCCCGAGGTGGGGTCCTTTATGGTTATCGCATTGATGGACCTC
GAAATTGGCATGAAGGGCATCGATTTGACGATAGCATTATTTTGATTGATCCTTACGCAAAACT
AATTGAAGGTCGACGAGCTTTTGGAGATGAAAGCAATAAAATGTGTAGATTTTTTGGAACTTAT
GATTTCAATAGCTTGCCTTTTGACTGGGGAGAAAATTACAAGCTTCCAAATGTACCGGAGAAAG
ATCTTGTTATATATGAGATGAATGTTCGTGCTTTTACTGCTGATGAAACAAGTAGTTTGGATCA
AGATCAACGGGGAAGTTACCTTGGCTTAATTGAAAAGATACCACATCTTCTCGAGCTTGGTGTC
AATACAGTAGAATTATTGCCTGTTTTTGAGTTTGATGAACTGGAATTACAAAGGCGACCTAATC
CGAGAGATCACATG
						
					

						Genomic sequence
						
							TGTTCATGATGGAATGATTGAATTAGCATTGGATCCACAGAAGAACCGCACCGGAGACATATGG
CACATATGCATTAAGGTAGTAATTTAACTATTTTATGTACCTTCATTACTGTATTCACTCAGCA
ATCTTCAAAGATTATATGATTTGGATGCTCATCGTATCATGTTGGCTGTCCACTTTCTACTCTC
TTTTTGCTATTAATTGACCTGCTCCCTATTGTAGGCAGTGTCAAATGATTGATCTCCTTCCTTA
ATGAATACTCAAATGTGTCCATAGTTTCAATATAAAGTAAACATATTGTGGTTTTCTGTTACAT
TTTTAAAAGAGAAGTTAACATATTGTAGTTAGAACTGAATGTCATCCAATTGTATGTCCAATGA
TTATTTGAATTTAATTTATCTTTCCTGTTATTCTGTCGAATAAAAACATTTCAAATCCTTTCTG
TAGAGTCATTGAGTTGTCCTAGTAAGTCAAATGACCTCACATATTTGGTAGGGTATCTAGCAAT
TCTTTGACCTTGACCTCACATGTTTCCAACTTTTATTGAGAATATCCCAACTAAGTAAAACACA
TAAACTAATGAAACTTTCTTTCCTTAAATTTCCATGCTGGAGCTGGAAGGAAGTAGTTCACTTC
AGATAGATGCATGGAATATGGATCTTGCTAATCTGAAAGGATTAAATAAAGGGATAAATTAAGA
TGAAAGAGAAGTAATGTAAATGTTGATTGTGTTAATTAATATGATTTTAGGAGACTTTATTTTT
CCTTTCCTAGCATTATTGTAGGAACAAAATATTTTTTTTTTATTGTAAATTGATTGTCTTTCCT
TAGTAAGGGTCCATTGCAAACTACCCCTTCTCTTTAAGAACCCTAATTGATTGTAGTAGACCTA
GTTAGCATATTAGGGATGATCATGTTTAAGCATATTAGGGATGATCATGTGTACTAGCAGATTC
AATTCAAGAACTTGGATGATTGCGATCTAGACCCCTAATTGAATAATTAAAGACAATAATAATA
CAAGACTAGTTACATTCTCCACTTAATCGAATAAGAACCATATATATCAAGCAAAGAGTTTAAT
ATTACCTCTTAAAAAATCGTTCTTGTAAGGTTGTACAAGAAATCCTAAGTAACCAATACACGAA
GATATGAATAAATAAAATCTCAATTTTATTGATAGCTATTCTGTGTCAAAAAGAATGAAATCAA
CGTGGGTGAATCTAGGGTAAATTTCTAAAACACTATCCCAAATAGCACGAGATTCAATATCTAC
TTTATGGAAATAATAGATAATAAAACCTAACTAGGAAACTTTAAACTAGGAAAATTGAACTAGA
CAATTTTTAAACCAGGAAAACATGGAAGATTAATGTCACACTAATTCTAGAACTACCTAACAAA
ATAAGGAAAGAAGTGTCCAATTTTCTCCTGAAAATACGCCTATTCCAACAGACTTGTGCATGTA
