Plant Circular RNA Database

Detail information of Solyc04g079320.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc04g079320.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_001557
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 63838617-63841525  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc04g079320.2						
					
						Parent gene annotation
						
							Uroporphyrinogen-III synthase, chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc04g079320.2_circ_g.3 						
					
						Support reads
						2
					
						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
						Solyc04g079320.2.1:6

General Information
CircRNA Name	Solyc04g079320.2_circ_g.2
ID in PlantcircBase	sly_circ_001557
Alias	NA
Organism	Solanum lycopersicum
Position	chr4: 63838617-63841525 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc04g079320.2
Parent gene annotation	Uroporphyrinogen-III synthase, chloroplastic
Parent gene strand	+
Alternative splicing	Solyc04g079320.2_circ_g.3
Support reads	2
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	Solyc04g079320.2.1:6

			
						 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  
						
							GGGACAATGCTGTTGCATGTATTGGGGAGACAACAGCTTCTGCAGCTAAAAAACTTGGGTTCAG
AAATATATACCATCCAACAAGTCCTGGTCTTGAAGGaggccacgttcgactggattatcattac
ttcaccagaggcgggaaaggtttttcttgatgcttggaagtaagtttaggttgaattaaccagt
aaagaggg

									
								

					

						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
						
							AGGCCACGTTCGACTGGATTATCATTACTTCACCAGAGGCGGGAAAGGTTTTTCTTGATGCTTG
GAAGTAAGTTTAGGTTGAATTAACCAGTAAAGAGGGTTAATTTTGTCTGACGTTCTTCACCTTC
TTATTTTAAATAACTAAACTATCTTCTTGACTAGTCTTTAGTACAGTTCCTTTGTTAGTTGAAT
AGGAGGATCACTTTGACTATAGGCTATTAGGCTATAGCCATTGGTAAGTTTTACCAAAGACGAA
AAATTATTTATTTGATATTATGGATAGCTGGTTGGAGAATATATCGGTGAAGTTGGCTTTAAAA
ATATAAAAAAATGCCGAGAAAGTTACAAGATCTGATGTTAAATTTAGTCATTTTGTGTTGGACT
TGTCAGTAAAACAAGTAATTGCAGTGTTTAAAAACGTTGTTGCTTGCTTGTGTAGACAAATCGG
GTTTTAAAACTATGTTCTCACTTCTCAGCATGTTTGAGAATCTTATCTACTCGTTGAAGATTTT
TCATTTGACTTTCACAAGTTTGAGAAAGACCAATTGTCCTGAGGTACAAATACTTCCTATATTA
TATGGTTATCAGCATATTAAGTTTGATTATTCACTGAATTGATGTGTTTATGTGACAAATAGCA
CCTGCTAAGCATTACGATACAACTTAGGGAGATTCACACCCAAGAAAGTAGTTATTGAGGTGGG
AGAACCCAAAGCTATAGAATCATAACAAACCACCACGCTCTGCATTGGTCGTCCTCGACGGCTG
