Plant Circular RNA Database

Detail information of Solyc04g008640.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc04g008640.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_001274
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 2264722-2270861  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc04g008640.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc04g008640.2_circ_g.1 						
					
						Support reads
						NA
					
						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
						Solyc04g008640.2.1:7

General Information
CircRNA Name	Solyc04g008640.2_circ_g.2
ID in PlantcircBase	sly_circ_001274
Alias	NA
Organism	Solanum lycopersicum
Position	chr4: 2264722-2270861 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc04g008640.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc04g008640.2_circ_g.1
Support reads	NA
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	Solyc04g008640.2.1:7

			
						 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  
						
							AATGCAGGAATTGGAGAAAAGCCTGAAAACTACTTGCGAGGAGTTCATTATGTCAGTGACTAAG
TTAGTTGTGGAACCATTGCTTTCTTTTGTGACAAAGattgcaaattaccttccttcagaggagg
atctggattaccctaaaaagttggagcaatctgtttcagcagaactggattcaccatctgtaag
tgccaaac

						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: 597
Transcript exons: 2264722-2264808,2265456-2265572,2265659-2265691,2265825-
2265911,2265989-2266051,2267143-2267259,2270769-2270861
ATTGCAAATTACCTTCCTTCAGAGGAGGATCTGGATTACCCTAAAAAGTTGGAGCAATCTGTTT
CAGCAGAACTGGATTCACCATCTACTGAACTAAATCAAGATGTTTCCGGAACTTGGTATCCTCC
ACTGGAGAAAACCATATCATGTCTATCAAAACTGTACTGTTCTCTAGAAACAGCTGTTTTTACT
GGATTGGCTCAGGAAGCTGTAGAGTTTTGCTCGTTATCCATTCAAAAAGCTAGCAAACTTATTG
GCAAAAGATCGTCATCAATGGATGCACAACTTTTCCTAATAAAGCATCTACTCATCCTGAGGGA
GCAGATTGCCCCATTCGACATAGAATTTTCAGTCACGCATAAGGAACTTGATTTTTCACATTTG
CTGGAGCATCTGAGGCGGATTCTAAGGGGTCAGGCATCAATCTTTGACTGGTCGAGATCAACTT
CATTAGCTAGAACTTTATCTCCACGAGTTTTGGAAAGTCAAATTGACGCCAAGAAGGAATTGGA
GAAAAGCCTGAAAACTACTTGCGAGGAGTTCATTATGTCAGTGACTAAGTTAGTTGTGGAACCA
TTGCTTTCTTTTGTGACAAAG
						
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	AATGCAGGAATTGGAGAAAAGCCTGAAAACTACTTGCGAGGAGTTCATTATGTCAGTGACTAAG TTAGTTGTGGAACCATTGCTTTCTTTTGTGACAAAGattgcaaattaccttccttcagaggagg atctggattaccctaaaaagttggagcaatctgtttcagcagaactggattcaccatctgtaag tgccaaac
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: 597 Transcript exons: 2264722-2264808,2265456-2265572,2265659-2265691,2265825- 2265911,2265989-2266051,2267143-2267259,2270769-2270861 ATTGCAAATTACCTTCCTTCAGAGGAGGATCTGGATTACCCTAAAAAGTTGGAGCAATCTGTTT CAGCAGAACTGGATTCACCATCTACTGAACTAAATCAAGATGTTTCCGGAACTTGGTATCCTCC ACTGGAGAAAACCATATCATGTCTATCAAAACTGTACTGTTCTCTAGAAACAGCTGTTTTTACT GGATTGGCTCAGGAAGCTGTAGAGTTTTGCTCGTTATCCATTCAAAAAGCTAGCAAACTTATTG GCAAAAGATCGTCATCAATGGATGCACAACTTTTCCTAATAAAGCATCTACTCATCCTGAGGGA GCAGATTGCCCCATTCGACATAGAATTTTCAGTCACGCATAAGGAACTTGATTTTTCACATTTG CTGGAGCATCTGAGGCGGATTCTAAGGGGTCAGGCATCAATCTTTGACTGGTCGAGATCAACTT CATTAGCTAGAACTTTATCTCCACGAGTTTTGGAAAGTCAAATTGACGCCAAGAAGGAATTGGA GAAAAGCCTGAAAACTACTTGCGAGGAGTTCATTATGTCAGTGACTAAGTTAGTTGTGGAACCA TTGCTTTCTTTTGTGACAAAG
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.331155851

