Plant Circular RNA Database

Detail information of Solyc10g005490.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc10g005490.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_003019
					
						Alias
						10:393403|394744, Slcirc154
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr10: 393403-394744  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc10g005490.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc10g005490.2_circ_g.1 						
					
						Support reads
						44/39
					
						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
						Solyc10g005490.2.1:6

General Information
CircRNA Name	Solyc10g005490.2_circ_g.2
ID in PlantcircBase	sly_circ_003019
Alias	10:393403\|394744, Slcirc154
Organism	Solanum lycopersicum
Position	chr10: 393403-394744 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc10g005490.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc10g005490.2_circ_g.1
Support reads	44/39
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	Solyc10g005490.2.1:6

			
						 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  
						
							ACGTATTTCGCGCCTGATAGGTGACACCTTTTCCATTAGCGGCCCTCACAAGCATGCCTTTTCT
CCCTGTTATTTCTGCCACTTTCTCCGGGCCCCCAAGctagaaccgagtctcttattattccaac
agaaacaagtgcagctttccccttcaaaataaaatcctgtatagcatccggtatatcagcagaa
caacctgg

									
								

					

						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: 646
Transcript exons: 393403-393523,393630-393717,393810-393905,394120-394226,
394435-394570,394647-394744
CTAGAACCGAGTCTCTTATTATTCCAACAGAAACAAGTGCAGCTTTCCCCTTCAAAATAAAATC
CTGTATAGCATCCGGTATATCAGCAGAACAACCTGGTGGTACAAGTGGAAAAGGATCCTGCTCC
ATGATCCCTCTATACAACATCACAAGGGCTCTTTTCCCATAGGAACTATCGTAGTTATAAGCAC
TAAGAGATGGTCCAGCTCGACGATCTCCCTGAGTCAATGCCCCAAGTGATTCAAGTCTCTTGGC
AACAACGGATGCAAACCGCCGTTCGCCGCCAAGATTAGTAAATAGTAGCTTATACTCGGGTGCA
GAAGCTTGATTAGAGCGATGAGTTCTTCCAAACTGCTGAATTGCCCGATCAGCACTCCAAGGTA
ACTCCAGAGTCAAATGGACCCTTCTTCTCTGGTTTAAGGCCCTTCTATCAGCTTGCAGAGAAAC
ACCAGCTGATCCAGCTTCAGATATTATAGCTACCAGCTTCTTCCCTTCCATGAAGAGCTGTTTC
TCATGTATATTGACCATTTCCATGCTTACATCCTTCGTATTTCGCGCCTGATAGGTGACACCTT
TTCCATTAGCGGCCCTCACAAGCATGCCTTTTCTCCCTGTTATTTCTGCCACTTTCTCCGGGCC
CCCAAG
						
					

