Plant Circular RNA Database

Detail information of Solyc06g083870.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc06g083870.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_002130
					
						Alias
						6:45464469|45465850
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr6: 49174469-49175850  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc06g083870.2						
					
						Parent gene annotation
						
							Structural maintenance of chromosomes protein 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc06g083870.2_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  
						
							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
						Solyc06g083870.2.1:2

General Information
CircRNA Name	Solyc06g083870.2_circ_g.2
ID in PlantcircBase	sly_circ_002130
Alias	6:45464469\|45465850
Organism	Solanum lycopersicum
Position	chr6: 49174469-49175850 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc06g083870.2
Parent gene annotation	Structural maintenance of chromosomes protein 1
Parent gene strand	+
Alternative splicing	Solyc06g083870.2_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	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	Solyc06g083870.2.1:2

			
						 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  
						
							TGTCTTGCAGAAAAGTATTGCAGACAAACTTCAAAATTTGGAACGCGAAAAGGGGAGTATTGAA
AATGAAATTAGACATATCCAGCCTGAACTTGAGCAGtgcttaagaagaaaaaagaaggtctcga
gtcagagttggaggagcttggatcaataagggagatgcagcttaaggagtctgaagcatctggc
agaatcag

									
								

					

						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: 230
Transcript exons: 49174469-49174608,49175761-49175850
TGCTTAAGAAGAAAAAAGAAGGTCTCGAGTCAGAGTTGGAGGAGCTTGGATCAATAAGGGAGAT
GCAGCTTAAGGAGTCTGAAGCATCTGGCAGAATCAGTGGACTTGAGAAAAAGATTCACTATGCT
GAGATTGAAAAGAAAAGTATTGCAGACAAACTTCAAAATTTGGAACGCGAAAAGGGGAGTATTG
AAAATGAAATTAGACATATCCAGCCTGAACTTGAGCAG
						
					

						Genomic sequence
						
							TGCTTAAGAAGAAAAAAGAAGGTCTCGAGTCAGAGTTGGAGGAGCTTGGATCAATAAGGGAGAT
GCAGCTTAAGGAGTCTGAAGCATCTGGCAGAATCAGTGGACTTGAGAAAAAGATTCACTATGCT
GAGATTGAAAAGGTTTTTGACTATCTATTTTTAAAGTTTTGTGAGCCCTCATATTAGTCATTTG
AGATTCATACATTGTCATCTATTTTCGGTTTAAGATGCCTTGTAGCTTCTTATATAGAAACTTC
CTTCCTGATAAAGTTTGATATTGTGAAGGGGGAGTATGGTTATTGTATCTCTAAACTTTGTAGT
TTGCTGAGGTTCTTGTGTGTTTTCTTGGGTCCAACTCCATGTTTATTGCCTTTGTGCCAGTTTC
TACAACACTATTTTGAGATTTCTCAAATACTTGACATGTTTTGCTGATAAAAAAGTACTCAAGA
CACATTATAGAAATAATATGGTTTAGTTAACTCAATTCTTTCAAGAAATAAAATTTATTTAACA
GTTTAAAATCCAAATTTGCTCTGATGTTTCAATTATTCTAATATTTTCTGCTGCTTTTGCTGTT
AATACACAAGTCAAGTGGACTGCCAAACTCTCTGTCTGATCATTTCATGTCAACATTAAACAGA
CTGAAGTAAGCTATTAGTGAGGACCACCAACAATATAGCTTGTTTTGTTTCTTTGAGGAAAGTA
ACTAGTTTATATATTTATATATATATATATATATATATAAGGATAAACAATTGCTTAATAATCA
ATTCCTATGATCATAAACATTGGTATTTTGTTCTTAGGGCCACCCTGAGCATCATATCCTCATG
TTGATTGGTTCTTTCAGTCTCAATCTAGTGCTCATCAAGTTGATGGCACTTTGGAAATGAAAGG
GTGTTAAAGTTTTGCTTTATACTCGACTGATTTATTGCTGCAACTTATTTGTTGATGGACAATA
TCTGAAGAAGGAACTCTGCCTATACTCTTCATTTCTTCTTTGATACATTATGGTAAAAAAAGAT
GGCATACTCACATTTATTTATACTTCCAAATGTTCAAATTCTTTGAAAAATAAACTTTATTTAC
ACTTTGGATCTACTTCTGTTTACATATTTTTGGAGAGTCCGAGCAACGTAGTGGCTCAATAGTC
GTGGTGTCTTTTGCCCTAGCTTTTCACTTCTTTCATAGCTTATTAATTCTGTATCCCTGTTAAT
GTACTGTCGCTTATTGGCCTTTTCATTTGTATATGTTCTGCATCTTGTAATGCTGACAGCTTGA
GTTGTCTTGCAGAAAAGTATTGCAGACAAACTTCAAAATTTGGAACGCGAAAAGGGGAGTATTG
AAAATGAAATTAGACATATCCAGCCTGAACTTGAGCAG
						
