Plant Circular RNA Database

Detail information of Solyc03g111570.2_circ_g.4

			
						 General Information
					
						CircRNA Name
						Solyc03g111570.2_circ_g.4
					
						ID in PlantcircBase
						sly_circ_001112
					
						Alias
						3:56255025|56255794
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr3: 62201975-62202744  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc03g111570.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc03g111570.2_circ_g.3 						
					
						Support reads
						6/4
					
						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
						Solyc03g111570.2.1:3

General Information
CircRNA Name	Solyc03g111570.2_circ_g.4
ID in PlantcircBase	sly_circ_001112
Alias	3:56255025\|56255794
Organism	Solanum lycopersicum
Position	chr3: 62201975-62202744 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc03g111570.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc03g111570.2_circ_g.3
Support reads	6/4
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	Solyc03g111570.2.1:3

			
						 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  
						
							GGTTCTGAGCAGGGATGTGTACAGAATTGGCCAACTTTTTGATTTCTTTAGGATGCTCTCGTTC
TTCTTCACCACAGTTGGTTATTATGTTTGTACAATGggttcgcatgcactatggacatcccgat
atcttcgaccggatctttcatatcacacggggtggcattagtaaagcatcacgtgttatcaaca
taagtgaa

						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: 343
Transcript exons: 62201975-62202087,62202440-62202492,62202568-62202744
GGTTCGCATGCACTATGGACATCCCGATATCTTCGACCGGATCTTTCATATCACACGGGGTGGC
ATTAGTAAAGCATCACGTGTTATCAACATAAGTGAAGACATCTATGCCGGTTTTAATTCCACTT
TAAGGCAGGGTAATATTACCCACCATGAGTATATTCAGGTTGGAAAGGGAAGAGATGTTGGTTT
AAATCAAATAGCTTTATTTGAAGGCAAGGTAGCTGGTGGAAACGGAGAGCAGGTTCTGAGCAGG
GATGTGTACAGAATTGGCCAACTTTTTGATTTCTTTAGGATGCTCTCGTTCTTCTTCACCACAG
TTGGTTATTATGTTTGTACAATG
						
						Genomic sequence
						
							GGTTCGCATGCACTATGGACATCCCGATATCTTCGACCGGATCTTTCATATCACACGGGGTGGC
ATTAGTAAAGCATCACGTGTTATCAACATAAGTGAAGACATCTATGCCGGTAAGTTTGAGAGAC
TTGGTGTACTCATAGTAGCTCCTATTTTCCACCTTTCCTAATTGCTTCCTGGCTAGTTCACATT
GTTTGGTGTATCTATAATGTGGACTAGGTATAGTGATTGACTGATATTCTTCAGATCATGAAAA
CAAATAGAGCTACTTCACATGATAGTTCCTATTGTTATTTGGATAGAGGATGACTTTCCGTGAT
GTTCAGCCAATAGTCTCTTCGAAAGGCAGTTTTTTTCTTTAAGCTAACAGTTCTACTTCTATGC
CTTCAACTGTTATGGTGTTTTTTTTTCCTGAAGTATATGATATTCTAGCTTTATATCTGTGGTT
TCCACCGTTCTTTGCAGGTTTTAATTCCACTTTAAGGCAGGGTAATATTACCCACCATGAGTAT
ATTCAGGTTGGTTTAGTTGCAGTTGCGTGCATTTGATTAGATTTCTTTTTACTATCCTGAAGGC
TGTGTTGATGAATGTAGGTTGGAAAGGGAAGAGATGTTGGTTTAAATCAAATAGCTTTATTTGA
AGGCAAGGTAGCTGGTGGAAACGGAGAGCAGGTTCTGAGCAGGGATGTGTACAGAATTGGCCAA
CTTTTTGATTTCTTTAGGATGCTCTCGTTCTTCTTCACCACAGTTGGTTATTATGTTTGTACAA
TG

