Plant Circular RNA Database

Detail information of Solyc12g009400.1_circ_ag.1

			
						 General Information
					
						CircRNA Name
						Solyc12g009400.1_circ_ag.1
					
						ID in PlantcircBase
						sly_circ_003521
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr12: 2685639-2689812  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							NA						
					
						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
						NA

General Information
CircRNA Name	Solyc12g009400.1_circ_ag.1
ID in PlantcircBase	sly_circ_003521
Alias	NA
Organism	Solanum lycopersicum
Position	chr12: 2685639-2689812 JBrowse»
Reference genome	SL2.50.38
Type	ag-circRNA
Identification method	CIRI
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	NA
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	NA

			
						 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  
						
							GCCAGAGCTAGGAGGGGCGATGGTCCCACTCTGGTTGAGTGTGAGACTTACCGGTTTAGAGGAC
ACTCTTTGGCCGATCCAGATGAGCTTCGTGACCCTGctgaaaagaaccattatgctgcacgaga
tcctatcagtgccttgaagaagtatatgtttgagaacaatctggcaagtgaagcagagttgaag
gccattga

									
								

					

						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
						
							CTGAAAAGAACCATTATGCTGCACGAGATCCTATCAGTGCCTTGAAGAAGTATATGTTTGAGAA
CAATCTGGCAAGTGAAGCAGAGTTGAAGGCCATTGATAAGAAGATTGATGAACTGGTTGAAGAA
GCTGTCGAATTTGCGGATGAAAGCCCTCATCCTGTTCGTAGCCAGCTGCTCGAGAACGTGTTTG
CTGATCCAAAGGGCTTTGGCATTGGGCCTGACGGAAGGTACAGATGTGAAGATCCCAAGTTCAC
CGAAGGCACTGCTCATGTCTAGGTCTCAAGGCACATTCAGTAATCAATAATATCAGGTTCTAAG
TTACTGAATTAGTGATTGCCAATTATACTTCTATATAAAGGTCTGGAAGTCCTCCTTATTAGGA
AGTTTGGTACAAAGGTACTTTATTATTTCAATTTTAGTTCAAAATTTTGTTGTTATTAGTTTCA
CATTGTTTTCAAGTTGTACTATATTATGAACAACAAAATCTATTTCAAACACACAATCTCTTAT
TTGGAAAAACCAAGTTGTATGGTTATAATAATCGTCTCGTATCCAAGGGTGTGGTTTAGTGGTC
AATGAAGTGGGTTGAGAGCCACGACAGGTTCAAATTCTAGCAAAGACCAAAAAAAAGCCATTAG