TTTCAGCCTCTTTTGGGGATCCATACATGCTATTAGGTTGGCTATATGAATCTTCACTGACCAT
ATTTCCTCATTTATGTTTAAGCTCATGTTAATCATATACTAAAATAAATAAAAGTGAAAATAAG
TCAAATTTCATTCCAATTACTTCCTTTGTATTTATTTGTTCAGATTGGACTTCTAACTCGTTCA
AATGCATAATTATCTTTAAGTTTAACATTCACTAGTATCAATTTTGTAATCACAAATTTCCTTG
GATGAATCAATAGTTTCCCATATTTTTGTACTGTTGGAACTGTGTAATGAAGGTATACATTTCT
CTTTTCAGCAGGCCTTTCCGTGGTTTCTATTTTACTCACAGTTTATGCTGCTATGTCACTATTA
TATGCTATTATTGTGCTTGCTATATAACCTTTTCTTACTGTATTATTTTTTCTCCGTCATCCGC
AGGAGTTGCCCCGAGGTGGGGTCCTTTATGGTTATCGCATTGATGGACCTCGAAATTGGCATGA
AGGGCATCGATTTGACGATAGCATTATTTTGATTGATCCTTACGCAAAACTAATTGAAGGTCGA
CGAGCTTTTGGAGATGAAAGCAATAAAATGTGTAGATTTTTTGGAACTTATGATTTCAATAGCT
TGCCTTTTGACTGGGGAGAAAATTACAAGCTTCCAAATGTACCGGAGGTAGATTGAGAAGAACT
ACTTGAATAACTTTTTTCCTCGTGTGCAAATCTAAAGATAATTTGCTTGCATGTTCAGCTATTT
GACTTATGAGCTATGACTAGTGACAGAGCTGTCATTTTGTAAGTGCTCAAATTGTCTGCCATTT
AGTTGATCTTGTTATTTCAAGTAAGAGGAGTTTCAGCTTAATCTTCTGTAGTAATATTATTGGT
TCTTTGGTAGATTGAGCTGTAAGATTATAGTACTTAGATCTTTTATAACATTTTACTCTTAAGG
ATAGTTCGATTTGCATTTTACTTATGAGTGGATTATAATGTAGGGACTGCTTGTGTGGTGATTA
ATATGTAACAGATTGCTATGCAGTCATTAACGATCAAGGAATTGTTGTGTAGTGATTAAGAGAT
TATTGCCATACAAGAATAACCTTTTTTTAGTGACATTCTTGTCTTTGAATAGTCTAATCTCTGT
ATGGCTAATACACGTATTCTTGTTTCACATTGTATCTAGTATATAATATCACATAGATTCTCGT
ATAACTGAAGTTGTATTATTTGGATACCACCAACCAAATGTTGCATTACATAATGCGCGATTGT
GCAACCAACCAAATGTTGTGTTATTCTATGCCCGAATATTTGCTGGATTTGTTACCACACAATC
AACCAAACCAACCATTAACTCCTTGCAGTATATCCTCTTTTCTTTGGGCAGAAAGATCTTGTTA
TATATGAGATGAATGTTCGTGCTTTTACTGCTGATGAAACAAGTAGTTTGGATCAAGATCAACG
GGGAAGTTACCTTGGCTTAATTGAAAAGGTACTTCCATATTCTACTTGTCTATTTTCTCTTTTA
CCAACTACTAGCATTTCATTTGTTTGTTGAAGTTTGGTGTATCTTCCTTAATAGCAGTACTGCA
AGTTACACCACGAGTTAACTTCCCAAATACTTACATTTTTGTTTTGGCAAGGTCCAATTTTAAA
ATTGCTTTATATGTTCTTTGGCCCTTTTTCTTAGATTAGATGTCTTTGATATTTTCATCATATA
CTAGTCACTTGCAGTAATCTGTTAAACTTATTTTAGTCTTTCAGTTATCTGACATTCATCTACA
AATGCAGATACCACATCTTCTCGAGCTTGGTGTCAATACAGTAGAATTATTGCCTGTTTTTGAG
TTTGATGAACTGGAATTACAAAGGCGACCTAATCCGAGAGATCACATG
						