Conservation Information
Conserved circRNAs	NA
PMCS	0.331155851

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2265862-2270858(+)
						
						Potential amino acid sequence
						
							MDAQLFLIKHLLILREQIAPFDIEFSVTHKELDFSHLLEHLRRILRGQASIFDWSRSTSLARTL
SPRVLESQIDAKKELEKSLKTTCEEFIMSVTKLVVEPLLSFVTKIANYLPSEEDLDYPKKLEQS
VSAELDSPSTELNQDVSGTWYPPLEKTISCLSKLYCSLETAVFTGLAQEAVEFCSLSIQKASKL
IGKRSSSMDAQLFLIKHLLILREQIAPFDIEFSVTHKELDFSHLLEHLRRILRGQASIFDWSRS
TSLARTLSPRVLESQIDAKKELEKSLKTTCEEFIMSVTKLVVEPLLSFVTKIANYLPSEEDLDY
PKKLEQSVSAELDSPSTELNQDVSGTWYPPLEKTISCLSKLYCSLETAVFTGLAQEAVEFCSLS
IQKASKLIGKRSSSMDAQLFLIKHLLILREQIAPFDIEFSVTHKELDFSHLLEHLRRILRGQAS
IFDWSRSTSLARTLSPRVLESQIDAKKELEKSLKTTCEEFIMSVTKLVVEPLLSFVTKIANYLP
SEEDLDYPKKLEQSVSAELDSPSTELNQDVSGTWYPPLEKTISCLSKLYCSLETAVFTGLAQEA
VEFCSLSIQKASKLIGKRSSSMDAQLFLIKHLLILREQIAPFDIEFSVTHKELDFSHLLEHLRR
ILRGQASIFDWSRSTSLARTLSPRVLESQIDAKKELEKSLKTTCEEFIMSVTKLVVEPLLSFVT
K(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2265862-2270858(+)
Potential amino acid sequence	MDAQLFLIKHLLILREQIAPFDIEFSVTHKELDFSHLLEHLRRILRGQASIFDWSRSTSLARTL SPRVLESQIDAKKELEKSLKTTCEEFIMSVTKLVVEPLLSFVTKIANYLPSEEDLDYPKKLEQS VSAELDSPSTELNQDVSGTWYPPLEKTISCLSKLYCSLETAVFTGLAQEAVEFCSLSIQKASKL IGKRSSSMDAQLFLIKHLLILREQIAPFDIEFSVTHKELDFSHLLEHLRRILRGQASIFDWSRS TSLARTLSPRVLESQIDAKKELEKSLKTTCEEFIMSVTKLVVEPLLSFVTKIANYLPSEEDLDY PKKLEQSVSAELDSPSTELNQDVSGTWYPPLEKTISCLSKLYCSLETAVFTGLAQEAVEFCSLS IQKASKLIGKRSSSMDAQLFLIKHLLILREQIAPFDIEFSVTHKELDFSHLLEHLRRILRGQAS IFDWSRSTSLARTLSPRVLESQIDAKKELEKSLKTTCEEFIMSVTKLVVEPLLSFVTKIANYLP SEEDLDYPKKLEQSVSAELDSPSTELNQDVSGTWYPPLEKTISCLSKLYCSLETAVFTGLAQEA VEFCSLSIQKASKLIGKRSSSMDAQLFLIKHLLILREQIAPFDIEFSVTHKELDFSHLLEHLRR ILRGQASIFDWSRSTSLARTLSPRVLESQIDAKKELEKSLKTTCEEFIMSVTKLVVEPLLSFVT K(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Tan et al., 2017

circRNA

Detail information of Solyc04g008640.2_circ_g.2

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