GTGATGTGTTCCCATCTGTCCTAACCTTTGGTGGATAGATTTACCTAGTACCTGTTGCTGGTGG
GAGGTGACGTGGAATTAATCGAGATGTGTACAAACTTGGAAAACATCACCTAAAAGTTTTTAAA
TTCTCACCCATCTGTTGCTCTGTATCGAAGTTCGATTAAATTTCAATCTTTAGTGAAATGTCTC
ATATTAAAAAAAATTAAAATTTTTATAACTGATTCAAACTCGAAATCTGATGAAGAATGAAGGA
TCTAGATGATTATTCTATTTCTAATTCTTTTTTAATTTTTTGGAGGCTAATGAGTATTTTGTTT
AGTTCCTTGTGGAATTATTTAATTTATTAAATAATTAGTATATTAGTTTTTTTTTTTGTCTATT
TATATATATTATGCCTAAATTACAGTCATATGAAGAAAATAATGTACACTTAACATAAGATAAA
ATAGTCAAATAATTGTAGTGATATATAATTTGTTAAAATTGTAAAGATTTATAACTAGAGAGAT
TAAAACTATGCATATATCAATTAGTTAAAGGTTAAATTTGTTTAGATATATCAGAGATAGCACA
AGAATAAAATTGAAGATTAAATTTGCTTAGATACACAATAATAAAAATTGAAATTTGGTGATAT
TTAAAGATTAAAATATTTTAAATTATTGGTTATTATAAATTATGGTCTATTTGATTTATCTTAA
ATATTTTTATTTTGATTAGACACTAATTTTTAGAAAAAAGCGAGTAACATCGACAAAGAGACAA
TCTTAAATCGAAAATGTGTTTTCATGAAGTATAAACATCTCAAAAAGATAATAGAGACGTATAA
AGATTTACTCAACTTAAACAAAAAGTGACCCGCATGTGCAAAAGCATAAGAGAGAATCTTCGTG
AAATTAATTATTATGAATTTTACAACAAAGTTAATTGACAGATTCAATGACAATATAAAGAGAA
TTCAATTAATTCGCTATTTAATACGAATTGATAAAATGCAAATTATTCAATAAGTAAAAATAAA
TTTTTTTTAAAAAATAAAACATATCTAAACCCTAGTTAATCAAAGTTTTCAATTTCAAACCTTA
GGTATGAAAATATTTTTAGATAACATTTTATTCTAATGAATCTTATCGTAATTATTTATAAGTT
TTAATAAATCATACGACAATATAAATATTAGACATCGAACGAAATCGAGAGGGTGAGGCCTTAA
TAGTTCTATCAAATTATTAGTCCAACATCCCCATTTTGAGTTCTTTGACGTTAAATCCAACAAT
TTGCTTACATTTTCCCTTCTTGTTTTCTCCGCTCACTTCTTCCTTTATATATCACGCTTCATCT
TCTGAACAATCCCATAAAATACATCAAGTTTTTCTCTGTAATCATGGCTGCATCAGCCTCTTCT
TTTGCTGCTAACAATTTTTTGCAGCCTATCAACTCCACCAGATCCATTGACAACAACAACAAGA
AGACCCTTTTGGGAAATCAGCTTAAAGACAGCTCCTTTTTTCTTGGATCAGCTAAGAAACTCTA
TATGAAGAAACCCTTTTCGTCTCAGAACTCGAAAAGCCGATCTAATGGTGTTTTCGCTGTTTCT
GAGGTTGTTAAGAACAAGAAGCCCAATACAGACTCCTCACTCTCCAATCTGGTACTTGCATGTT
TTTAGTTTCTTCTTAAAAAATGTTTCTTTTTGATAATTGTGTTGTTCAGGCCAGCTTGTGTGCA