					

			
		

Sequences
Splice junction sequence	ACATCTTCTCGAGCTTGGTGTCAATACAGTAGAATTATTGCCTGTTTTTGAGTTTGATGAACTG GAATTACAAAGGCGACCTAATCCGAGAGATCACATGtgttcatgatggaatgattgaattagca ttggatccacagaagaaccgcaccggagacatatggcacatatgcattaaggtagtaatttaac tattttat
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: 526 Transcript exons: 3159038-3159116,3160960-3161196,3161905-3162009,3162309- 3162413 TGTTCATGATGGAATGATTGAATTAGCATTGGATCCACAGAAGAACCGCACCGGAGACATATGG CACATATGCATTAAGGAGTTGCCCCGAGGTGGGGTCCTTTATGGTTATCGCATTGATGGACCTC GAAATTGGCATGAAGGGCATCGATTTGACGATAGCATTATTTTGATTGATCCTTACGCAAAACT AATTGAAGGTCGACGAGCTTTTGGAGATGAAAGCAATAAAATGTGTAGATTTTTTGGAACTTAT GATTTCAATAGCTTGCCTTTTGACTGGGGAGAAAATTACAAGCTTCCAAATGTACCGGAGAAAG ATCTTGTTATATATGAGATGAATGTTCGTGCTTTTACTGCTGATGAAACAAGTAGTTTGGATCA AGATCAACGGGGAAGTTACCTTGGCTTAATTGAAAAGATACCACATCTTCTCGAGCTTGGTGTC AATACAGTAGAATTATTGCCTGTTTTTGAGTTTGATGAACTGGAATTACAAAGGCGACCTAATC CGAGAGATCACATG
Genomic sequence	TGTTCATGATGGAATGATTGAATTAGCATTGGATCCACAGAAGAACCGCACCGGAGACATATGG CACATATGCATTAAGGTAGTAATTTAACTATTTTATGTACCTTCATTACTGTATTCACTCAGCA ATCTTCAAAGATTATATGATTTGGATGCTCATCGTATCATGTTGGCTGTCCACTTTCTACTCTC TTTTTGCTATTAATTGACCTGCTCCCTATTGTAGGCAGTGTCAAATGATTGATCTCCTTCCTTA ATGAATACTCAAATGTGTCCATAGTTTCAATATAAAGTAAACATATTGTGGTTTTCTGTTACAT TTTTAAAAGAGAAGTTAACATATTGTAGTTAGAACTGAATGTCATCCAATTGTATGTCCAATGA TTATTTGAATTTAATTTATCTTTCCTGTTATTCTGTCGAATAAAAACATTTCAAATCCTTTCTG TAGAGTCATTGAGTTGTCCTAGTAAGTCAAATGACCTCACATATTTGGTAGGGTATCTAGCAAT TCTTTGACCTTGACCTCACATGTTTCCAACTTTTATTGAGAATATCCCAACTAAGTAAAACACA TAAACTAATGAAACTTTCTTTCCTTAAATTTCCATGCTGGAGCTGGAAGGAAGTAGTTCACTTC AGATAGATGCATGGAATATGGATCTTGCTAATCTGAAAGGATTAAATAAAGGGATAAATTAAGA TGAAAGAGAAGTAATGTAAATGTTGATTGTGTTAATTAATATGATTTTAGGAGACTTTATTTTT CCTTTCCTAGCATTATTGTAGGAACAAAATATTTTTTTTTTATTGTAAATTGATTGTCTTTCCT TAGTAAGGGTCCATTGCAAACTACCCCTTCTCTTTAAGAACCCTAATTGATTGTAGTAGACCTA GTTAGCATATTAGGGATGATCATGTTTAAGCATATTAGGGATGATCATGTGTACTAGCAGATTC AATTCAAGAACTTGGATGATTGCGATCTAGACCCCTAATTGAATAATTAAAGACAATAATAATA CAAGACTAGTTACATTCTCCACTTAATCGAATAAGAACCATATATATCAAGCAAAGAGTTTAAT ATTACCTCTTAAAAAATCGTTCTTGTAAGGTTGTACAAGAAATCCTAAGTAACCAATACACGAA GATATGAATAAATAAAATCTCAATTTTATTGATAGCTATTCTGTGTCAAAAAGAATGAAATCAA CGTGGGTGAATCTAGGGTAAATTTCTAAAACACTATCCCAAATAGCACGAGATTCAATATCTAC