					

			
		

Sequences
Splice junction sequence	TGTCTTGCAGAAAAGTATTGCAGACAAACTTCAAAATTTGGAACGCGAAAAGGGGAGTATTGAA AATGAAATTAGACATATCCAGCCTGAACTTGAGCAGtgcttaagaagaaaaaagaaggtctcga gtcagagttggaggagcttggatcaataagggagatgcagcttaaggagtctgaagcatctggc agaatcag
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: 230 Transcript exons: 49174469-49174608,49175761-49175850 TGCTTAAGAAGAAAAAAGAAGGTCTCGAGTCAGAGTTGGAGGAGCTTGGATCAATAAGGGAGAT GCAGCTTAAGGAGTCTGAAGCATCTGGCAGAATCAGTGGACTTGAGAAAAAGATTCACTATGCT GAGATTGAAAAGAAAAGTATTGCAGACAAACTTCAAAATTTGGAACGCGAAAAGGGGAGTATTG AAAATGAAATTAGACATATCCAGCCTGAACTTGAGCAG
Genomic sequence	TGCTTAAGAAGAAAAAAGAAGGTCTCGAGTCAGAGTTGGAGGAGCTTGGATCAATAAGGGAGAT GCAGCTTAAGGAGTCTGAAGCATCTGGCAGAATCAGTGGACTTGAGAAAAAGATTCACTATGCT GAGATTGAAAAGGTTTTTGACTATCTATTTTTAAAGTTTTGTGAGCCCTCATATTAGTCATTTG AGATTCATACATTGTCATCTATTTTCGGTTTAAGATGCCTTGTAGCTTCTTATATAGAAACTTC CTTCCTGATAAAGTTTGATATTGTGAAGGGGGAGTATGGTTATTGTATCTCTAAACTTTGTAGT TTGCTGAGGTTCTTGTGTGTTTTCTTGGGTCCAACTCCATGTTTATTGCCTTTGTGCCAGTTTC TACAACACTATTTTGAGATTTCTCAAATACTTGACATGTTTTGCTGATAAAAAAGTACTCAAGA CACATTATAGAAATAATATGGTTTAGTTAACTCAATTCTTTCAAGAAATAAAATTTATTTAACA GTTTAAAATCCAAATTTGCTCTGATGTTTCAATTATTCTAATATTTTCTGCTGCTTTTGCTGTT AATACACAAGTCAAGTGGACTGCCAAACTCTCTGTCTGATCATTTCATGTCAACATTAAACAGA CTGAAGTAAGCTATTAGTGAGGACCACCAACAATATAGCTTGTTTTGTTTCTTTGAGGAAAGTA ACTAGTTTATATATTTATATATATATATATATATATATAAGGATAAACAATTGCTTAATAATCA ATTCCTATGATCATAAACATTGGTATTTTGTTCTTAGGGCCACCCTGAGCATCATATCCTCATG TTGATTGGTTCTTTCAGTCTCAATCTAGTGCTCATCAAGTTGATGGCACTTTGGAAATGAAAGG GTGTTAAAGTTTTGCTTTATACTCGACTGATTTATTGCTGCAACTTATTTGTTGATGGACAATA TCTGAAGAAGGAACTCTGCCTATACTCTTCATTTCTTCTTTGATACATTATGGTAAAAAAAGAT GGCATACTCACATTTATTTATACTTCCAAATGTTCAAATTCTTTGAAAAATAAACTTTATTTAC ACTTTGGATCTACTTCTGTTTACATATTTTTGGAGAGTCCGAGCAACGTAGTGGCTCAATAGTC GTGGTGTCTTTTGCCCTAGCTTTTCACTTCTTTCATAGCTTATTAATTCTGTATCCCTGTTAAT GTACTGTCGCTTATTGGCCTTTTCATTTGTATATGTTCTGCATCTTGTAATGCTGACAGCTTGA GTTGTCTTGCAGAAAAGTATTGCAGACAAACTTCAAAATTTGGAACGCGAAAAGGGGAGTATTG AAAATGAAATTAGACATATCCAGCCTGAACTTGAGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.728136172

Conservation Information
Conserved circRNAs	NA
PMCS	0.728136172

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							49174593-49174472(+)
49174532-49174522(+)
						
						Potential amino acid sequence
						
							MLRLKRKVLQTNFKIWNAKRGVLKMKLDISSLNLSSA*(+)
MQLKESEASGRISGLEKKIHYAEIEKKSIADKLQNLEREKGSIENEIRHIQPELEQCLRRKKKV
SSQSWRSLDQ*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	49174593-49174472(+) 49174532-49174522(+)
Potential amino acid sequence	MLRLKRKVLQTNFKIWNAKRGVLKMKLDISSLNLSSA(+) MQLKESEASGRISGLEKKIHYAEIEKKSIADKLQNLEREKGSIENEIRHIQPELEQCLRRKKKV SSQSWRSLDQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc06g083870.2_circ_g.2

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