GATGGGAAGAAATCACAATTGATGTTTGTTTTTGGTCTTATGAGTTGTTTTTTACAATTGGGTT
ATGATTGTTTAGATCAATGGTGTTTTGAACTGGATTTCTGTTAATTAAGTGCTTATATTTTGTT
TTACCAAAAGTATGATGATTTAGCATTACAATTTTGGTGTGAATTCCGATTTGGAGTATAAAAT
TTACATACTTAGAATCTGTAAGATTAGTAGCATTGTGTGAATTTGGATATTGATTAAGTGTTGT
TTTGAAAACACGATTTACATATTTCACAACTAAGTAAACTAATGCACAACGTTTTGTGATTGTT
AGAACGGGTAAGAATCTCACATTGGTTGGGGTATGGACGGAACGTGTGTTGATATGGAATTAAT
CCTCCCCTCGAGATCTAGCTTTTGGGTTGAGTTAGACTCTGTGCTATTTGGTGGGCCAAAGTAG
TCTACCGGCGGTGAAAAGACGATAGTAGACCAGACGGGGGCACCACTAGAACACCCGAATAAGG
ATCTATTTTCTTTTGAAGCTATAGTACATATGCACTTTATACGTTTGTCTTACTAATAATATTC
CTTAGCGTACATCTGTACTATAAACCTCCCCTCTGGGAGGTGTTTTCAAGGGAAGGCGGACTCC
GCAGCTAGGTATCATATTTGGGATTCGCGTCCACGTTCTAGTTGGGCGTAGATGTTAGGGGGTG
GTGGTGTTAGAGTGTGTTAGAGTTTCACATTGGTTGGGAATAGACGGATGATTTGCTAATATGG
ACTTGCACAATCCTTCCCTTAAGAGCTAGTTCATGGGGTTGAGTTAGGGTCTAGTGCCACATCT
TTACCGCAATGAAAAATATCTATAAATGTTCCAAAAGTTGTAGTCAAAGAAAAATGGTAATAAG
CTCTAACGCTAGTAAAAGTATTATATAAAATTGGACCAGCGTAGTTATTTTTGTATTTGCTTGT
GTTAATTCACTTACTGTAAGCAAATCTAGTTTTAATTCAATTTTTTGTTTGTGTTGTCAATCTA
GTTAATTACCAAGGATGAAGGGTTGGAGTTGTATGAAGATATGGTTCTTGGAAGAGCGTTTGAG
GACATGTGTGCCCAAATGTATTACAGGGGAAAAATGTTTGGTTTTGTGCATTTGTACAACGGCC
AAGAGGCAGTCTCTACTGGGTTCATTAAGCTACTGAAGAAGGAGGATTCTGTGGTTAGCACTTA
TCGTGATCACGTCCATGCATTGAGCAAAGGGGTTCCAGCACGTCAAGTGATGAGCGAGCTCTTT
GGGAAGACCACTGGCTGTTGCAGAGGCCAGGGTGGCTCCATGCACATGTTCTCTAAAGAGCACA
ACGTTCTTGGTGGTTTCGCTTTCATTGGTGAGGGTATCCCTGTGGCAACAGGTGCCGCCTTCAC
TAGCAAGTATAGAAGGGAGGTCATGAAAGAGGCAGATTGTGATCATGTAACTATGGCCTTCTTT
GGTGATGGAACTTGCAACAATGGCCAGTTCTTTGAGTGTTTGAACATGGCTGCTCTTTGGAAAT
TGCCCATTATATTTGTTGTTGAGAACAATTTGTGGGCAATTGGAATGTCTCACTTGAGATCTAC
TTCAGATCCTGAAATTTGGAAGAAAGGTCCCGCCTTCGGGATGCCTGGGGTTCATGTTGATGGC
ATGGATGTGTTGAAGGTGAGGGAGGTAGCAAAGGAAGCTGTTGCCAGAGCTAGGAGGGGCGATG
GTCCCACTCTGGTTGAGTGTGAGACTTACCGGTTTAGAGGACACTCTTTGGCCGATCCAGATGA
GCTTCGTGACCCTG
						
