Plant Circular RNA Database

Detail information of Solyc05g009870.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc05g009870.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_001649
					
						Alias
						5:4080912|4083836
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr5: 4080912-4083836  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI, circseq_cup
					
						Parent gene
						
							Solyc05g009870.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc05g009870.2_circ_g.2 						
					
						Support reads
						45
					
						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
						Solyc05g009870.2.1:5

General Information
CircRNA Name	Solyc05g009870.2_circ_g.1
ID in PlantcircBase	sly_circ_001649
Alias	5:4080912\|4083836
Organism	Solanum lycopersicum
Position	chr5: 4080912-4083836 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI, circseq_cup
Parent gene	Solyc05g009870.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc05g009870.2_circ_g.2
Support reads	45
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	Solyc05g009870.2.1:5

			
						 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  
						
							GTGTCATACATGTCGATCATGAGGCATTGATGGAGCAGGTAATGAGAATCTACCCCTTGCTACA
ACCACATGAAACAACCAAAGTGGAACGAAAACAACCcgcaaatcttcagaagagtaaatgctgt
tgctgctatgaagaagaccatagcgattgcaacccagaagtgctgagacatagatgataagacg
acttttag

									
								

					

						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: 386
Transcript exons: 4080912-4083836
CGCAAATCTTCAGAAGAGTAAATGCTGTTGCTGCTATGAAGAAGACCATAGCGATTGCAACCCA
GAAGTGAGGAAGGGTCTCCCATATAGCCTCATCACTCATGCTTTCTTCATCTCCAGGCATCAGC
GCCCTGCACATTCTAACATTATCAACCAAGATAGCAATTTCAAGTGCAAGCAGGGGAAAGAACA
CAATCTTCAAACTTACAGCATAGGCGCTGTCGAGATGGATACAAAGAAGTAGTTCAAAAGCAAC
AAGCAGCGGTGTTGCCATGACAGCATGAAATGGTGCCCAATGTCGATCATGAGGCATTGATGGA
GCAGGTAATGAGAATCTACCCCTTGCTACAACCACATGAAACAACCAAAGTGGAACGAAAACAA
CC
						
					

						Genomic sequence
						
							CGCAAATCTTCAGAAGAGTAAATGCTGTTGCTGCTATGAAGAAGACCATAGCGATTGCAACCCA
GAAGTGCTGAGACATAGATGATAAGACGACTTTTAGAAACTACCAATGTGCACATATTAGTGGA
AATTGTATGTACCAATCAATCACAGTTTCAAATAGCTTTCACATCAATAGGGTACAACACAAAG
CATATGAATTCAAGGCACATAACACCAGACTGCATATAGCTGAAAAAAGTACTTAAAAAGTCTG
GTTCAAATATGCAATTAAACTGTTTGTTCCTAATATGTGCAACTCCTCAGCATAAACTGTGTTT
GAACGCTATTTTCACAGGTGAGGAGATAGCAGTCAACTCACAAAAGATCCGAATTTAAGAGTGC
ACTTCCTTTGAAACCCCGTAAAATAACATCTACGCTCTTTCGTTTACAGATTCATGCAAGTGAA
GAAATCAGGTTTCTAAGCTGGTCATTCTAAAAGGTATAATAGATATTACTATTAGATTCTTCCC
AATAAATAAGCTACAGGAATGACATGATTGTTAACTGTAGTTTCTTAAAATGAATGGGATATCT
TTACTTACAGGAAGGGTCTCCCATATAGCCTCATCACTCATGCTTTCTTCATCTCCAGGCATCA
GCGCCCTGCACATTCTGAGCATGGGGAGAAGTTCAAAAGGAATTAGATAAACATCCAAAACCAA
GACCAATAATTTACATGCTTTGAAGTACCGCAAAAAATATATGTTTGGACATCTTATCACAAAT
CTCTTTATTCCAAAAAGGCATAATACATAAACACAGACACTCAAACATGGCCTCAAATGGCCAA
ATAAACACTCCAACTTTGAGTATGCACATCTAGAAACTTCAACTCTTCTCCACTATATCAGCTG
CACATTCCAACTTAAAGAATGTTCATCTAGACACCTCCAAAGTTTATGTGCCACATCAGCATCT
GCTGTCTACGAGACACACTGGGGACGAGTTGGAGTATTCTGTTGCCAGTTGAGACCAAATTGAG
GTGTCTATATGTGCACTCCTCAAAGTTGGAGTGCTTATTGTCAACTGAGGCCAAGTTTGAGTGT
GTGTTTAAGGGCCCGTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGT
ATTATGCCTCCCCAAAAATAATTCAACTGCCACCAGATGGCTTAAAAGTTCAGCATTTCTTGGC
AGGAAAAGTATCTTACCTAACATTATCAACCAAGATAGCAATTTCAAGTGCAAGCAGGGGAAAG
AACACAATCTTCAAACTTACAGCTGCAATTATCCACAGTTCACAAATAAGTGGCTTCGCTTATA
TGAAGTAGCATTGCATATCAAATTTAAAGAGAGAAAGAAATGATACAAGATTTAAACAGATGAA
ATTAAGATTTTGCACGATCAAGGCACTGAAAGGTAAGTAATAGGTTAAAGGAAAAAGGTTAAGG
TAGAGTTGCAAGTCTAGTGAAAATGCCCCTAGTAACTAGACGTGAGTGAACAACATTACGAATC
AGCAAGAAGGCAGTAAGCAGTTGCTTATAGATGCATCAGATAATGATGTTCTAAGGAAATTTTC
TTGTTTACCATAGGCGCTGTCGAGATGGATACAAAGAAGTAGTTCAAAAGCAACAAGCAGCGGT
GTCGCCATGACAGCATGAAATGGTGCCCACTGTTCATGAAGGAATATGTGCTTGTGTCACTATT
CAGCTTTTTGAAAATATACAAACAGCAATGACTGGCACATGAAACGTTGAATCTAAAAATCAGA
AATGTTAATGTGTCATACATGTCGATCATGAGGCATTGATGGAGCAGGTAATGAGAATCTACCC
CTTGCTACAACCACATGAAACAACCAAAGTGGAACGAAAACAACC
						
