Plant Circular RNA Database

Detail information of Solyc09g091820.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc09g091820.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_002987
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr9: 71033789-71034923  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI; find_circ
					
						Parent gene
						
							Solyc09g091820.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						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  
						
							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
						Solyc09g091820.2.1:6

General Information
CircRNA Name	Solyc09g091820.2_circ_g.1
ID in PlantcircBase	sly_circ_002987
Alias	NA
Organism	Solanum lycopersicum
Position	chr9: 71033789-71034923 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI; find_circ
Parent gene	Solyc09g091820.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	NA
Support reads	NA
Tissues	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	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	Solyc09g091820.2.1:6

			
						 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  
						
							CACCCATAAGATTCAAAGAGCAATGGAGAAGCACCAAGATTTGTCTGGAGCTGTGCACCATCCA
TCTGAGCTAATTTCTGGAAAATTTGATGGCCTTAAGataagttccttgtctctttccgatgttg
gtgctactgtatcaatcttgcttggttttgcacctcctgctactctttcctctgctagttcatc
aaaggtag

									
								

					

						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: 543
Transcript exons: 71033789-71033884,71033965-71034040,71034252-71034317,71
034424-71034503,71034601-71034687,71034786-71034923
ATAAGTTCCTTGTCTCTTTCCGATGTTGGTGCTACTGTATCAATCTTGCTTGGTTTTGCACCTC
CTGCTACTCTTTCCTCTGCTAGTTCATCAAAGTTGAATGAGGTACTTGTACCAAATCCATTTGA
TAGGCCGGGTTCTGTCCTCATCCTAGAAGTTACAGGAGCTGAAGGTGTTGCTTTTGAGGCCCTT
AGGAGCAATGTAGTAAACGAAAATAGAGCTGACATTCAACTTCCAGATGCAGATAAAGTTTCTC
TTTTTTCATTGGATGAACCAAAAACAGATGCTGAACATTCAGAGAAAGAATTAAGTGAATTTGC
ATCATGGTTGAGTGGTTCATATGTGAATGGAGAGCTGACAATCCCCTTGGAGGATGACGCTAAT
TTGAAATTTCAATTGTCAAAGGAAGCAGATAGGGACTTTGTAACAAGTCTTGTTTCACTCACCC
ATAAGATTCAAAGAGCAATGGAGAAGCACCAAGATTTGTCTGGAGCTGTGCACCATCCATCTGA
GCTAATTTCTGGAAAATTTGATGGCCTTAAG
						
					

						Genomic sequence
						
							ATAAGTTCCTTGTCTCTTTCCGATGTTGGTGCTACTGTATCAATCTTGCTTGGTTTTGCACCTC
CTGCTACTCTTTCCTCTGCTAGTTCATCAAAGGTAGGAAGGATGAATCATTTATTAGCTAATTT
TTTTACTTTAAAGCGAAATATACATCATCAAATATCCATTGGTTGCAGTTGAATGAGGTACTTG
TACCAAATCCATTTGATAGGCCGGGTTCTGTCCTCATCCTAGAAGTTACAGGAGCTGAAGGTAT
GCAAGCTGGAATAAATATATAGTACAGTAGATTAACATACCGAGTTTCTCTTTCTCTCTCTCAC
TCCTGTGTGAGCGTGCACCTGTTTGTGTATATAAGATAAATAATATACTTATTCAAGATTCTAG
TGTGCTTTTTTTGTCTATTAAGCCTCTATCTGGTGATTATATAAGATTGTACTTATTTGATGCC
CATTTGTTGTTATAGGTGTTGCTTTTGAGGCCCTTAGGAGCAATGTAGTAAACGAAAATAGAGC
TGACATTCAACTTCCAGGTAGTTGTCGTTTACTCTTAACGTGTTGTAAGGTGTTTTACTAGTTT
GATATGTAAAAAAAGAGAATTAGATTGGTTTACGTCTAATTAATTTGTCATGCATGCAGATGCA
GATAAAGTTTCTCTTTTTTCATTGGATGAACCAAAAACAGATGCTGAACATTCAGAGAAAGAAT
TAAGTGAATTTGTGAGCGTCTGTTAGCAGTTGCATTGCATGATTATTTTTTCACATTGAATAAC
TTCAAGGTCATACAACTCATGAGAGGATTGATATTTGTAAGCAGGCATCATGGTTGAGTGGTTC
ATATGTGAATGGAGAGCTGACAATCCCCTTGGAGGATGACGCTAATTTGAAATTTCAATTGTCA
AAGGTACTTTTTTAGGCTTAACAACCTATACTATGACTTCTTTTTGTGGTGTTCTTTCCAATTA
GGCCTTTATTGATTGTCCTTTATTACTTGCGGCACAGGAAGCAGATAGGGACTTTGTAACAAGT
CTTGTTTCACTCACCCATAAGATTCAAAGAGCAATGGAGAAGCACCAAGATTTGTCTGGAGCTG
TGCACCATCCATCTGAGCTAATTTCTGGAAAATTTGATGGCCTTAAG
						