						Genomic sequence
						
							CTAGAACCGAGTCTCTTATTATTCCAACAGAAACAAGTGCAGCTTTCCCCTTCAAAATAAAATC
CTGTATAGCATCCGGTATATCAGCAGAACAACCTGGTGGTACAAGTGGAAAAGGATCCTGCAAA
CCATATAGCATGTTGAATATTCACTTGTACACATACATGCTTAAGTGGGAAAAGAATGTAATAC
AAGAAATGACAGTATCAAGCAAAAGGCATAGACACCTGCTCCATGATCCCTCTATACAACATCA
CAAGGGCTCTTTTCCCATAGGAACTATCGTAGTTATAAGCACTAAGAGATGGTCCAGCTCTGCA
ATATATAAAGAGCAATTAAAAAGAGCCGTAACTTTGCATGTTTTCATAATCGCACTTCCAACAT
ATGCTAAACAATAACGCACTCACCGACGATCTCCCTGAGTCAATGCCCCAAGTGATTCAAGTCT
CTTGGCAACAACGGATGCAAACCGCCGTTCGCCGCCAAGATTAGTAAATAGTAGCCTGTATATT
GAGAAAAAGAAAAATATCATAAGTGCAAAATATGAAAAAGTGATTGTTACAGGGATTTATTTCT
GGCAAGTATGAAAAGCATATTTTATGGCAACTTGTAACAATCCAGGTACGCCACCAAATAGTTA
CAATGGTAATTTGTATAAACCAGGTTGCCATCATATAGCATAACCATTATTCACATGTAACCAG
ACACGGTACCTACTTATACTCGGGTGCAGAAGCTTGATTAGAGCGATGAGTTCTTCCAAACTGC
TGAATTGCCCGATCAGCACTCCAAGGTAACTCCAGAGTCAAATGGACCCTTCTTCTCTGACACA
AGAGAAGGAATACAAACGGCATAATCAGAAAACAACTATCAAGAGCAGCTCATTCCTTGAGGAT
CGGAGGATATATGTAGAGAGAGAGAGAGAGAGAAAAGAGTGTCTACTACATTTCCACACACACA
TATATACATATAAGAGATGATGTCTTTTGCTCCATGCAGTAAATGATGAAAACAAAAAAACAAA
AAAGCTACCTGGTTTAAGGCCCTTCTATCAGCTTGCAGAGAAACACCAGCTGATCCAGCTTCAG
ATATTATAGCTACCAGCTTCTTCCCTTCCATGAAGAGCTGTTTCTCATGTATATTGACCATTTC
CATGCTTACATCCTTCCTAAAGCAAGAAAAAATCGCTCAGCCATTATGAGAAAAAAACAATCTA
TAATTTAATTTAAACATCAGAAACTCACGTATTTCGCGCCTGATAGGTGACACCTTTTCCATTA
GCGGCCCTCACAAGCATGCCTTTTCTCCCTGTTATTTCTGCCACTTTCTCCGGGCCCCCAAG
						
					

			
		

Sequences
Splice junction sequence	ACGTATTTCGCGCCTGATAGGTGACACCTTTTCCATTAGCGGCCCTCACAAGCATGCCTTTTCT CCCTGTTATTTCTGCCACTTTCTCCGGGCCCCCAAGctagaaccgagtctcttattattccaac agaaacaagtgcagctttccccttcaaaataaaatcctgtatagcatccggtatatcagcagaa caacctgg
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: 646 Transcript exons: 393403-393523,393630-393717,393810-393905,394120-394226, 394435-394570,394647-394744 CTAGAACCGAGTCTCTTATTATTCCAACAGAAACAAGTGCAGCTTTCCCCTTCAAAATAAAATC CTGTATAGCATCCGGTATATCAGCAGAACAACCTGGTGGTACAAGTGGAAAAGGATCCTGCTCC ATGATCCCTCTATACAACATCACAAGGGCTCTTTTCCCATAGGAACTATCGTAGTTATAAGCAC TAAGAGATGGTCCAGCTCGACGATCTCCCTGAGTCAATGCCCCAAGTGATTCAAGTCTCTTGGC AACAACGGATGCAAACCGCCGTTCGCCGCCAAGATTAGTAAATAGTAGCTTATACTCGGGTGCA GAAGCTTGATTAGAGCGATGAGTTCTTCCAAACTGCTGAATTGCCCGATCAGCACTCCAAGGTA ACTCCAGAGTCAAATGGACCCTTCTTCTCTGGTTTAAGGCCCTTCTATCAGCTTGCAGAGAAAC ACCAGCTGATCCAGCTTCAGATATTATAGCTACCAGCTTCTTCCCTTCCATGAAGAGCTGTTTC TCATGTATATTGACCATTTCCATGCTTACATCCTTCGTATTTCGCGCCTGATAGGTGACACCTT TTCCATTAGCGGCCCTCACAAGCATGCCTTTTCTCCCTGTTATTTCTGCCACTTTCTCCGGGCC CCCAAG
Genomic sequence	CTAGAACCGAGTCTCTTATTATTCCAACAGAAACAAGTGCAGCTTTCCCCTTCAAAATAAAATC CTGTATAGCATCCGGTATATCAGCAGAACAACCTGGTGGTACAAGTGGAAAAGGATCCTGCAAA CCATATAGCATGTTGAATATTCACTTGTACACATACATGCTTAAGTGGGAAAAGAATGTAATAC AAGAAATGACAGTATCAAGCAAAAGGCATAGACACCTGCTCCATGATCCCTCTATACAACATCA CAAGGGCTCTTTTCCCATAGGAACTATCGTAGTTATAAGCACTAAGAGATGGTCCAGCTCTGCA ATATATAAAGAGCAATTAAAAAGAGCCGTAACTTTGCATGTTTTCATAATCGCACTTCCAACAT ATGCTAAACAATAACGCACTCACCGACGATCTCCCTGAGTCAATGCCCCAAGTGATTCAAGTCT CTTGGCAACAACGGATGCAAACCGCCGTTCGCCGCCAAGATTAGTAAATAGTAGCCTGTATATT GAGAAAAAGAAAAATATCATAAGTGCAAAATATGAAAAAGTGATTGTTACAGGGATTTATTTCT GGCAAGTATGAAAAGCATATTTTATGGCAACTTGTAACAATCCAGGTACGCCACCAAATAGTTA CAATGGTAATTTGTATAAACCAGGTTGCCATCATATAGCATAACCATTATTCACATGTAACCAG ACACGGTACCTACTTATACTCGGGTGCAGAAGCTTGATTAGAGCGATGAGTTCTTCCAAACTGC TGAATTGCCCGATCAGCACTCCAAGGTAACTCCAGAGTCAAATGGACCCTTCTTCTCTGACACA AGAGAAGGAATACAAACGGCATAATCAGAAAACAACTATCAAGAGCAGCTCATTCCTTGAGGAT CGGAGGATATATGTAGAGAGAGAGAGAGAGAGAAAAGAGTGTCTACTACATTTCCACACACACA TATATACATATAAGAGATGATGTCTTTTGCTCCATGCAGTAAATGATGAAAACAAAAAAACAAA AAAGCTACCTGGTTTAAGGCCCTTCTATCAGCTTGCAGAGAAACACCAGCTGATCCAGCTTCAG ATATTATAGCTACCAGCTTCTTCCCTTCCATGAAGAGCTGTTTCTCATGTATATTGACCATTTC CATGCTTACATCCTTCCTAAAGCAAGAAAAAATCGCTCAGCCATTATGAGAAAAAAACAATCTA TAATTTAATTTAAACATCAGAAACTCACGTATTTCGCGCCTGATAGGTGACACCTTTTCCATTA GCGGCCCTCACAAGCATGCCTTTTCTCCCTGTTATTTCTGCCACTTTCTCCGGGCCCCCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.803288531