					

			
		

Sequences
Splice junction sequence	GCCAGAGCTAGGAGGGGCGATGGTCCCACTCTGGTTGAGTGTGAGACTTACCGGTTTAGAGGAC ACTCTTTGGCCGATCCAGATGAGCTTCGTGACCCTGctgaaaagaaccattatgctgcacgaga tcctatcagtgccttgaagaagtatatgtttgagaacaatctggcaagtgaagcagagttgaag gccattga
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	CTGAAAAGAACCATTATGCTGCACGAGATCCTATCAGTGCCTTGAAGAAGTATATGTTTGAGAA CAATCTGGCAAGTGAAGCAGAGTTGAAGGCCATTGATAAGAAGATTGATGAACTGGTTGAAGAA GCTGTCGAATTTGCGGATGAAAGCCCTCATCCTGTTCGTAGCCAGCTGCTCGAGAACGTGTTTG CTGATCCAAAGGGCTTTGGCATTGGGCCTGACGGAAGGTACAGATGTGAAGATCCCAAGTTCAC CGAAGGCACTGCTCATGTCTAGGTCTCAAGGCACATTCAGTAATCAATAATATCAGGTTCTAAG TTACTGAATTAGTGATTGCCAATTATACTTCTATATAAAGGTCTGGAAGTCCTCCTTATTAGGA AGTTTGGTACAAAGGTACTTTATTATTTCAATTTTAGTTCAAAATTTTGTTGTTATTAGTTTCA CATTGTTTTCAAGTTGTACTATATTATGAACAACAAAATCTATTTCAAACACACAATCTCTTAT TTGGAAAAACCAAGTTGTATGGTTATAATAATCGTCTCGTATCCAAGGGTGTGGTTTAGTGGTC AATGAAGTGGGTTGAGAGCCACGACAGGTTCAAATTCTAGCAAAGACCAAAAAAAAGCCATTAG GTGATGTGTTCCCATCTGTCCTAACCTTTGGTGGATAGATTTACCTAGTACCTGTTGCTGGTGG GAGGTGACGTGGAATTAATCGAGATGTGTACAAACTTGGAAAACATCACCTAAAAGTTTTTAAA TTCTCACCCATCTGTTGCTCTGTATCGAAGTTCGATTAAATTTCAATCTTTAGTGAAATGTCTC ATATTAAAAAAAATTAAAATTTTTATAACTGATTCAAACTCGAAATCTGATGAAGAATGAAGGA TCTAGATGATTATTCTATTTCTAATTCTTTTTTAATTTTTTGGAGGCTAATGAGTATTTTGTTT AGTTCCTTGTGGAATTATTTAATTTATTAAATAATTAGTATATTAGTTTTTTTTTTTGTCTATT TATATATATTATGCCTAAATTACAGTCATATGAAGAAAATAATGTACACTTAACATAAGATAAA ATAGTCAAATAATTGTAGTGATATATAATTTGTTAAAATTGTAAAGATTTATAACTAGAGAGAT TAAAACTATGCATATATCAATTAGTTAAAGGTTAAATTTGTTTAGATATATCAGAGATAGCACA AGAATAAAATTGAAGATTAAATTTGCTTAGATACACAATAATAAAAATTGAAATTTGGTGATAT TTAAAGATTAAAATATTTTAAATTATTGGTTATTATAAATTATGGTCTATTTGATTTATCTTAA ATATTTTTATTTTGATTAGACACTAATTTTTAGAAAAAAGCGAGTAACATCGACAAAGAGACAA TCTTAAATCGAAAATGTGTTTTCATGAAGTATAAACATCTCAAAAAGATAATAGAGACGTATAA AGATTTACTCAACTTAAACAAAAAGTGACCCGCATGTGCAAAAGCATAAGAGAGAATCTTCGTG AAATTAATTATTATGAATTTTACAACAAAGTTAATTGACAGATTCAATGACAATATAAAGAGAA TTCAATTAATTCGCTATTTAATACGAATTGATAAAATGCAAATTATTCAATAAGTAAAAATAAA TTTTTTTTAAAAAATAAAACATATCTAAACCCTAGTTAATCAAAGTTTTCAATTTCAAACCTTA GGTATGAAAATATTTTTAGATAACATTTTATTCTAATGAATCTTATCGTAATTATTTATAAGTT TTAATAAATCATACGACAATATAAATATTAGACATCGAACGAAATCGAGAGGGTGAGGCCTTAA TAGTTCTATCAAATTATTAGTCCAACATCCCCATTTTGAGTTCTTTGACGTTAAATCCAACAAT TTGCTTACATTTTCCCTTCTTGTTTTCTCCGCTCACTTCTTCCTTTATATATCACGCTTCATCT TCTGAACAATCCCATAAAATACATCAAGTTTTTCTCTGTAATCATGGCTGCATCAGCCTCTTCT