					

			
		

Sequences
Splice junction sequence	GTGTCATACATGTCGATCATGAGGCATTGATGGAGCAGGTAATGAGAATCTACCCCTTGCTACA ACCACATGAAACAACCAAAGTGGAACGAAAACAACCcgcaaatcttcagaagagtaaatgctgt tgctgctatgaagaagaccatagcgattgcaacccagaagtgctgagacatagatgataagacg acttttag
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: 386 Transcript exons: 4080912-4083836 CGCAAATCTTCAGAAGAGTAAATGCTGTTGCTGCTATGAAGAAGACCATAGCGATTGCAACCCA GAAGTGAGGAAGGGTCTCCCATATAGCCTCATCACTCATGCTTTCTTCATCTCCAGGCATCAGC GCCCTGCACATTCTAACATTATCAACCAAGATAGCAATTTCAAGTGCAAGCAGGGGAAAGAACA CAATCTTCAAACTTACAGCATAGGCGCTGTCGAGATGGATACAAAGAAGTAGTTCAAAAGCAAC AAGCAGCGGTGTTGCCATGACAGCATGAAATGGTGCCCAATGTCGATCATGAGGCATTGATGGA GCAGGTAATGAGAATCTACCCCTTGCTACAACCACATGAAACAACCAAAGTGGAACGAAAACAA CC
Genomic sequence	CGCAAATCTTCAGAAGAGTAAATGCTGTTGCTGCTATGAAGAAGACCATAGCGATTGCAACCCA GAAGTGCTGAGACATAGATGATAAGACGACTTTTAGAAACTACCAATGTGCACATATTAGTGGA AATTGTATGTACCAATCAATCACAGTTTCAAATAGCTTTCACATCAATAGGGTACAACACAAAG CATATGAATTCAAGGCACATAACACCAGACTGCATATAGCTGAAAAAAGTACTTAAAAAGTCTG GTTCAAATATGCAATTAAACTGTTTGTTCCTAATATGTGCAACTCCTCAGCATAAACTGTGTTT GAACGCTATTTTCACAGGTGAGGAGATAGCAGTCAACTCACAAAAGATCCGAATTTAAGAGTGC ACTTCCTTTGAAACCCCGTAAAATAACATCTACGCTCTTTCGTTTACAGATTCATGCAAGTGAA GAAATCAGGTTTCTAAGCTGGTCATTCTAAAAGGTATAATAGATATTACTATTAGATTCTTCCC AATAAATAAGCTACAGGAATGACATGATTGTTAACTGTAGTTTCTTAAAATGAATGGGATATCT TTACTTACAGGAAGGGTCTCCCATATAGCCTCATCACTCATGCTTTCTTCATCTCCAGGCATCA GCGCCCTGCACATTCTGAGCATGGGGAGAAGTTCAAAAGGAATTAGATAAACATCCAAAACCAA GACCAATAATTTACATGCTTTGAAGTACCGCAAAAAATATATGTTTGGACATCTTATCACAAAT CTCTTTATTCCAAAAAGGCATAATACATAAACACAGACACTCAAACATGGCCTCAAATGGCCAA ATAAACACTCCAACTTTGAGTATGCACATCTAGAAACTTCAACTCTTCTCCACTATATCAGCTG CACATTCCAACTTAAAGAATGTTCATCTAGACACCTCCAAAGTTTATGTGCCACATCAGCATCT GCTGTCTACGAGACACACTGGGGACGAGTTGGAGTATTCTGTTGCCAGTTGAGACCAAATTGAG GTGTCTATATGTGCACTCCTCAAAGTTGGAGTGCTTATTGTCAACTGAGGCCAAGTTTGAGTGT GTGTTTAAGGGCCCGTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGT ATTATGCCTCCCCAAAAATAATTCAACTGCCACCAGATGGCTTAAAAGTTCAGCATTTCTTGGC AGGAAAAGTATCTTACCTAACATTATCAACCAAGATAGCAATTTCAAGTGCAAGCAGGGGAAAG AACACAATCTTCAAACTTACAGCTGCAATTATCCACAGTTCACAAATAAGTGGCTTCGCTTATA TGAAGTAGCATTGCATATCAAATTTAAAGAGAGAAAGAAATGATACAAGATTTAAACAGATGAA ATTAAGATTTTGCACGATCAAGGCACTGAAAGGTAAGTAATAGGTTAAAGGAAAAAGGTTAAGG TAGAGTTGCAAGTCTAGTGAAAATGCCCCTAGTAACTAGACGTGAGTGAACAACATTACGAATC AGCAAGAAGGCAGTAAGCAGTTGCTTATAGATGCATCAGATAATGATGTTCTAAGGAAATTTTC TTGTTTACCATAGGCGCTGTCGAGATGGATACAAAGAAGTAGTTCAAAAGCAACAAGCAGCGGT GTCGCCATGACAGCATGAAATGGTGCCCACTGTTCATGAAGGAATATGTGCTTGTGTCACTATT CAGCTTTTTGAAAATATACAAACAGCAATGACTGGCACATGAAACGTTGAATCTAAAAATCAGA AATGTTAATGTGTCATACATGTCGATCATGAGGCATTGATGGAGCAGGTAATGAGAATCTACCC CTTGCTACAACCACATGAAACAACCAAAGTGGAACGAAAACAACC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.073970692