Conservation Information
Conserved circRNAs	NA
PMCS	0.803288531

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							394538-393459(+)
394701-394682(-)
						
						Potential amino acid sequence
						
							MYIDHFHAYILRISRLIGDTFSISGPHKHAFSPCYFCHFLRAPKLEPSLLLFQQKQVQLSPSK*
(+)
MLVRAANGKGVTYQARNTKDVSMEMVNIHEKQLFMEGKKLVAIISEAGSAGVSLQADRRALNQR
RRVHLTLELPWSADRAIQQFGRTHRSNQASAPEYKLLFTNLGGERRFASVVAKRLESLGALTQG
DRRAGPSLSAYNYDSSYGKRALVMLYRGIMEQDPFPLVPPGCSADIPDAIQDFILKGKAALVSV
GIIRDSVLAWGPGESGRNNREKRHACEGR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	394538-393459(+) 394701-394682(-)
Potential amino acid sequence	MYIDHFHAYILRISRLIGDTFSISGPHKHAFSPCYFCHFLRAPKLEPSLLLFQQKQVQLSPSK* (+) MLVRAANGKGVTYQARNTKDVSMEMVNIHEKQLFMEGKKLVAIISEAGSAGVSLQADRRALNQR RRVHLTLELPWSADRAIQQFGRTHRSNQASAPEYKLLFTNLGGERRFASVVAKRLESLGALTQG DRRAGPSLSAYNYDSSYGKRALVMLYRGIMEQDPFPLVPPGCSADIPDAIQDFILKGKAALVSV GIIRDSVLAWGPGESGRNNREKRHACEGR*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

			
						 Other Information
					
						References
						Zuo et al., 2016; Tan et al., 2017; Yin et al., 2018; Wang et al., 2018b

circRNA

Detail information of Solyc10g005490.2_circ_g.2

Address

Any questions?

Supported by