Plant Circular RNA Database

Detail information of Solyc03g114460.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc03g114460.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_001136
					
						Alias
						3:58506811|58509586
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr3: 64453761-64456536  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc03g114460.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc03g114460.2_circ_g.1 						
					
						Support reads
						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
						Solyc03g114460.2.1:3

General Information
CircRNA Name	Solyc03g114460.2_circ_g.2
ID in PlantcircBase	sly_circ_001136
Alias	3:58506811\|58509586
Organism	Solanum lycopersicum
Position	chr3: 64453761-64456536 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc03g114460.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc03g114460.2_circ_g.1
Support reads	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	Solyc03g114460.2.1:3

			
						 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  
						
							TATTGCGGGTTATGTGGTTGTCTCAATCGCTGACAGTTTTGCTCCAACTGAAATTGCAACGAGG
CTCATGATATCAAAAGCAAAGGCTATTTTCACTCAGggaagctgctaagttgactaacattggt
aagttattggagcggcgaggaaaggagttactggggtcaagttataaaaatcctatttcaagct
tctctgat

									
								

					

						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: 586
Transcript exons: 64453761-64453890,64454015-64454265,64456332-64456536
GGAAGCTGCTAAGTTGACTAACATTGGTAAGTTATTGGAGCGGCGAGGAAAGGAGTTACTGGGG
TCAAGTTATAAAAATCCTATTTCAAGCTTCTCTGATTTTCAAGAATTTACAGTCTCAAACTTGG
AGATGTACTGGAAGATCGTATTTGAGGAAATGGATATTTTTTTCTCTGTTAGTCCTGAATGTAT
TCTGCATGAAACTCCTTTGCACCCTGGTGGTCAATGGCTTCCTGGGGCACGTCTAAATCCTGCC
AAGAATTGTTTGAGGTTGAATGCAAAGAGGAGTTTAAGTGACATAGTTGTGATAACACGTGATG
AAGGAGATGATGAGGCACCTGTTACCAAATTGACTCTTGAGGAACTAAGATCTGCAGTATGGAG
AGTCGCATATTGCATTGATACACTGGGATTGGACAAAGGATCTGCCATTGCCATAGATATGCCA
ATGGATGTCAATTCCGTAGTGATCTACTTGGCCATTGTTATTGCGGGTTATGTGGTTGTCTCAA
TCGCTGACAGTTTTGCTCCAACTGAAATTGCAACGAGGCTCATGATATCAAAAGCAAAGGCTAT
TTTCACTCAG
						
					

