Plant Circular RNA Database

Detail information of Solyc06g009220.2_circ_g.6

			
						 General Information
					
						CircRNA Name
						Solyc06g009220.2_circ_g.6
					
						ID in PlantcircBase
						sly_circ_001885
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr6: 3160960-3162413  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc06g009220.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc06g009220.2_circ_g.1 Solyc06g009220.2_circ_g.2 Solyc06g009220.2_circ_g.3 Solyc06g009220.2_circ_g.4 Solyc06g009220.2_circ_g.5 						
					
						Support reads
						NA
					
						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
						Solyc06g009220.2.1:3

General Information
CircRNA Name	Solyc06g009220.2_circ_g.6
ID in PlantcircBase	sly_circ_001885
Alias	NA
Organism	Solanum lycopersicum
Position	chr6: 3160960-3162413 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc06g009220.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc06g009220.2_circ_g.1 Solyc06g009220.2_circ_g.2 Solyc06g009220.2_circ_g.3 Solyc06g009220.2_circ_g.4 Solyc06g009220.2_circ_g.5
Support reads	NA
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	Solyc06g009220.2.1:3

			
						 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  
						
							ACATCTTCTCGAGCTTGGTGTCAATACAGTAGAATTATTGCCTGTTTTTGAGTTTGATGAACTG
GAATTACAAAGGCGACCTAATCCGAGAGATCACATGgagttgccccgaggtggggtcctttatg
gttatcgcattgatggacctcgaaattggcatgaagggcatcgatttgacgatagcattatttt
gattgatc

									
								

					

						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: 447
Transcript exons: 3160960-3161196,3161905-3162009,3162309-3162413
GAGTTGCCCCGAGGTGGGGTCCTTTATGGTTATCGCATTGATGGACCTCGAAATTGGCATGAAG
GGCATCGATTTGACGATAGCATTATTTTGATTGATCCTTACGCAAAACTAATTGAAGGTCGACG
AGCTTTTGGAGATGAAAGCAATAAAATGTGTAGATTTTTTGGAACTTATGATTTCAATAGCTTG
CCTTTTGACTGGGGAGAAAATTACAAGCTTCCAAATGTACCGGAGAAAGATCTTGTTATATATG
AGATGAATGTTCGTGCTTTTACTGCTGATGAAACAAGTAGTTTGGATCAAGATCAACGGGGAAG
TTACCTTGGCTTAATTGAAAAGATACCACATCTTCTCGAGCTTGGTGTCAATACAGTAGAATTA
TTGCCTGTTTTTGAGTTTGATGAACTGGAATTACAAAGGCGACCTAATCCGAGAGATCACATG
						
					

						Genomic sequence
						
							GAGTTGCCCCGAGGTGGGGTCCTTTATGGTTATCGCATTGATGGACCTCGAAATTGGCATGAAG
GGCATCGATTTGACGATAGCATTATTTTGATTGATCCTTACGCAAAACTAATTGAAGGTCGACG
AGCTTTTGGAGATGAAAGCAATAAAATGTGTAGATTTTTTGGAACTTATGATTTCAATAGCTTG
CCTTTTGACTGGGGAGAAAATTACAAGCTTCCAAATGTACCGGAGGTAGATTGAGAAGAACTAC
TTGAATAACTTTTTTCCTCGTGTGCAAATCTAAAGATAATTTGCTTGCATGTTCAGCTATTTGA
CTTATGAGCTATGACTAGTGACAGAGCTGTCATTTTGTAAGTGCTCAAATTGTCTGCCATTTAG
TTGATCTTGTTATTTCAAGTAAGAGGAGTTTCAGCTTAATCTTCTGTAGTAATATTATTGGTTC
TTTGGTAGATTGAGCTGTAAGATTATAGTACTTAGATCTTTTATAACATTTTACTCTTAAGGAT
AGTTCGATTTGCATTTTACTTATGAGTGGATTATAATGTAGGGACTGCTTGTGTGGTGATTAAT
ATGTAACAGATTGCTATGCAGTCATTAACGATCAAGGAATTGTTGTGTAGTGATTAAGAGATTA
TTGCCATACAAGAATAACCTTTTTTTAGTGACATTCTTGTCTTTGAATAGTCTAATCTCTGTAT
GGCTAATACACGTATTCTTGTTTCACATTGTATCTAGTATATAATATCACATAGATTCTCGTAT
AACTGAAGTTGTATTATTTGGATACCACCAACCAAATGTTGCATTACATAATGCGCGATTGTGC
AACCAACCAAATGTTGTGTTATTCTATGCCCGAATATTTGCTGGATTTGTTACCACACAATCAA
CCAAACCAACCATTAACTCCTTGCAGTATATCCTCTTTTCTTTGGGCAGAAAGATCTTGTTATA
TATGAGATGAATGTTCGTGCTTTTACTGCTGATGAAACAAGTAGTTTGGATCAAGATCAACGGG
GAAGTTACCTTGGCTTAATTGAAAAGGTACTTCCATATTCTACTTGTCTATTTTCTCTTTTACC
AACTACTAGCATTTCATTTGTTTGTTGAAGTTTGGTGTATCTTCCTTAATAGCAGTACTGCAAG
TTACACCACGAGTTAACTTCCCAAATACTTACATTTTTGTTTTGGCAAGGTCCAATTTTAAAAT
TGCTTTATATGTTCTTTGGCCCTTTTTCTTAGATTAGATGTCTTTGATATTTTCATCATATACT
AGTCACTTGCAGTAATCTGTTAAACTTATTTTAGTCTTTCAGTTATCTGACATTCATCTACAAA
TGCAGATACCACATCTTCTCGAGCTTGGTGTCAATACAGTAGAATTATTGCCTGTTTTTGAGTT
TGATGAACTGGAATTACAAAGGCGACCTAATCCGAGAGATCACATG
						