					

			
		

Sequences
Splice junction sequence	CACCCATAAGATTCAAAGAGCAATGGAGAAGCACCAAGATTTGTCTGGAGCTGTGCACCATCCA TCTGAGCTAATTTCTGGAAAATTTGATGGCCTTAAGataagttccttgtctctttccgatgttg gtgctactgtatcaatcttgcttggttttgcacctcctgctactctttcctctgctagttcatc aaaggtag
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: 543 Transcript exons: 71033789-71033884,71033965-71034040,71034252-71034317,71 034424-71034503,71034601-71034687,71034786-71034923 ATAAGTTCCTTGTCTCTTTCCGATGTTGGTGCTACTGTATCAATCTTGCTTGGTTTTGCACCTC CTGCTACTCTTTCCTCTGCTAGTTCATCAAAGTTGAATGAGGTACTTGTACCAAATCCATTTGA TAGGCCGGGTTCTGTCCTCATCCTAGAAGTTACAGGAGCTGAAGGTGTTGCTTTTGAGGCCCTT AGGAGCAATGTAGTAAACGAAAATAGAGCTGACATTCAACTTCCAGATGCAGATAAAGTTTCTC TTTTTTCATTGGATGAACCAAAAACAGATGCTGAACATTCAGAGAAAGAATTAAGTGAATTTGC ATCATGGTTGAGTGGTTCATATGTGAATGGAGAGCTGACAATCCCCTTGGAGGATGACGCTAAT TTGAAATTTCAATTGTCAAAGGAAGCAGATAGGGACTTTGTAACAAGTCTTGTTTCACTCACCC ATAAGATTCAAAGAGCAATGGAGAAGCACCAAGATTTGTCTGGAGCTGTGCACCATCCATCTGA GCTAATTTCTGGAAAATTTGATGGCCTTAAG
Genomic sequence	ATAAGTTCCTTGTCTCTTTCCGATGTTGGTGCTACTGTATCAATCTTGCTTGGTTTTGCACCTC CTGCTACTCTTTCCTCTGCTAGTTCATCAAAGGTAGGAAGGATGAATCATTTATTAGCTAATTT TTTTACTTTAAAGCGAAATATACATCATCAAATATCCATTGGTTGCAGTTGAATGAGGTACTTG TACCAAATCCATTTGATAGGCCGGGTTCTGTCCTCATCCTAGAAGTTACAGGAGCTGAAGGTAT GCAAGCTGGAATAAATATATAGTACAGTAGATTAACATACCGAGTTTCTCTTTCTCTCTCTCAC TCCTGTGTGAGCGTGCACCTGTTTGTGTATATAAGATAAATAATATACTTATTCAAGATTCTAG TGTGCTTTTTTTGTCTATTAAGCCTCTATCTGGTGATTATATAAGATTGTACTTATTTGATGCC CATTTGTTGTTATAGGTGTTGCTTTTGAGGCCCTTAGGAGCAATGTAGTAAACGAAAATAGAGC TGACATTCAACTTCCAGGTAGTTGTCGTTTACTCTTAACGTGTTGTAAGGTGTTTTACTAGTTT GATATGTAAAAAAAGAGAATTAGATTGGTTTACGTCTAATTAATTTGTCATGCATGCAGATGCA GATAAAGTTTCTCTTTTTTCATTGGATGAACCAAAAACAGATGCTGAACATTCAGAGAAAGAAT TAAGTGAATTTGTGAGCGTCTGTTAGCAGTTGCATTGCATGATTATTTTTTCACATTGAATAAC TTCAAGGTCATACAACTCATGAGAGGATTGATATTTGTAAGCAGGCATCATGGTTGAGTGGTTC ATATGTGAATGGAGAGCTGACAATCCCCTTGGAGGATGACGCTAATTTGAAATTTCAATTGTCA AAGGTACTTTTTTAGGCTTAACAACCTATACTATGACTTCTTTTTGTGGTGTTCTTTCCAATTA GGCCTTTATTGATTGTCCTTTATTACTTGCGGCACAGGAAGCAGATAGGGACTTTGTAACAAGT CTTGTTTCACTCACCCATAAGATTCAAAGAGCAATGGAGAAGCACCAAGATTTGTCTGGAGCTG TGCACCATCCATCTGAGCTAATTTCTGGAAAATTTGATGGCCTTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.531728048