						Genomic sequence
						
							GGAAGCTGCTAAGTTGACTAACATTGGTAAGTTATTGGAGCGGCGAGGAAAGGAGTTACTGGGG
TCAAGTTATAAAAATCCTATTTCAAGCTTCTCTGATTTTCAAGAATTTACAGTCTCAAACTTGG
AGGTACTTGTATGTTTTGCCGGCATTATTTGCAGCTTTACTTTCTTGTTTGTGAATGAGTAAAT
ATTGATGCAGTGTCCTTTTTTACCTCTTACTGAAACTTTTCCGTCTCAAAATATCTTTGTAGAT
GTACTGGAAGATCGTATTTGAGGAAATGGATATTTTTTTCTCTGTTAGTCCTGAATGTATTCTG
CATGAAACTCCTTTGCACCCTGGTGGTCAATGGCTTCCTGGGGCACGTCTAAATCCTGCCAAGA
ATTGTTTGAGGTTGAATGCAAAGAGGAGTTTAAGTGACATAGTTGTGATAACACGTGATGAAGG
AGATGATGAGGCACCTGTTACCAAATTGACTCTTGAGGAACTAAGATCTGCAGTATGGTACAAT
GATTTTTGTTAATGTGGATTACAAAATTAAGTTGTAGTACATATATCAATTGTTTTTTCAAGTC
AGAATACTTTTGCTTGTTATTTGGATATCTGAAATATTTCATCTGAGTCTTCCTGCTGAATGGC
CTAAAATATATCATTATGTTCATCATAAAATGTTGGTCCTTTAGTAATTGTGCGTACTGCTGAA
CTTGCTGACTATTTATGACTTTAAGGTGACTCAGCTCTGGTCATGGCACATATCTGAAAAAAAA
ATGTTAAGATGCACACTATCAACAAGATCCAGTGGCAAGAGACTCCAGTTCAAACAATGAGGTT
GAAGTCACCATAGGAGTATAGTGGGAGAAGACCACTACTGACTTCTGCCTCGGCAGGGGGAATG
GGGGGAGGGGTTTAGGAGTTCATGTATATTAAATAAATGTACTTCCTCAGCAGTTCCAGTGTTG
AGCCATCCACATTCCATGTGATACATGGGGAAATATGATTTGTTAGTAATATAGGAAATATTGT
ACCCAAAGAAACATTAAAAAAAAGGGTGGGAGGCTGCACCGTGGATATTACCTCTTATTATTTG
TCTATTACTAAGTCAAGGAGGTGGGAAAACCAAATGATGAATGCTGTAAATTGATGTTCAGATC
TTCTACTAGCATCTGAATGTTTATATCATATGTTTCCTGGTCTGCTTGTGAGTTGGACTGGAAC
GAAAATCTGGAAACTTAAGCAAGGATTGCTGTGAGATGGTGTCAAGGACATATAAAACAATATT
TTATGTTACTTGAAAACAAGAGAAAACACTTATGAACCAATTTATTCGACTTCTAACAAGGTTC
ACACACCATTGGCATCGCTTATGTGTGAGCATCAAGTCAGTGAATCTTTTGCACATGCCAGTAG
TACAATCAAATCACTTCTTGTTAAAGTAGGCGATGACTGGACGACAAGGCTTTAGAGAGGTAAC
TGGGTAGACTGGCTGCCACCCAGGAACTCCGGGTGCATGGTCTAATAATGGCTCTGCTCTATTC
AATTCTACAACGAATTACTGTTGAATGGGGTGACTGGGATCTCCTTTCTACATCAAACAAACCC
CGAGTGAACTGTTGCAAATGCGTTTCCATTTCCTTAACTTCTCATGAAAAGCATTTCTGATCTT
ATTTTCCACAGTGCATTGGTTAGACAATTATGGCCTTAAACATGTTATGTTTGTATAATTGTAT
CCACTGGGTTATGCCTTCTAAAATAGTAAAACTTTAGAGCAGTCCAACTCTGACATGCAAAGTT
TTGTTGGGAAGAATGAGAGACTGATTTGATATATACTCCATGCTTGTTGTGAAGAAAGAAGAGA
ATTTTGAGTATTGTGAGGTTGAGCAATCTGATTTTTCCCAGAATGGATAAATGCTACCTTCAAT
TATATGAAACCTATTTAGTAGCCACTTTCTTTTTCTTTTATTGCAGATCCGCTTTTTCCCCCTA
AAAATGAAAAATTACCTAGCACCCAGAAGGATAAAATCAAAGAAAGTTGCTTGAGATGGTTGAT
CATGTTTTGCATCACTTACATATGCATCTGTTCATAGGTGTGAAACTATGGTGAGTGAAGGTGT
TAAATGGTACGAGGTACACCTAAAATCAGATGGAAGGAAAATGTCTTGAAAAGACATAATTTCT
TGGAATTAGTGCGGAATTATCTAAAGATAGGACGAAATGAAAGAAAAAGAGTCCTATAGATGAT
ATCTACTAGTTGAGAATGTCGATCTGAACCTACTGCTTGGTTGAAGTATTTTGACCTTACGATA
TATTTATATGCCAGTAAAAATATAGTGAACTTCTTATATTATTGTAATTACTATTACTATTGTT
CATATATAATTAACTTATCTTTTCACTTCTATTTTTTATTTGGTATGTGATGATAATATGAGTT
GAACTGAAATGGAGAAACATGGTCAGAGAAGATTCATATAACTAACCCGACTTATTAGGGACTA
AGATGTAATTGTTATATGTTTGTTCTGTTTTTATGAGTTATGACTACTAATTGTAAAAACCTTT
CTAAATCACAGGAGAGTCGCATATTGCATTGATACACTGGGATTGGACAAAGGATCTGCCATTG
CCATAGATATGCCAATGGATGTCAATTCCGTAGTGATCTACTTGGCCATTGTTATTGCGGGTTA
TGTGGTTGTCTCAATCGCTGACAGTTTTGCTCCAACTGAAATTGCAACGAGGCTCATGATATCA
AAAGCAAAGGCTATTTTCACTCAG
						
					

			
		