TTTATGGAAATAATAGATAATAAAACCTAACTAGGAAACTTTAAACTAGGAAAATTGAACTAGA CAATTTTTAAACCAGGAAAACATGGAAGATTAATGTCACACTAATTCTAGAACTACCTAACAAA ATAAGGAAAGAAGTGTCCAATTTTCTCCTGAAAATACGCCTATTCCAACAGACTTGTGCATGTA TTTCAGCCTCTTTTGGGGATCCATACATGCTATTAGGTTGGCTATATGAATCTTCACTGACCAT ATTTCCTCATTTATGTTTAAGCTCATGTTAATCATATACTAAAATAAATAAAAGTGAAAATAAG TCAAATTTCATTCCAATTACTTCCTTTGTATTTATTTGTTCAGATTGGACTTCTAACTCGTTCA AATGCATAATTATCTTTAAGTTTAACATTCACTAGTATCAATTTTGTAATCACAAATTTCCTTG GATGAATCAATAGTTTCCCATATTTTTGTACTGTTGGAACTGTGTAATGAAGGTATACATTTCT CTTTTCAGCAGGCCTTTCCGTGGTTTCTATTTTACTCACAGTTTATGCTGCTATGTCACTATTA TATGCTATTATTGTGCTTGCTATATAACCTTTTCTTACTGTATTATTTTTTCTCCGTCATCCGC AGGAGTTGCCCCGAGGTGGGGTCCTTTATGGTTATCGCATTGATGGACCTCGAAATTGGCATGA AGGGCATCGATTTGACGATAGCATTATTTTGATTGATCCTTACGCAAAACTAATTGAAGGTCGA CGAGCTTTTGGAGATGAAAGCAATAAAATGTGTAGATTTTTTGGAACTTATGATTTCAATAGCT TGCCTTTTGACTGGGGAGAAAATTACAAGCTTCCAAATGTACCGGAGGTAGATTGAGAAGAACT ACTTGAATAACTTTTTTCCTCGTGTGCAAATCTAAAGATAATTTGCTTGCATGTTCAGCTATTT GACTTATGAGCTATGACTAGTGACAGAGCTGTCATTTTGTAAGTGCTCAAATTGTCTGCCATTT AGTTGATCTTGTTATTTCAAGTAAGAGGAGTTTCAGCTTAATCTTCTGTAGTAATATTATTGGT TCTTTGGTAGATTGAGCTGTAAGATTATAGTACTTAGATCTTTTATAACATTTTACTCTTAAGG ATAGTTCGATTTGCATTTTACTTATGAGTGGATTATAATGTAGGGACTGCTTGTGTGGTGATTA ATATGTAACAGATTGCTATGCAGTCATTAACGATCAAGGAATTGTTGTGTAGTGATTAAGAGAT TATTGCCATACAAGAATAACCTTTTTTTAGTGACATTCTTGTCTTTGAATAGTCTAATCTCTGT ATGGCTAATACACGTATTCTTGTTTCACATTGTATCTAGTATATAATATCACATAGATTCTCGT ATAACTGAAGTTGTATTATTTGGATACCACCAACCAAATGTTGCATTACATAATGCGCGATTGT GCAACCAACCAAATGTTGTGTTATTCTATGCCCGAATATTTGCTGGATTTGTTACCACACAATC AACCAAACCAACCATTAACTCCTTGCAGTATATCCTCTTTTCTTTGGGCAGAAAGATCTTGTTA TATATGAGATGAATGTTCGTGCTTTTACTGCTGATGAAACAAGTAGTTTGGATCAAGATCAACG GGGAAGTTACCTTGGCTTAATTGAAAAGGTACTTCCATATTCTACTTGTCTATTTTCTCTTTTA CCAACTACTAGCATTTCATTTGTTTGTTGAAGTTTGGTGTATCTTCCTTAATAGCAGTACTGCA AGTTACACCACGAGTTAACTTCCCAAATACTTACATTTTTGTTTTGGCAAGGTCCAATTTTAAA ATTGCTTTATATGTTCTTTGGCCCTTTTTCTTAGATTAGATGTCTTTGATATTTTCATCATATA CTAGTCACTTGCAGTAATCTGTTAAACTTATTTTAGTCTTTCAGTTATCTGACATTCATCTACA AATGCAGATACCACATCTTCTCGAGCTTGGTGTCAATACAGTAGAATTATTGCCTGTTTTTGAG TTTGATGAACTGGAATTACAAAGGCGACCTAATCCGAGAGATCACATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.517210323