TTTGCTGCTAACAATTTTTTGCAGCCTATCAACTCCACCAGATCCATTGACAACAACAACAAGA AGACCCTTTTGGGAAATCAGCTTAAAGACAGCTCCTTTTTTCTTGGATCAGCTAAGAAACTCTA TATGAAGAAACCCTTTTCGTCTCAGAACTCGAAAAGCCGATCTAATGGTGTTTTCGCTGTTTCT GAGGTTGTTAAGAACAAGAAGCCCAATACAGACTCCTCACTCTCCAATCTGGTACTTGCATGTT TTTAGTTTCTTCTTAAAAAATGTTTCTTTTTGATAATTGTGTTGTTCAGGCCAGCTTGTGTGCA GATGGGAAGAAATCACAATTGATGTTTGTTTTTGGTCTTATGAGTTGTTTTTTACAATTGGGTT ATGATTGTTTAGATCAATGGTGTTTTGAACTGGATTTCTGTTAATTAAGTGCTTATATTTTGTT TTACCAAAAGTATGATGATTTAGCATTACAATTTTGGTGTGAATTCCGATTTGGAGTATAAAAT TTACATACTTAGAATCTGTAAGATTAGTAGCATTGTGTGAATTTGGATATTGATTAAGTGTTGT TTTGAAAACACGATTTACATATTTCACAACTAAGTAAACTAATGCACAACGTTTTGTGATTGTT AGAACGGGTAAGAATCTCACATTGGTTGGGGTATGGACGGAACGTGTGTTGATATGGAATTAAT CCTCCCCTCGAGATCTAGCTTTTGGGTTGAGTTAGACTCTGTGCTATTTGGTGGGCCAAAGTAG TCTACCGGCGGTGAAAAGACGATAGTAGACCAGACGGGGGCACCACTAGAACACCCGAATAAGG ATCTATTTTCTTTTGAAGCTATAGTACATATGCACTTTATACGTTTGTCTTACTAATAATATTC CTTAGCGTACATCTGTACTATAAACCTCCCCTCTGGGAGGTGTTTTCAAGGGAAGGCGGACTCC GCAGCTAGGTATCATATTTGGGATTCGCGTCCACGTTCTAGTTGGGCGTAGATGTTAGGGGGTG GTGGTGTTAGAGTGTGTTAGAGTTTCACATTGGTTGGGAATAGACGGATGATTTGCTAATATGG ACTTGCACAATCCTTCCCTTAAGAGCTAGTTCATGGGGTTGAGTTAGGGTCTAGTGCCACATCT TTACCGCAATGAAAAATATCTATAAATGTTCCAAAAGTTGTAGTCAAAGAAAAATGGTAATAAG CTCTAACGCTAGTAAAAGTATTATATAAAATTGGACCAGCGTAGTTATTTTTGTATTTGCTTGT GTTAATTCACTTACTGTAAGCAAATCTAGTTTTAATTCAATTTTTTGTTTGTGTTGTCAATCTA GTTAATTACCAAGGATGAAGGGTTGGAGTTGTATGAAGATATGGTTCTTGGAAGAGCGTTTGAG GACATGTGTGCCCAAATGTATTACAGGGGAAAAATGTTTGGTTTTGTGCATTTGTACAACGGCC AAGAGGCAGTCTCTACTGGGTTCATTAAGCTACTGAAGAAGGAGGATTCTGTGGTTAGCACTTA TCGTGATCACGTCCATGCATTGAGCAAAGGGGTTCCAGCACGTCAAGTGATGAGCGAGCTCTTT GGGAAGACCACTGGCTGTTGCAGAGGCCAGGGTGGCTCCATGCACATGTTCTCTAAAGAGCACA ACGTTCTTGGTGGTTTCGCTTTCATTGGTGAGGGTATCCCTGTGGCAACAGGTGCCGCCTTCAC TAGCAAGTATAGAAGGGAGGTCATGAAAGAGGCAGATTGTGATCATGTAACTATGGCCTTCTTT GGTGATGGAACTTGCAACAATGGCCAGTTCTTTGAGTGTTTGAACATGGCTGCTCTTTGGAAAT TGCCCATTATATTTGTTGTTGAGAACAATTTGTGGGCAATTGGAATGTCTCACTTGAGATCTAC TTCAGATCCTGAAATTTGGAAGAAAGGTCCCGCCTTCGGGATGCCTGGGGTTCATGTTGATGGC ATGGATGTGTTGAAGGTGAGGGAGGTAGCAAAGGAAGCTGTTGCCAGAGCTAGGAGGGGCGATG GTCCCACTCTGGTTGAGTGTGAGACTTACCGGTTTAGAGGACACTCTTTGGCCGATCCAGATGA GCTTCGTGACCCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						1.099886872

Conservation Information
Conserved circRNAs	NA
PMCS	1.099886872

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc12g009400.1_circ_ag.1

Address

Any questions?

Supported by