TGTGCGCTAGACCATATCTAACCCTGGGCATCACTACAATATTGGCATCACCATCCAAGGCACG
AAGGGCAGTGGGTACGACCTAGGGAGAACCACACCCGAAAGCTAGTTTTTAGGTGAGAAATCCA
AAGCTATATAAGTCCTACATCAGCTTCCCCATTTAACCAATGTGAGACTCAAGTCCCGTACCTT
GCAATAGGATCATAACATACTATCATCAACCCCAAGTTCTGGTTGAACCTTCCATCCATCAACT
GTATACTTTTTCCTAAATGAAGCATTGAAACTTGTATAAAAGACTCTCAGTTGATTGTCAGCAT
ACACAAAAAGCGAGAGTCATTAGAGTGTGTCCTGTTATGTGTGTACTTATGTTGTCAAATGAAA
TATTGAACTAAAGATGGTACAATAATTAATTCCCCAAAATATGAAGTATTACTATATATGTTTT
TCATTACTGTTTATTGGTTGAAAGAAGCCTCAAATTCTTCAAGCTGTCTAGATGATCTATATTT
ACTTTTGCTGTCTCTGGTCCCTCATACTTATTCCAATTTATCACTTAGAGCTGCTGGGACCCCA
TCTGTCAGAGTAGGAGTTGTTGGATCTGGTACAGCCAGCATATTTGATGAAGCTGTTCAGTCTT
CAAAGCAGTATCTTGATATGGCATTTGCACCATCGAAGGGTATTCAGTAAACTTCCCACTTGCT
CTTTTGACATTTAGAAATAGCATATGCACACATGTGCATCAGGGATGACATTTGCATTTGTCAT
TCATTTAAATACCTTTTTTTCCTTGCAAACTGTTCCGCAGTAAAAAATTGACTGACGGTAATGT
TATTGCCTGAGTGACTGAAAATTTCATTCTATTTGCATTTTTAGCAACTGGCAAGGTTTTAGCT
TTAGAGCTTCCGAAGAATGGAAATGACAAGTGCACTGTTCTCTATCCTGCTTCAGCAAAAGCCA
GCACTGACATCGGTGTGTGCATATTACTCCATCTCTTTATGTTTCTGTCTCTCCTAATTCTCCC
ATCTATCTGATTTCGTACAGAGATTTTTTTCCTTGTATTCTCGTTCTGATTTTTTCTGGTTCTG
TAGGGATCTTTAGTTTCCGTGGAGGTGCCTTTTCTATTGTAAACCATTATTCAGAAAAAAATTG
AAAAGGAAGAACAAAATAAACAGATTAACCACAAAAGTCTTAGCTCATTATCTTTCCTCATGGC
CATAATCTGTACAAGAGTCTCATTCATCCGATATTTTGCAACTGTCTCACCTTGATAGTTCATG
TTTAGTATGCAAATTTTCCTCTGAATATAGAAGTATTTTGAGTAGTTTTAAACTGACATATGGC
TCCGTCATTTCAGAGGAAGGACTTTCTGGGCGGGGATTCGAGGTTACTCGGCTGAACACTTACA
CAACGGTATGATATTTCTCTATTGCCTAATTGGAGAAGAAAATTCATTTTTACTCACAAGAGAC
CACCGTGCTTGCAAATTTGATAATACACACTTGCCCTGAAAAAGAGGGTCACTTGTCATCTTTT
CCTGACATTTGGTCAAAGTTCAGATAGAGCACCACATCTTAGATCCTTCTCTTGAGAGAAAACT
AATTAGATTTCATCCTGCTGCCTATGACCTTTCCATTTCTTGCAGGCACCAGTCAATCACGTTG
ATCAATATCTTCTTGAACTAGCACTCTCTGTTCCCGTTGTTACTGTAGCATCTCCTTCTGCCCT
CAGGTACGATATTCCAAATTATTCATTTTTATAGCAAAAGTAGATGGATGACAGGTTGATATCT
AATATTGGCTTAAGCAAGTGCACTAATTCTATAGCTGATGACTGTAATTCCACCAACATGCTAG
AAAATATTAGACAGATGTGTTCAGACATAGTTCATTGAGCCAGGGAACAGAATTGTATCCTTAT
GTTCTTCATCCTTCTACCTTATATTTTTAGAGGCTTTATTCTCTTTCTCCTTTCTCATTCCTTT
TTCCTTCTGCTGGGTTATTTGACAGGGTATGGGCTAATCTTACTGCATCGAGACAGTGGGACAA
TGCTGTTGCATGTATTGGGGAGACAACAGCTTCTGCAGCTAAAAAACTTGGGTTCAGAAATATA
TACCATCCAACAAGTCCTGGTCTTGAAGG
						
					

			
		