Conservation Information
Conserved circRNAs	NA
PMCS	0.531728048

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							71034847-71034920(+)
71034308-71034838(-)
						
						Potential amino acid sequence
						
							MEKHQDLSGAVHHPSELISGKFDGLKISSLSLSDVGATVSILLGFAPPATLSSASSSKLNEVLV
PNPFDRPGSVLILEVTGAEGVAFEALRSNVVNENRADIQLPDADKVSLFSLDEPKTDAEHSEKE
LSEFASWLSGSYVNGELTIPLEDDANLKFQLSKEADRDFVTSLVSLTHKIQRAMEKHQDLSGAV
HHPSELISGKFDGLKISSLSLSDVGATVSILLGFAPPATLSSASSSKLNEVLVPNPFDRPGSVL
ILEVTGAEGVAFEALRSNVVNENRADIQLPDADKVSLFSLDEPKTDAEHSEKELSEFASWLSGS
YVNGELTIPLEDDANLKFQLSKEADRDFVTSLVSLTHKIQRAMEKHQDLSGAVHHPSELISGKF
DGLKISSLSLSDVGATVSILLGFAPPATLSSASSSKLNEVLVPNPFDRPGSVLILEVTGAEGVA
FEALRSNVVNENRADIQLPDADKVSLFSLDEPKTDAEHSEKELSEFASWLSGSYVNGELTIPLE
DDANLKFQLSKEADRDFVTSLVSLTHKIQRAMEKHQDLSGAVHHPSELISGKFDGLK(+)
MSALFSFTTLLLRASKATPSAPVTSRMRTEPGLSNGFGTSTSFNFDELAEERVAGGAKPSKIDT
VAPTSERDKELILRPSNFPEISSDGWCTAPDKSWCFSIAL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	71034847-71034920(+) 71034308-71034838(-)
Potential amino acid sequence	MEKHQDLSGAVHHPSELISGKFDGLKISSLSLSDVGATVSILLGFAPPATLSSASSSKLNEVLV PNPFDRPGSVLILEVTGAEGVAFEALRSNVVNENRADIQLPDADKVSLFSLDEPKTDAEHSEKE LSEFASWLSGSYVNGELTIPLEDDANLKFQLSKEADRDFVTSLVSLTHKIQRAMEKHQDLSGAV HHPSELISGKFDGLKISSLSLSDVGATVSILLGFAPPATLSSASSSKLNEVLVPNPFDRPGSVL ILEVTGAEGVAFEALRSNVVNENRADIQLPDADKVSLFSLDEPKTDAEHSEKELSEFASWLSGS YVNGELTIPLEDDANLKFQLSKEADRDFVTSLVSLTHKIQRAMEKHQDLSGAVHHPSELISGKF DGLKISSLSLSDVGATVSILLGFAPPATLSSASSSKLNEVLVPNPFDRPGSVLILEVTGAEGVA FEALRSNVVNENRADIQLPDADKVSLFSLDEPKTDAEHSEKELSEFASWLSGSYVNGELTIPLE DDANLKFQLSKEADRDFVTSLVSLTHKIQRAMEKHQDLSGAVHHPSELISGKFDGLK(+) MSALFSFTTLLLRASKATPSAPVTSRMRTEPGLSNGFGTSTSFNFDELAEERVAGGAKPSKIDT VAPTSERDKELILRPSNFPEISSDGWCTAPDKSWCFSIAL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yang et al., 2020

circRNA

Detail information of Solyc09g091820.2_circ_g.1

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