Sequences
Splice junction sequence	TATTGCGGGTTATGTGGTTGTCTCAATCGCTGACAGTTTTGCTCCAACTGAAATTGCAACGAGG CTCATGATATCAAAAGCAAAGGCTATTTTCACTCAGggaagctgctaagttgactaacattggt aagttattggagcggcgaggaaaggagttactggggtcaagttataaaaatcctatttcaagct tctctgat
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: 586 Transcript exons: 64453761-64453890,64454015-64454265,64456332-64456536 GGAAGCTGCTAAGTTGACTAACATTGGTAAGTTATTGGAGCGGCGAGGAAAGGAGTTACTGGGG TCAAGTTATAAAAATCCTATTTCAAGCTTCTCTGATTTTCAAGAATTTACAGTCTCAAACTTGG AGATGTACTGGAAGATCGTATTTGAGGAAATGGATATTTTTTTCTCTGTTAGTCCTGAATGTAT TCTGCATGAAACTCCTTTGCACCCTGGTGGTCAATGGCTTCCTGGGGCACGTCTAAATCCTGCC AAGAATTGTTTGAGGTTGAATGCAAAGAGGAGTTTAAGTGACATAGTTGTGATAACACGTGATG AAGGAGATGATGAGGCACCTGTTACCAAATTGACTCTTGAGGAACTAAGATCTGCAGTATGGAG AGTCGCATATTGCATTGATACACTGGGATTGGACAAAGGATCTGCCATTGCCATAGATATGCCA ATGGATGTCAATTCCGTAGTGATCTACTTGGCCATTGTTATTGCGGGTTATGTGGTTGTCTCAA TCGCTGACAGTTTTGCTCCAACTGAAATTGCAACGAGGCTCATGATATCAAAAGCAAAGGCTAT TTTCACTCAG
Genomic sequence	GGAAGCTGCTAAGTTGACTAACATTGGTAAGTTATTGGAGCGGCGAGGAAAGGAGTTACTGGGG TCAAGTTATAAAAATCCTATTTCAAGCTTCTCTGATTTTCAAGAATTTACAGTCTCAAACTTGG AGGTACTTGTATGTTTTGCCGGCATTATTTGCAGCTTTACTTTCTTGTTTGTGAATGAGTAAAT ATTGATGCAGTGTCCTTTTTTACCTCTTACTGAAACTTTTCCGTCTCAAAATATCTTTGTAGAT GTACTGGAAGATCGTATTTGAGGAAATGGATATTTTTTTCTCTGTTAGTCCTGAATGTATTCTG CATGAAACTCCTTTGCACCCTGGTGGTCAATGGCTTCCTGGGGCACGTCTAAATCCTGCCAAGA ATTGTTTGAGGTTGAATGCAAAGAGGAGTTTAAGTGACATAGTTGTGATAACACGTGATGAAGG AGATGATGAGGCACCTGTTACCAAATTGACTCTTGAGGAACTAAGATCTGCAGTATGGTACAAT GATTTTTGTTAATGTGGATTACAAAATTAAGTTGTAGTACATATATCAATTGTTTTTTCAAGTC AGAATACTTTTGCTTGTTATTTGGATATCTGAAATATTTCATCTGAGTCTTCCTGCTGAATGGC CTAAAATATATCATTATGTTCATCATAAAATGTTGGTCCTTTAGTAATTGTGCGTACTGCTGAA CTTGCTGACTATTTATGACTTTAAGGTGACTCAGCTCTGGTCATGGCACATATCTGAAAAAAAA ATGTTAAGATGCACACTATCAACAAGATCCAGTGGCAAGAGACTCCAGTTCAAACAATGAGGTT GAAGTCACCATAGGAGTATAGTGGGAGAAGACCACTACTGACTTCTGCCTCGGCAGGGGGAATG GGGGGAGGGGTTTAGGAGTTCATGTATATTAAATAAATGTACTTCCTCAGCAGTTCCAGTGTTG AGCCATCCACATTCCATGTGATACATGGGGAAATATGATTTGTTAGTAATATAGGAAATATTGT ACCCAAAGAAACATTAAAAAAAAGGGTGGGAGGCTGCACCGTGGATATTACCTCTTATTATTTG TCTATTACTAAGTCAAGGAGGTGGGAAAACCAAATGATGAATGCTGTAAATTGATGTTCAGATC TTCTACTAGCATCTGAATGTTTATATCATATGTTTCCTGGTCTGCTTGTGAGTTGGACTGGAAC GAAAATCTGGAAACTTAAGCAAGGATTGCTGTGAGATGGTGTCAAGGACATATAAAACAATATT