					

			
		

Sequences
Splice junction sequence	ACATCTTCTCGAGCTTGGTGTCAATACAGTAGAATTATTGCCTGTTTTTGAGTTTGATGAACTG GAATTACAAAGGCGACCTAATCCGAGAGATCACATGgagttgccccgaggtggggtcctttatg gttatcgcattgatggacctcgaaattggcatgaagggcatcgatttgacgatagcattatttt gattgatc
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: 447 Transcript exons: 3160960-3161196,3161905-3162009,3162309-3162413 GAGTTGCCCCGAGGTGGGGTCCTTTATGGTTATCGCATTGATGGACCTCGAAATTGGCATGAAG GGCATCGATTTGACGATAGCATTATTTTGATTGATCCTTACGCAAAACTAATTGAAGGTCGACG AGCTTTTGGAGATGAAAGCAATAAAATGTGTAGATTTTTTGGAACTTATGATTTCAATAGCTTG CCTTTTGACTGGGGAGAAAATTACAAGCTTCCAAATGTACCGGAGAAAGATCTTGTTATATATG AGATGAATGTTCGTGCTTTTACTGCTGATGAAACAAGTAGTTTGGATCAAGATCAACGGGGAAG TTACCTTGGCTTAATTGAAAAGATACCACATCTTCTCGAGCTTGGTGTCAATACAGTAGAATTA TTGCCTGTTTTTGAGTTTGATGAACTGGAATTACAAAGGCGACCTAATCCGAGAGATCACATG
Genomic sequence	GAGTTGCCCCGAGGTGGGGTCCTTTATGGTTATCGCATTGATGGACCTCGAAATTGGCATGAAG GGCATCGATTTGACGATAGCATTATTTTGATTGATCCTTACGCAAAACTAATTGAAGGTCGACG AGCTTTTGGAGATGAAAGCAATAAAATGTGTAGATTTTTTGGAACTTATGATTTCAATAGCTTG CCTTTTGACTGGGGAGAAAATTACAAGCTTCCAAATGTACCGGAGGTAGATTGAGAAGAACTAC TTGAATAACTTTTTTCCTCGTGTGCAAATCTAAAGATAATTTGCTTGCATGTTCAGCTATTTGA CTTATGAGCTATGACTAGTGACAGAGCTGTCATTTTGTAAGTGCTCAAATTGTCTGCCATTTAG TTGATCTTGTTATTTCAAGTAAGAGGAGTTTCAGCTTAATCTTCTGTAGTAATATTATTGGTTC TTTGGTAGATTGAGCTGTAAGATTATAGTACTTAGATCTTTTATAACATTTTACTCTTAAGGAT AGTTCGATTTGCATTTTACTTATGAGTGGATTATAATGTAGGGACTGCTTGTGTGGTGATTAAT ATGTAACAGATTGCTATGCAGTCATTAACGATCAAGGAATTGTTGTGTAGTGATTAAGAGATTA TTGCCATACAAGAATAACCTTTTTTTAGTGACATTCTTGTCTTTGAATAGTCTAATCTCTGTAT GGCTAATACACGTATTCTTGTTTCACATTGTATCTAGTATATAATATCACATAGATTCTCGTAT AACTGAAGTTGTATTATTTGGATACCACCAACCAAATGTTGCATTACATAATGCGCGATTGTGC AACCAACCAAATGTTGTGTTATTCTATGCCCGAATATTTGCTGGATTTGTTACCACACAATCAA CCAAACCAACCATTAACTCCTTGCAGTATATCCTCTTTTCTTTGGGCAGAAAGATCTTGTTATA TATGAGATGAATGTTCGTGCTTTTACTGCTGATGAAACAAGTAGTTTGGATCAAGATCAACGGG GAAGTTACCTTGGCTTAATTGAAAAGGTACTTCCATATTCTACTTGTCTATTTTCTCTTTTACC AACTACTAGCATTTCATTTGTTTGTTGAAGTTTGGTGTATCTTCCTTAATAGCAGTACTGCAAG TTACACCACGAGTTAACTTCCCAAATACTTACATTTTTGTTTTGGCAAGGTCCAATTTTAAAAT TGCTTTATATGTTCTTTGGCCCTTTTTCTTAGATTAGATGTCTTTGATATTTTCATCATATACT AGTCACTTGCAGTAATCTGTTAAACTTATTTTAGTCTTTCAGTTATCTGACATTCATCTACAAA TGCAGATACCACATCTTCTCGAGCTTGGTGTCAATACAGTAGAATTATTGCCTGTTTTTGAGTT TGATGAACTGGAATTACAAAGGCGACCTAATCCGAGAGATCACATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.524245911

