Plant Circular RNA Database

Detail information of Solyc08g065810.1_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc08g065810.1_circ_g.2
					
						ID in PlantcircBase
						sly_circ_002560
					
						Alias
						Slcirc123
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr8: 54124803-54125996  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc08g065810.1						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc08g065810.1_circ_g.1 Solyc08g065810.1_circ_ag.1 Solyc08g065820.1_circ_g.1 						
					
						Support reads
						8/39
					
						Tissues
						fruit/leaf
					
						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
						Solyc08g065810.1.1:3

General Information
CircRNA Name	Solyc08g065810.1_circ_g.2
ID in PlantcircBase	sly_circ_002560
Alias	Slcirc123
Organism	Solanum lycopersicum
Position	chr8: 54124803-54125996 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc08g065810.1
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc08g065810.1_circ_g.1 Solyc08g065810.1_circ_ag.1 Solyc08g065820.1_circ_g.1
Support reads	8/39
Tissues	fruit/leaf
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	Solyc08g065810.1.1:3

			
						 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  
						
							ATATGCCTGAATTCCTTGAAGTGCTTCCTAAGATATTCCTCCAACTTAGGAATATCTTGCCTTC
TAAAGATGTCCCACAATGCACCTCCATCTATATCATcttcaaatttctaacttgataagggcag
cctgcaggaatgaaaactgcatcccctaattttttaacaaaggtccatggttcaattcctgcga
aatagaaa

						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: 281
Transcript exons: 54124803-54124888,54124996-54125068,54125875-54125996
CTTCAAATTTCTAACTTGATAAGGGCAGCCTGCAGGAATGAAAACTGCATCCCCTAATTTTTTA
ACAAAGGTCCATGGTTCAATTCCACATTCTTCCTTAAGCTTATTTTTGTGATCCTTAGTCAAGT
AAAATGTTTGATCATGTATAGGGTGAATAACCTTTGGTATACGACAACAATTAATATGCCTGAA
TTCCTTGAAGTGCTTCCTAAGATATTCCTCCAACTTAGGAATATCTTGCCTTCTAAAGATGTCC
CACAATGCACCTCCATCTATATCAT
						
						Genomic sequence
						
							CTTCAAATTTCTAACTTGATAAGGGCAGCCTGCAGGAATGAAAACTGCATCCCCTAATTTTTTA
ACAAAGGTCCATGGTTCAATTCCTGCGAAATAGAAAATAATTCAAATAAAATGTAAGAAGAAAA
AAGAGAGAGTTCCACATCGAAATAGGAACATTTCAAGCTGTGAGATTCATACATGGAAAACTCA
CCACATTCTTCCTTAAGCTTATTTTTGTGATCCTTAGTCAAGTAAAATGTTTGATCATGTATAG
GGTGAATAACCTACAATGAAAAACAAAATGGAGTTGGTAGTTGGTATATACAGAAAACAGTATT
TTAAATAACAAGACAGAAAAACAAAGAATGAAATGTCTCACAGTTATCATTCTTGTATTAAATT
ATGAAGATATGAATAAGAAAAAAGGTAAATTCTTTAAACATTAGAAGAAATAGAGTGATGTTTA
TTTTCTTCATAAGTTCAACTTTACGTCTCTAGCAAAAACATCTCCATGGTAAATTTGATAATAT
ACAAACAACAAGCTTCATCATGCGTATGGATTTCAAGATCAAGCAATGTTTTCTTAAATTTCTT
GTTTCATCGTTTACAATTTCAGAAGATCATGTTTCGAAACATTCCCTCCTCCGTACTTGAATAA
TGAGTTTAAAGGCAAATTTGGGAGATCTAAAAAATATTTTAATGTCTAGGTAGGAAATATGTCA
GATGTTGAAATTTCTTACTCAAGATTTTAAATTGGCACGAAGTGTAACATTATAGGTCCTGCTC
TTAGGCAAAAGTTGAGGAACTGGTGACTTGGGTCACAGGTTTGAGCCTTGCGCCATGTGAACTA
AGCTTGGTATTTAAGTGAAAAAGGGTATAAGTGCAGGCACAATATCCCCGAGTTTCAAAGGTTG
CAGTAAGTCTTATGGGCTGACCCCATATGGATTTCTCTGTCGTTTAAAAACACCTTGTTAATGA
AAGAAACATTCTACAACCAATTATTCTTAACCCCCAAGCCAAAGCCACGAAGAAACAATAGGAC
TCAATACTCATCCCAAAAGTATGAATGCTAAGCAAATTTCGTTCATACCTTTGGTATACGACAA
CAATTAATATGCCTGAATTCCTTGAAGTGCTTCCTAAGATATTCCTCCAACTTAGGAATATCTT
GCCTTCTAAAGATGTCCCACAATGCACCTCCATCTATATCAT

