Plant Circular RNA Database

Detail information of Solyc04g054740.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc04g054740.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_001448
					
						Alias
						SL3.0ch04:53123215|53123968
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 53183057-53183810  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						CIRI; find_circ
					
						Parent gene
						
							Solyc04g054740.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc04g054740.2_circ_g.1 Solyc04g054740.2_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						Exon boundary  
						
							No-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-TA							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
						Solyc04g054740.2.1:3

General Information
CircRNA Name	Solyc04g054740.2_circ_g.3
ID in PlantcircBase	sly_circ_001448
Alias	SL3.0ch04:53123215\|53123968
Organism	Solanum lycopersicum
Position	chr4: 53183057-53183810 JBrowse»
Reference genome	SL2.50.38
Type	ei-circRNA
Identification method	CIRI; find_circ
Parent gene	Solyc04g054740.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc04g054740.2_circ_g.1 Solyc04g054740.2_circ_g.2
Support reads	NA
Tissues	leaf
Exon boundary	No-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-TA 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	Solyc04g054740.2.1:3

			
						 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  
						
							AAAGGAGATCTCGAAAAGCAACGTTGTCGATGACATGGTTTCTAGTAACGCCATCCTTTATGAG
CCTGGAGAGCATCCTGACCATGTTGTTGTGATTAAGgggagtttaaggagaacaacaaagtgga
cagggtggtggtcctgtggactgccaacactgaaagatacagcagtgtggctgttggctttaat
gataccat

						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
						
							GGGAGTTTAAGGAGAACAACAAAGTGGACAGGGTGGTGGTCCTGTGGACTGCCAACACTGAAAG
ATACAGCAGTGTGGCTGTTGGCTTTAATGATACCATGGAAAACCTCTTTGCTTCTGTGGATAGA
AATGAGGCTGAAATATCTCCTTCCACCTTGTATGCTATTGCTTGTATTCTTGAAAATGTACCCT
TCATCAATGGAAGCCCACAAAATACTTTTGTCCCAGGTATGTTCCAGTTTCAAATTAAAAATCT
TGCTTCGTTGTTGTTGTTATTGTTGTTGTTTGTTTGGGAAATCAGTTGTGTGCTAGTCTTATGT
ATTCATTGAAAATTTGTTAGGCCTCATTGATTTGGCCATCAAGAGGAACACTTTGATTGGTGGT
GATGACTTTAAGAGTGGTCAAACCAAGATGAAGTCAGTGCTGGTTGATTTCCTTGTTGGAGCTG
GTATTAAGGTATGGCTATGCTGCTTCTAATTTCACACAGCTTTTAAACTAATAAAGCAAATTTG
ATATGTAAAATATGGTATCTTGAAAGAGGAAAGCTGAGTGGTAGTGAAATTTGTGTTTTTTACA
GCCAACATCAATCGTGAGCTACAACCATTTGGGTAACAATGATGGAATGAATCTGTCTGCCCCT
CAAACTTTCCGTTCAAAGGAGATCTCGAAAAGCAACGTTGTCGATGACATGGTTTCTAGTAACG
CCATCCTTTATGAGCCTGGAGAGCATCCTGACCATGTTGTTGTGATTAAG

Sequences
Splice junction sequence	AAAGGAGATCTCGAAAAGCAACGTTGTCGATGACATGGTTTCTAGTAACGCCATCCTTTATGAG CCTGGAGAGCATCCTGACCATGTTGTTGTGATTAAGgggagtttaaggagaacaacaaagtgga cagggtggtggtcctgtggactgccaacactgaaagatacagcagtgtggctgttggctttaat gataccat
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	GGGAGTTTAAGGAGAACAACAAAGTGGACAGGGTGGTGGTCCTGTGGACTGCCAACACTGAAAG ATACAGCAGTGTGGCTGTTGGCTTTAATGATACCATGGAAAACCTCTTTGCTTCTGTGGATAGA AATGAGGCTGAAATATCTCCTTCCACCTTGTATGCTATTGCTTGTATTCTTGAAAATGTACCCT TCATCAATGGAAGCCCACAAAATACTTTTGTCCCAGGTATGTTCCAGTTTCAAATTAAAAATCT TGCTTCGTTGTTGTTGTTATTGTTGTTGTTTGTTTGGGAAATCAGTTGTGTGCTAGTCTTATGT ATTCATTGAAAATTTGTTAGGCCTCATTGATTTGGCCATCAAGAGGAACACTTTGATTGGTGGT GATGACTTTAAGAGTGGTCAAACCAAGATGAAGTCAGTGCTGGTTGATTTCCTTGTTGGAGCTG GTATTAAGGTATGGCTATGCTGCTTCTAATTTCACACAGCTTTTAAACTAATAAAGCAAATTTG ATATGTAAAATATGGTATCTTGAAAGAGGAAAGCTGAGTGGTAGTGAAATTTGTGTTTTTTACA GCCAACATCAATCGTGAGCTACAACCATTTGGGTAACAATGATGGAATGAATCTGTCTGCCCCT CAAACTTTCCGTTCAAAGGAGATCTCGAAAAGCAACGTTGTCGATGACATGGTTTCTAGTAACG CCATCCTTTATGAGCCTGGAGAGCATCCTGACCATGTTGTTGTGATTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.306230449

Conservation Information
Conserved circRNAs	NA
PMCS	0.306230449

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to low-temperature stress

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to low-temperature stress

			
						 Other Information
					
						References
						Yang et al., 2020

circRNA

Detail information of Solyc04g054740.2_circ_g.3

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