Sequences
Splice junction sequence	GGTTCTGAGCAGGGATGTGTACAGAATTGGCCAACTTTTTGATTTCTTTAGGATGCTCTCGTTC TTCTTCACCACAGTTGGTTATTATGTTTGTACAATGggttcgcatgcactatggacatcccgat atcttcgaccggatctttcatatcacacggggtggcattagtaaagcatcacgtgttatcaaca taagtgaa
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: 343 Transcript exons: 62201975-62202087,62202440-62202492,62202568-62202744 GGTTCGCATGCACTATGGACATCCCGATATCTTCGACCGGATCTTTCATATCACACGGGGTGGC ATTAGTAAAGCATCACGTGTTATCAACATAAGTGAAGACATCTATGCCGGTTTTAATTCCACTT TAAGGCAGGGTAATATTACCCACCATGAGTATATTCAGGTTGGAAAGGGAAGAGATGTTGGTTT AAATCAAATAGCTTTATTTGAAGGCAAGGTAGCTGGTGGAAACGGAGAGCAGGTTCTGAGCAGG GATGTGTACAGAATTGGCCAACTTTTTGATTTCTTTAGGATGCTCTCGTTCTTCTTCACCACAG TTGGTTATTATGTTTGTACAATG
Genomic sequence	GGTTCGCATGCACTATGGACATCCCGATATCTTCGACCGGATCTTTCATATCACACGGGGTGGC ATTAGTAAAGCATCACGTGTTATCAACATAAGTGAAGACATCTATGCCGGTAAGTTTGAGAGAC TTGGTGTACTCATAGTAGCTCCTATTTTCCACCTTTCCTAATTGCTTCCTGGCTAGTTCACATT GTTTGGTGTATCTATAATGTGGACTAGGTATAGTGATTGACTGATATTCTTCAGATCATGAAAA CAAATAGAGCTACTTCACATGATAGTTCCTATTGTTATTTGGATAGAGGATGACTTTCCGTGAT GTTCAGCCAATAGTCTCTTCGAAAGGCAGTTTTTTTCTTTAAGCTAACAGTTCTACTTCTATGC CTTCAACTGTTATGGTGTTTTTTTTTCCTGAAGTATATGATATTCTAGCTTTATATCTGTGGTT TCCACCGTTCTTTGCAGGTTTTAATTCCACTTTAAGGCAGGGTAATATTACCCACCATGAGTAT ATTCAGGTTGGTTTAGTTGCAGTTGCGTGCATTTGATTAGATTTCTTTTTACTATCCTGAAGGC TGTGTTGATGAATGTAGGTTGGAAAGGGAAGAGATGTTGGTTTAAATCAAATAGCTTTATTTGA AGGCAAGGTAGCTGGTGGAAACGGAGAGCAGGTTCTGAGCAGGGATGTGTACAGAATTGGCCAA CTTTTTGATTTCTTTAGGATGCTCTCGTTCTTCTTCACCACAGTTGGTTATTATGTTTGTACAA TG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.886870561

Conservation Information
Conserved circRNAs	NA
PMCS	0.886870561

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							62201983-62202040(+)
62202660-62202040(+)
62202025-62202715(-)
62201985-62202609(-)
						
						Potential amino acid sequence
						
							MHYGHPDIFDRIFHITRGGISKASRVINISEDIYAGFNSTLRQGNITHHEYIQVGKGRDVGLNQ
IALFEGKVAGGNGEQVLSRDVYRIGQLFDFFRMLSFFFTTVGYYVCTMGSHALWTSRYLRPDLS
YHTGWH*(+)
MCTELANFLISLGCSRSSSPQLVIMFVQWVRMHYGHPDIFDRIFHITRGGISKASRVINISEDI
YAGFNSTLRQGNITHHEYIQVGKGRDVGLNQIALFEGKVAGGNGEQVLSRDVYRIGQLFDFFRM
LSFFFTTVGYYVCTMGSHALWTSRYLRPDLSYHTGWH*(+)
MKDPVEDIGMSIVHANPLYKHNNQLW*(-)
MRTHCTNIITNCGEEEREHPKEIKKLANSVHIPAQNLLSVSTSYLAFK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	62201983-62202040(+) 62202660-62202040(+) 62202025-62202715(-) 62201985-62202609(-)
Potential amino acid sequence	MHYGHPDIFDRIFHITRGGISKASRVINISEDIYAGFNSTLRQGNITHHEYIQVGKGRDVGLNQ IALFEGKVAGGNGEQVLSRDVYRIGQLFDFFRMLSFFFTTVGYYVCTMGSHALWTSRYLRPDLS YHTGWH(+) MCTELANFLISLGCSRSSSPQLVIMFVQWVRMHYGHPDIFDRIFHITRGGISKASRVINISEDI YAGFNSTLRQGNITHHEYIQVGKGRDVGLNQIALFEGKVAGGNGEQVLSRDVYRIGQLFDFFRM LSFFFTTVGYYVCTMGSHALWTSRYLRPDLSYHTGWH(+) MKDPVEDIGMSIVHANPLYKHNNQLW(-) MRTHCTNIITNCGEEEREHPKEIKKLANSVHIPAQNLLSVSTSYLAFK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

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

circRNA

Detail information of Solyc03g111570.2_circ_g.4

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