Conservation Information
Conserved circRNAs	NA
PMCS	0.517210323

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3159052-3159043(+)
3162371-3159043(+)
						
						Potential amino acid sequence
						
							MIELALDPQKNRTGDIWHICIKELPRGGVLYGYRIDGPRNWHEGHRFDDSIILIDPYAKLIEGR
RAFGDESNKMCRFFGTYDFNSLPFDWGENYKLPNVPEKDLVIYEMNVRAFTADETSSLDQDQRG
SYLGLIEKIPHLLELGVNTVELLPVFEFDELELQRRPNPRDHMCS*(+)
MNWNYKGDLIREITCVHDGMIELALDPQKNRTGDIWHICIKELPRGGVLYGYRIDGPRNWHEGH
RFDDSIILIDPYAKLIEGRRAFGDESNKMCRFFGTYDFNSLPFDWGENYKLPNVPEKDLVIYEM
NVRAFTADETSSLDQDQRGSYLGLIEKIPHLLELGVNTVELLPVFEFDELELQRRPNPRDHMCS
*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3159052-3159043(+) 3162371-3159043(+)
Potential amino acid sequence	MIELALDPQKNRTGDIWHICIKELPRGGVLYGYRIDGPRNWHEGHRFDDSIILIDPYAKLIEGR RAFGDESNKMCRFFGTYDFNSLPFDWGENYKLPNVPEKDLVIYEMNVRAFTADETSSLDQDQRG SYLGLIEKIPHLLELGVNTVELLPVFEFDELELQRRPNPRDHMCS(+) MNWNYKGDLIREITCVHDGMIELALDPQKNRTGDIWHICIKELPRGGVLYGYRIDGPRNWHEGH RFDDSIILIDPYAKLIEGRRAFGDESNKMCRFFGTYDFNSLPFDWGENYKLPNVPEKDLVIYEM NVRAFTADETSSLDQDQRGSYLGLIEKIPHLLELGVNTVELLPVFEFDELELQRRPNPRDHMCS (+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016; Tan et al., 2017; Yin et al., 2018

circRNA

Detail information of Solyc06g009220.2_circ_g.4

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