Conservation Information
Conserved circRNAs	NA
PMCS	0.073970692

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4083620-4083574(+)
4083807-4080979(+)
4081513-4083798(-)
4083765-4083798(-)
						
						Potential amino acid sequence
						
							MVPNVDHEALMEQVMRIYPLLQPHETTKVERKQPANLQKSKCCCCYEEDHSDCNPEVRKGLPYS
LITHAFFISRHQRPAHSNIINQDSNFKCKQGKEHNLQTYSIGAVEMDTKK*(+)
MKQPKWNENNPQIFRRVNAVAAMKKTIAIATQK*(+)
MGDPSSLLGCNRYGLLHSSNSIYSSEDLRVVFVPLWLFHVVVARGRFSLPAPSMPHDRHWAPFH
AVMATPLLVAFELLLCIHLDSAYAVSLKIVFFPLLALEIAILVDNVRMCRALMPGDEESMSDEA
IWETLPHFWVAIAMVFFIAATAFTLLKICGLFSFHFGCFMWL*(-)
MPHDRHWAPFHAVMATPLLVAFELLLCIHLDSAYAVSLKIVFFPLLALEIAILVDNVRMCRALM
PGDEESMSDEAIWETLPHFWVAIAMVFFIAATAFTLLKICGLFSFHFGCFMWL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4083620-4083574(+) 4083807-4080979(+) 4081513-4083798(-) 4083765-4083798(-)
Potential amino acid sequence	MVPNVDHEALMEQVMRIYPLLQPHETTKVERKQPANLQKSKCCCCYEEDHSDCNPEVRKGLPYS LITHAFFISRHQRPAHSNIINQDSNFKCKQGKEHNLQTYSIGAVEMDTKK(+) MKQPKWNENNPQIFRRVNAVAAMKKTIAIATQK(+) MGDPSSLLGCNRYGLLHSSNSIYSSEDLRVVFVPLWLFHVVVARGRFSLPAPSMPHDRHWAPFH AVMATPLLVAFELLLCIHLDSAYAVSLKIVFFPLLALEIAILVDNVRMCRALMPGDEESMSDEA IWETLPHFWVAIAMVFFIAATAFTLLKICGLFSFHFGCFMWL(-) MPHDRHWAPFHAVMATPLLVAFELLLCIHLDSAYAVSLKIVFFPLLALEIAILVDNVRMCRALM PGDEESMSDEAIWETLPHFWVAIAMVFFIAATAFTLLKICGLFSFHFGCFMWL(-)
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 Solyc05g009870.2_circ_g.1

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