TTATGTTACTTGAAAACAAGAGAAAACACTTATGAACCAATTTATTCGACTTCTAACAAGGTTC ACACACCATTGGCATCGCTTATGTGTGAGCATCAAGTCAGTGAATCTTTTGCACATGCCAGTAG TACAATCAAATCACTTCTTGTTAAAGTAGGCGATGACTGGACGACAAGGCTTTAGAGAGGTAAC TGGGTAGACTGGCTGCCACCCAGGAACTCCGGGTGCATGGTCTAATAATGGCTCTGCTCTATTC AATTCTACAACGAATTACTGTTGAATGGGGTGACTGGGATCTCCTTTCTACATCAAACAAACCC CGAGTGAACTGTTGCAAATGCGTTTCCATTTCCTTAACTTCTCATGAAAAGCATTTCTGATCTT ATTTTCCACAGTGCATTGGTTAGACAATTATGGCCTTAAACATGTTATGTTTGTATAATTGTAT CCACTGGGTTATGCCTTCTAAAATAGTAAAACTTTAGAGCAGTCCAACTCTGACATGCAAAGTT TTGTTGGGAAGAATGAGAGACTGATTTGATATATACTCCATGCTTGTTGTGAAGAAAGAAGAGA ATTTTGAGTATTGTGAGGTTGAGCAATCTGATTTTTCCCAGAATGGATAAATGCTACCTTCAAT TATATGAAACCTATTTAGTAGCCACTTTCTTTTTCTTTTATTGCAGATCCGCTTTTTCCCCCTA AAAATGAAAAATTACCTAGCACCCAGAAGGATAAAATCAAAGAAAGTTGCTTGAGATGGTTGAT CATGTTTTGCATCACTTACATATGCATCTGTTCATAGGTGTGAAACTATGGTGAGTGAAGGTGT TAAATGGTACGAGGTACACCTAAAATCAGATGGAAGGAAAATGTCTTGAAAAGACATAATTTCT TGGAATTAGTGCGGAATTATCTAAAGATAGGACGAAATGAAAGAAAAAGAGTCCTATAGATGAT ATCTACTAGTTGAGAATGTCGATCTGAACCTACTGCTTGGTTGAAGTATTTTGACCTTACGATA TATTTATATGCCAGTAAAAATATAGTGAACTTCTTATATTATTGTAATTACTATTACTATTGTT CATATATAATTAACTTATCTTTTCACTTCTATTTTTTATTTGGTATGTGATGATAATATGAGTT GAACTGAAATGGAGAAACATGGTCAGAGAAGATTCATATAACTAACCCGACTTATTAGGGACTA AGATGTAATTGTTATATGTTTGTTCTGTTTTTATGAGTTATGACTACTAATTGTAAAAACCTTT CTAAATCACAGGAGAGTCGCATATTGCATTGATACACTGGGATTGGACAAAGGATCTGCCATTG CCATAGATATGCCAATGGATGTCAATTCCGTAGTGATCTACTTGGCCATTGTTATTGCGGGTTA TGTGGTTGTCTCAATCGCTGACAGTTTTGCTCCAACTGAAATTGCAACGAGGCTCATGATATCA AAAGCAAAGGCTATTTTCACTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.351703279

Conservation Information
Conserved circRNAs	NA
PMCS	0.351703279

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							64454016-64453769(+)
						
						Potential amino acid sequence
						
							MYWKIVFEEMDIFFSVSPECILHETPLHPGGQWLPGARLNPAKNCLRLNAKRSLSDIVVITRDE
GDDEAPVTKLTLEELRSAVWRVAYCIDTLGLDKGSAIAIDMPMDVNSVVIYLAIVIAGYVVVSI
ADSFAPTEIATRLMISKAKAIFTQGSC*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	64454016-64453769(+)
Potential amino acid sequence	MYWKIVFEEMDIFFSVSPECILHETPLHPGGQWLPGARLNPAKNCLRLNAKRSLSDIVVITRDE GDDEAPVTKLTLEELRSAVWRVAYCIDTLGLDKGSAIAIDMPMDVNSVVIYLAIVIAGYVVVSI ADSFAPTEIATRLMISKAKAIFTQGSC*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc03g114460.2_circ_g.2

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