Plant Circular RNA Database

Detail information of Solyc04g078460.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc04g078460.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_001548
					
						Alias
						4:60778783|60779200
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 63185413-63185830  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc04g078460.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						3
					
						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
						Solyc04g078460.2.1:2

General Information
CircRNA Name	Solyc04g078460.2_circ_g.1
ID in PlantcircBase	sly_circ_001548
Alias	4:60778783\|60779200
Organism	Solanum lycopersicum
Position	chr4: 63185413-63185830 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc04g078460.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	NA
Support reads	3
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	Solyc04g078460.2.1:2

			
						 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  
						
							CGCCGTCCATAATGCTCGCCTCCATTTCCACTGTTCCATTTGCAGTTAATGCAGATCCACGACC
CGAATTGAATAGAGGATCACTTTCAAGTTCTCTCACcaaaatggtgttagcctctttggctagc
ttcagcataccaacattgtcctcagttatgaaatattcattgtctaccatttccacgccctgat
aataaaaa

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							CAAAATGGTGTTAGCCTCTTTGGCTAGCTTCAGCATACCAACATTGTCCTCAGTTATGAAATAT
TCATTGTCTACCATTTCCACGCCCTGATAATAAAAATTAATTCATTATTAAATTATTGTTAGGA
TTTAACAATTGCAATGATTTGATTTTTTTATAAAAAAAATCTGGTAATTTATTGACCTGTTGTT
TGGCGAATTCTTCGGCGCCGGAGAAACCGAGGTAAGAATGAGGAGATTTATCCATGACAAGGCG
AGCGAGAGAAATTGGGTTTTTCACGGTGGAGATACCAGAAACGGCGCCGCATCGTCTACCATCG
CCGTCCATAATGCTCGCCTCCATTTCCACTGTTCCATTTGCAGTTAATGCAGATCCACGACCCG
AATTGAATAGAGGATCACTTTCAAGTTCTCTCAC

Sequences
Splice junction sequence	CGCCGTCCATAATGCTCGCCTCCATTTCCACTGTTCCATTTGCAGTTAATGCAGATCCACGACC CGAATTGAATAGAGGATCACTTTCAAGTTCTCTCACcaaaatggtgttagcctctttggctagc ttcagcataccaacattgtcctcagttatgaaatattcattgtctaccatttccacgccctgat aataaaaa
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CAAAATGGTGTTAGCCTCTTTGGCTAGCTTCAGCATACCAACATTGTCCTCAGTTATGAAATAT TCATTGTCTACCATTTCCACGCCCTGATAATAAAAATTAATTCATTATTAAATTATTGTTAGGA TTTAACAATTGCAATGATTTGATTTTTTTATAAAAAAAATCTGGTAATTTATTGACCTGTTGTT TGGCGAATTCTTCGGCGCCGGAGAAACCGAGGTAAGAATGAGGAGATTTATCCATGACAAGGCG AGCGAGAGAAATTGGGTTTTTCACGGTGGAGATACCAGAAACGGCGCCGCATCGTCTACCATCG CCGTCCATAATGCTCGCCTCCATTTCCACTGTTCCATTTGCAGTTAATGCAGATCCACGACCCG AATTGAATAGAGGATCACTTTCAAGTTCTCTCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.317239932

Conservation Information
Conserved circRNAs	NA
PMCS	0.317239932

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							63185659-63185636(+)
63185757-63185415(-)
						
						Potential amino acid sequence
						
							MTRRAREIGFFTVEIPETAPHRLPSPSIMLASISTVPFAVNADPRPELNRGSLSSSLTKMVLAS
LASFSIPTLSSVMKYSLSTISTPCCLANSSAPEKPR*(+)
MEASIMDGDGRRCGAVSGISTVKNPISLARLVMDKSPHSYLGFSGAEEFAKQQGVEMVDNEYFI
TEDNVGMLKLAKEANTILVRELESDPLFNSGRGSALTANGTVEMEASIMDGDGRRCGAVSGIST
VKNPISLARLVMDKSPHSYLGFSGAEEFAKQQGVEMVDNEYFITEDNVGMLKLAKEANTILVRE
LESDPLFNSGRGSALTANGTVEMEASIMDGDGRRCGAVSGISTVKNPISLARLVMDKSPHSYLG
FSGAEEFAKQQGVEMVDNEYFITEDNVGMLKLAKEANTILVRELESDPLFNSGRGSALTANGTV
EMEASIMDGDGRRCGAVSGISTVKNPISLARLVMDKSPHSYLGFSGAEEFAKQQGVEMVDNEYF
ITEDNVGMLKLAKEANTIL(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	63185659-63185636(+) 63185757-63185415(-)
Potential amino acid sequence	MTRRAREIGFFTVEIPETAPHRLPSPSIMLASISTVPFAVNADPRPELNRGSLSSSLTKMVLAS LASFSIPTLSSVMKYSLSTISTPCCLANSSAPEKPR*(+) MEASIMDGDGRRCGAVSGISTVKNPISLARLVMDKSPHSYLGFSGAEEFAKQQGVEMVDNEYFI TEDNVGMLKLAKEANTILVRELESDPLFNSGRGSALTANGTVEMEASIMDGDGRRCGAVSGIST VKNPISLARLVMDKSPHSYLGFSGAEEFAKQQGVEMVDNEYFITEDNVGMLKLAKEANTILVRE LESDPLFNSGRGSALTANGTVEMEASIMDGDGRRCGAVSGISTVKNPISLARLVMDKSPHSYLG FSGAEEFAKQQGVEMVDNEYFITEDNVGMLKLAKEANTILVRELESDPLFNSGRGSALTANGTV EMEASIMDGDGRRCGAVSGISTVKNPISLARLVMDKSPHSYLGFSGAEEFAKQQGVEMVDNEYF ITEDNVGMLKLAKEANTIL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc04g078460.2_circ_g.1

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