Sequences
Splice junction sequence	GGGACAATGCTGTTGCATGTATTGGGGAGACAACAGCTTCTGCAGCTAAAAAACTTGGGTTCAG AAATATATACCATCCAACAAGTCCTGGTCTTGAAGGaggccacgttcgactggattatcattac ttcaccagaggcgggaaaggtttttcttgatgcttggaagtaagtttaggttgaattaaccagt aaagaggg
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	AGGCCACGTTCGACTGGATTATCATTACTTCACCAGAGGCGGGAAAGGTTTTTCTTGATGCTTG GAAGTAAGTTTAGGTTGAATTAACCAGTAAAGAGGGTTAATTTTGTCTGACGTTCTTCACCTTC TTATTTTAAATAACTAAACTATCTTCTTGACTAGTCTTTAGTACAGTTCCTTTGTTAGTTGAAT AGGAGGATCACTTTGACTATAGGCTATTAGGCTATAGCCATTGGTAAGTTTTACCAAAGACGAA AAATTATTTATTTGATATTATGGATAGCTGGTTGGAGAATATATCGGTGAAGTTGGCTTTAAAA ATATAAAAAAATGCCGAGAAAGTTACAAGATCTGATGTTAAATTTAGTCATTTTGTGTTGGACT TGTCAGTAAAACAAGTAATTGCAGTGTTTAAAAACGTTGTTGCTTGCTTGTGTAGACAAATCGG GTTTTAAAACTATGTTCTCACTTCTCAGCATGTTTGAGAATCTTATCTACTCGTTGAAGATTTT TCATTTGACTTTCACAAGTTTGAGAAAGACCAATTGTCCTGAGGTACAAATACTTCCTATATTA TATGGTTATCAGCATATTAAGTTTGATTATTCACTGAATTGATGTGTTTATGTGACAAATAGCA CCTGCTAAGCATTACGATACAACTTAGGGAGATTCACACCCAAGAAAGTAGTTATTGAGGTGGG AGAACCCAAAGCTATAGAATCATAACAAACCACCACGCTCTGCATTGGTCGTCCTCGACGGCTG TGTGCGCTAGACCATATCTAACCCTGGGCATCACTACAATATTGGCATCACCATCCAAGGCACG AAGGGCAGTGGGTACGACCTAGGGAGAACCACACCCGAAAGCTAGTTTTTAGGTGAGAAATCCA AAGCTATATAAGTCCTACATCAGCTTCCCCATTTAACCAATGTGAGACTCAAGTCCCGTACCTT GCAATAGGATCATAACATACTATCATCAACCCCAAGTTCTGGTTGAACCTTCCATCCATCAACT GTATACTTTTTCCTAAATGAAGCATTGAAACTTGTATAAAAGACTCTCAGTTGATTGTCAGCAT ACACAAAAAGCGAGAGTCATTAGAGTGTGTCCTGTTATGTGTGTACTTATGTTGTCAAATGAAA TATTGAACTAAAGATGGTACAATAATTAATTCCCCAAAATATGAAGTATTACTATATATGTTTT TCATTACTGTTTATTGGTTGAAAGAAGCCTCAAATTCTTCAAGCTGTCTAGATGATCTATATTT ACTTTTGCTGTCTCTGGTCCCTCATACTTATTCCAATTTATCACTTAGAGCTGCTGGGACCCCA TCTGTCAGAGTAGGAGTTGTTGGATCTGGTACAGCCAGCATATTTGATGAAGCTGTTCAGTCTT CAAAGCAGTATCTTGATATGGCATTTGCACCATCGAAGGGTATTCAGTAAACTTCCCACTTGCT CTTTTGACATTTAGAAATAGCATATGCACACATGTGCATCAGGGATGACATTTGCATTTGTCAT TCATTTAAATACCTTTTTTTCCTTGCAAACTGTTCCGCAGTAAAAAATTGACTGACGGTAATGT TATTGCCTGAGTGACTGAAAATTTCATTCTATTTGCATTTTTAGCAACTGGCAAGGTTTTAGCT TTAGAGCTTCCGAAGAATGGAAATGACAAGTGCACTGTTCTCTATCCTGCTTCAGCAAAAGCCA GCACTGACATCGGTGTGTGCATATTACTCCATCTCTTTATGTTTCTGTCTCTCCTAATTCTCCC ATCTATCTGATTTCGTACAGAGATTTTTTTCCTTGTATTCTCGTTCTGATTTTTTCTGGTTCTG TAGGGATCTTTAGTTTCCGTGGAGGTGCCTTTTCTATTGTAAACCATTATTCAGAAAAAAATTG AAAAGGAAGAACAAAATAAACAGATTAACCACAAAAGTCTTAGCTCATTATCTTTCCTCATGGC CATAATCTGTACAAGAGTCTCATTCATCCGATATTTTGCAACTGTCTCACCTTGATAGTTCATG TTTAGTATGCAAATTTTCCTCTGAATATAGAAGTATTTTGAGTAGTTTTAAACTGACATATGGC TCCGTCATTTCAGAGGAAGGACTTTCTGGGCGGGGATTCGAGGTTACTCGGCTGAACACTTACA CAACGGTATGATATTTCTCTATTGCCTAATTGGAGAAGAAAATTCATTTTTACTCACAAGAGAC CACCGTGCTTGCAAATTTGATAATACACACTTGCCCTGAAAAAGAGGGTCACTTGTCATCTTTT CCTGACATTTGGTCAAAGTTCAGATAGAGCACCACATCTTAGATCCTTCTCTTGAGAGAAAACT AATTAGATTTCATCCTGCTGCCTATGACCTTTCCATTTCTTGCAGGCACCAGTCAATCACGTTG ATCAATATCTTCTTGAACTAGCACTCTCTGTTCCCGTTGTTACTGTAGCATCTCCTTCTGCCCT CAGGTACGATATTCCAAATTATTCATTTTTATAGCAAAAGTAGATGGATGACAGGTTGATATCT AATATTGGCTTAAGCAAGTGCACTAATTCTATAGCTGATGACTGTAATTCCACCAACATGCTAG AAAATATTAGACAGATGTGTTCAGACATAGTTCATTGAGCCAGGGAACAGAATTGTATCCTTAT GTTCTTCATCCTTCTACCTTATATTTTTAGAGGCTTTATTCTCTTTCTCCTTTCTCATTCCTTT TTCCTTCTGCTGGGTTATTTGACAGGGTATGGGCTAATCTTACTGCATCGAGACAGTGGGACAA TGCTGTTGCATGTATTGGGGAGACAACAGCTTCTGCAGCTAAAAAACTTGGGTTCAGAAATATA TACCATCCAACAAGTCCTGGTCTTGAAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.153018199

