Plant Circular RNA Database

Detail information of Solyc03g032150.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc03g032150.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_000946
					
						Alias
						3:8936459|8936821
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr3: 4656225-4656587  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI, circseq_cup
					
						Parent gene
						
							Solyc03g032150.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc03g032150.2_circ_g.1 Solyc03g032150.2_circ_g.2 Solyc03g032150.2_circ_g.4 Solyc03g032150.2_circ_g.5 						
					
						Support reads
						21/35
					
						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
						Solyc03g032150.2.1:2

General Information
CircRNA Name	Solyc03g032150.2_circ_g.3
ID in PlantcircBase	sly_circ_000946
Alias	3:8936459\|8936821
Organism	Solanum lycopersicum
Position	chr3: 4656225-4656587 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI, circseq_cup
Parent gene	Solyc03g032150.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc03g032150.2_circ_g.1 Solyc03g032150.2_circ_g.2 Solyc03g032150.2_circ_g.4 Solyc03g032150.2_circ_g.5
Support reads	21/35
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	Solyc03g032150.2.1:2

			
						 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  
						
							AATTGCCATAGGAGCAGCACGGGGCTTAGCGTTCTTACATACTTCAGAAAAGAAAGTTATTTAC
AGAGACTTCAAAGCCTCAAACATACTGCTTGATGGGtcagaagtgaactttttaggaaggcttt
cgcatcctaaccttgttaaactactgggatattgtcatgaggacaaggaactgttactcgttta
cgaattta

						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: 279
Transcript exons: 4656225-4656360,4656445-4656587
TCAGAAGTGAACTTTTTAGGAAGGCTTTCGCATCCTAACCTTGTTAAACTACTGGGATATTGTC
ATGAGGACAAGGAACTGTTACTCGTTTACGAATTTATGCCCAAGGGGAGCTTGGAAAACCATCT
TTTTAGAAGGAGTGCTGCTATTGAACCGCTTTCTTGGGACTTGCGGCTCAAAATTGCCATAGGA
GCAGCACGGGGCTTAGCGTTCTTACATACTTCAGAAAAGAAAGTTATTTACAGAGACTTCAAAG
CCTCAAACATACTGCTTGATGGG
						
						Genomic sequence
						
							TCAGAAGTGAACTTTTTAGGAAGGCTTTCGCATCCTAACCTTGTTAAACTACTGGGATATTGTC
ATGAGGACAAGGAACTGTTACTCGTTTACGAATTTATGCCCAAGGGGAGCTTGGAAAACCATCT
TTTTAGAAGTAAGAAGTTAGTGTTAGAAATTCAATAAACCATAGCTCGATTAATTATACAGTGA
GCTGACCTTCAGCGTGTTTGCTTTGTAGGGAGTGCTGCTATTGAACCGCTTTCTTGGGACTTGC
GGCTCAAAATTGCCATAGGAGCAGCACGGGGCTTAGCGTTCTTACATACTTCAGAAAAGAAAGT
TATTTACAGAGACTTCAAAGCCTCAAACATACTGCTTGATGGG

Sequences
Splice junction sequence	AATTGCCATAGGAGCAGCACGGGGCTTAGCGTTCTTACATACTTCAGAAAAGAAAGTTATTTAC AGAGACTTCAAAGCCTCAAACATACTGCTTGATGGGtcagaagtgaactttttaggaaggcttt cgcatcctaaccttgttaaactactgggatattgtcatgaggacaaggaactgttactcgttta cgaattta
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: 279 Transcript exons: 4656225-4656360,4656445-4656587 TCAGAAGTGAACTTTTTAGGAAGGCTTTCGCATCCTAACCTTGTTAAACTACTGGGATATTGTC ATGAGGACAAGGAACTGTTACTCGTTTACGAATTTATGCCCAAGGGGAGCTTGGAAAACCATCT TTTTAGAAGGAGTGCTGCTATTGAACCGCTTTCTTGGGACTTGCGGCTCAAAATTGCCATAGGA GCAGCACGGGGCTTAGCGTTCTTACATACTTCAGAAAAGAAAGTTATTTACAGAGACTTCAAAG CCTCAAACATACTGCTTGATGGG
Genomic sequence	TCAGAAGTGAACTTTTTAGGAAGGCTTTCGCATCCTAACCTTGTTAAACTACTGGGATATTGTC ATGAGGACAAGGAACTGTTACTCGTTTACGAATTTATGCCCAAGGGGAGCTTGGAAAACCATCT TTTTAGAAGTAAGAAGTTAGTGTTAGAAATTCAATAAACCATAGCTCGATTAATTATACAGTGA GCTGACCTTCAGCGTGTTTGCTTTGTAGGGAGTGCTGCTATTGAACCGCTTTCTTGGGACTTGC GGCTCAAAATTGCCATAGGAGCAGCACGGGGCTTAGCGTTCTTACATACTTCAGAAAAGAAAGT TATTTACAGAGACTTCAAAGCCTCAAACATACTGCTTGATGGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						1.069111173

Conservation Information
Conserved circRNAs	NA
PMCS	1.069111173

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4656325-4656584(+)
						
						Potential amino acid sequence
						
							MPKGSLENHLFRRSAAIEPLSWDLRLKIAIGAARGLAFLHTSEKKVIYRDFKASNILLDGSEVN
FLGRLSHPNLVKLLGYCHEDKELLLVYEFMPKGSLENHLFRRSAAIEPLSWDLRLKIAIGAARG
LAFLHTSEKKVIYRDFKASNILLDGSEVNFLGRLSHPNLVKLLGYCHEDKELLLVYEFMPKGSL
ENHLFRRSAAIEPLSWDLRLKIAIGAARGLAFLHTSEKKVIYRDFKASNILLDGSEVNFLGRLS
HPNLVKLLGYCHEDKELLLVYEFMPKGSLENHLFRRSAAIEPLSWDLRLKIAIGAARGLAFLHT
SEKKVIYRDFKASNILLDG(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4656325-4656584(+)
Potential amino acid sequence	MPKGSLENHLFRRSAAIEPLSWDLRLKIAIGAARGLAFLHTSEKKVIYRDFKASNILLDGSEVN FLGRLSHPNLVKLLGYCHEDKELLLVYEFMPKGSLENHLFRRSAAIEPLSWDLRLKIAIGAARG LAFLHTSEKKVIYRDFKASNILLDGSEVNFLGRLSHPNLVKLLGYCHEDKELLLVYEFMPKGSL ENHLFRRSAAIEPLSWDLRLKIAIGAARGLAFLHTSEKKVIYRDFKASNILLDGSEVNFLGRLS HPNLVKLLGYCHEDKELLLVYEFMPKGSLENHLFRRSAAIEPLSWDLRLKIAIGAARGLAFLHT SEKKVIYRDFKASNILLDG(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Solyc03g032150.2_circ_g.3

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