Conservation Information
Conserved circRNAs	NA
PMCS	0.524245911

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3161114-3162410(+)
3162371-3161050(+)
3161030-3162383(-)
						
						Potential amino acid sequence
						
							MCRFFGTYDFNSLPFDWGENYKLPNVPEKDLVIYEMNVRAFTADETSSLDQDQRGSYLGLIEKI
PHLLELGVNTVELLPVFEFDELELQRRPNPRDHMELPRGGVLYGYRIDGPRNWHEGHRFDDSII
LIDPYAKLIEGRRAFGDESNKMCRFFGTYDFNSLPFDWGENYKLPNVPEKDLVIYEMNVRAFTA
DETSSLDQDQRGSYLGLIEKIPHLLELGVNTVELLPVFEFDELELQRRPNPRDHMELPRGGVLY
GYRIDGPRNWHEGHRFDDSIILIDPYAKLIEGRRAFGDESNKMCRFFGTYDFNSLPFDWGENYK
LPNVPEKDLVIYEMNVRAFTADETSSLDQDQRGSYLGLIEKIPHLLELGVNTVELLPVFEFDEL
ELQRRPNPRDHMELPRGGVLYGYRIDGPRNWHEGHRFDDSIILIDPYAKLIEGRRAFGDESNKM
CRFFGTYDFNSLPFDWGENYKLPNVPEKDLVIYEMNVRAFTADETSSLDQDQRGSYLGLIEKIP
HLLELGVNTVELLPVFEFDELELQRRPNPRDHM(+)
MNWNYKGDLIREITWSCPEVGSFMVIALMDLEIGMKGIDLTIALF*(+)
MPFMPISRSINAITIKDPTSGQLHVISRIRSPL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3161114-3162410(+) 3162371-3161050(+) 3161030-3162383(-)
Potential amino acid sequence	MCRFFGTYDFNSLPFDWGENYKLPNVPEKDLVIYEMNVRAFTADETSSLDQDQRGSYLGLIEKI PHLLELGVNTVELLPVFEFDELELQRRPNPRDHMELPRGGVLYGYRIDGPRNWHEGHRFDDSII LIDPYAKLIEGRRAFGDESNKMCRFFGTYDFNSLPFDWGENYKLPNVPEKDLVIYEMNVRAFTA DETSSLDQDQRGSYLGLIEKIPHLLELGVNTVELLPVFEFDELELQRRPNPRDHMELPRGGVLY GYRIDGPRNWHEGHRFDDSIILIDPYAKLIEGRRAFGDESNKMCRFFGTYDFNSLPFDWGENYK LPNVPEKDLVIYEMNVRAFTADETSSLDQDQRGSYLGLIEKIPHLLELGVNTVELLPVFEFDEL ELQRRPNPRDHMELPRGGVLYGYRIDGPRNWHEGHRFDDSIILIDPYAKLIEGRRAFGDESNKM CRFFGTYDFNSLPFDWGENYKLPNVPEKDLVIYEMNVRAFTADETSSLDQDQRGSYLGLIEKIP HLLELGVNTVELLPVFEFDELELQRRPNPRDHM(+) MNWNYKGDLIREITWSCPEVGSFMVIALMDLEIGMKGIDLTIALF(+) MPFMPISRSINAITIKDPTSGQLHVISRIRSPL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Tan et al., 2017

circRNA

Detail information of Solyc06g009220.2_circ_g.6

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