Sequences
Splice junction sequence	ATATGCCTGAATTCCTTGAAGTGCTTCCTAAGATATTCCTCCAACTTAGGAATATCTTGCCTTC TAAAGATGTCCCACAATGCACCTCCATCTATATCATcttcaaatttctaacttgataagggcag cctgcaggaatgaaaactgcatcccctaattttttaacaaaggtccatggttcaattcctgcga aatagaaa
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: 281 Transcript exons: 54124803-54124888,54124996-54125068,54125875-54125996 CTTCAAATTTCTAACTTGATAAGGGCAGCCTGCAGGAATGAAAACTGCATCCCCTAATTTTTTA ACAAAGGTCCATGGTTCAATTCCACATTCTTCCTTAAGCTTATTTTTGTGATCCTTAGTCAAGT AAAATGTTTGATCATGTATAGGGTGAATAACCTTTGGTATACGACAACAATTAATATGCCTGAA TTCCTTGAAGTGCTTCCTAAGATATTCCTCCAACTTAGGAATATCTTGCCTTCTAAAGATGTCC CACAATGCACCTCCATCTATATCAT
Genomic sequence	CTTCAAATTTCTAACTTGATAAGGGCAGCCTGCAGGAATGAAAACTGCATCCCCTAATTTTTTA ACAAAGGTCCATGGTTCAATTCCTGCGAAATAGAAAATAATTCAAATAAAATGTAAGAAGAAAA AAGAGAGAGTTCCACATCGAAATAGGAACATTTCAAGCTGTGAGATTCATACATGGAAAACTCA CCACATTCTTCCTTAAGCTTATTTTTGTGATCCTTAGTCAAGTAAAATGTTTGATCATGTATAG GGTGAATAACCTACAATGAAAAACAAAATGGAGTTGGTAGTTGGTATATACAGAAAACAGTATT TTAAATAACAAGACAGAAAAACAAAGAATGAAATGTCTCACAGTTATCATTCTTGTATTAAATT ATGAAGATATGAATAAGAAAAAAGGTAAATTCTTTAAACATTAGAAGAAATAGAGTGATGTTTA TTTTCTTCATAAGTTCAACTTTACGTCTCTAGCAAAAACATCTCCATGGTAAATTTGATAATAT ACAAACAACAAGCTTCATCATGCGTATGGATTTCAAGATCAAGCAATGTTTTCTTAAATTTCTT GTTTCATCGTTTACAATTTCAGAAGATCATGTTTCGAAACATTCCCTCCTCCGTACTTGAATAA TGAGTTTAAAGGCAAATTTGGGAGATCTAAAAAATATTTTAATGTCTAGGTAGGAAATATGTCA GATGTTGAAATTTCTTACTCAAGATTTTAAATTGGCACGAAGTGTAACATTATAGGTCCTGCTC TTAGGCAAAAGTTGAGGAACTGGTGACTTGGGTCACAGGTTTGAGCCTTGCGCCATGTGAACTA AGCTTGGTATTTAAGTGAAAAAGGGTATAAGTGCAGGCACAATATCCCCGAGTTTCAAAGGTTG CAGTAAGTCTTATGGGCTGACCCCATATGGATTTCTCTGTCGTTTAAAAACACCTTGTTAATGA AAGAAACATTCTACAACCAATTATTCTTAACCCCCAAGCCAAAGCCACGAAGAAACAATAGGAC TCAATACTCATCCCAAAAGTATGAATGCTAAGCAAATTTCGTTCATACCTTTGGTATACGACAA CAATTAATATGCCTGAATTCCTTGAAGTGCTTCCTAAGATATTCCTCCAACTTAGGAATATCTT GCCTTCTAAAGATGTCCCACAATGCACCTCCATCTATATCAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.556762321

Conservation Information
Conserved circRNAs	NA
PMCS	0.556762321

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							54125052-54124818(+)
54125977-54124856(+)
						
						Potential amino acid sequence
						
							MYRVNNLWYTTTINMPEFLEVLPKIFLQLRNILPSKDVPQCTSIYIIFKFLT*(+)
MHLHLYHLQISNLIRAACRNENCIP*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	54125052-54124818(+) 54125977-54124856(+)
Potential amino acid sequence	MYRVNNLWYTTTINMPEFLEVLPKIFLQLRNILPSKDVPQCTSIYIIFKFLT(+) MHLHLYHLQISNLIRAACRNENCIP(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016; Wang et al., 2018b

circRNA

Detail information of Solyc08g065810.1_circ_g.2

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