Conservation Information
Conserved circRNAs	NA
PMCS	0.153018199

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							63841433-63838671(+)
63840043-63838671(+)
63840003-63841068(-)
						
						Potential amino acid sequence
						
							MLLHVLGRQQLLQLKNLGSEIYTIQQVLVLKEATFDWIIITSPEAGKVFLDAWKAAGTPSVRVG
VVGSGTASIFDEAVQSSKQYLDMAFAPSKATGKVLALELPKNGNDKCTVLYPASAKASTDIEEG
LSGRGFEVTRLNTYTTAPVNHVDQYLLELALSVPVVTVASPSALRVWANLTASRQWDNAVACIG
ETTASAAKKLGFRNIYHPTSPGLEGGHVRLDYHYFTRGGKGFS*(+)
MAFAPSKATGKVLALELPKNGNDKCTVLYPASAKASTDIEEGLSGRGFEVTRLNTYTTAPVNHV
DQYLLELALSVPVVTVASPSALRVWANLTASRQWDNAVACIGETTASAAKKLGFRNIYHPTSPG
LEGGHVRLDYHYFTRGGKGFS*(+)
MLAVPDPTTPTLTDGVPAAFQASRKTFPASGEVMIIQSNVASFKTRTCWMVYISEPKFFSCRSC
CLPNTCNSIVPLSRCSKISPYPEGRRRCYSNNGNREC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	63841433-63838671(+) 63840043-63838671(+) 63840003-63841068(-)
Potential amino acid sequence	MLLHVLGRQQLLQLKNLGSEIYTIQQVLVLKEATFDWIIITSPEAGKVFLDAWKAAGTPSVRVG VVGSGTASIFDEAVQSSKQYLDMAFAPSKATGKVLALELPKNGNDKCTVLYPASAKASTDIEEG LSGRGFEVTRLNTYTTAPVNHVDQYLLELALSVPVVTVASPSALRVWANLTASRQWDNAVACIG ETTASAAKKLGFRNIYHPTSPGLEGGHVRLDYHYFTRGGKGFS(+) MAFAPSKATGKVLALELPKNGNDKCTVLYPASAKASTDIEEGLSGRGFEVTRLNTYTTAPVNHV DQYLLELALSVPVVTVASPSALRVWANLTASRQWDNAVACIGETTASAAKKLGFRNIYHPTSPG LEGGHVRLDYHYFTRGGKGFS(+) MLAVPDPTTPTLTDGVPAAFQASRKTFPASGEVMIIQSNVASFKTRTCWMVYISEPKFFSCRSC CLPNTCNSIVPLSRCSKISPYPEGRRRCYSNNGNREC*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc04g079320.2_circ_g.2

Address

Any questions?

Supported by