Plant Circular RNA Database

Detail information of Solyc03g033540.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc03g033540.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_000953
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr3: 5077212-5078880  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc03g033540.2						
					
						Parent gene annotation
						
							Calcium-dependent protein kinase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc03g033540.2_circ_g.1 						
					
						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  
						
							CT-AC							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
						Solyc03g033540.2.1:4

General Information
CircRNA Name	Solyc03g033540.2_circ_g.2
ID in PlantcircBase	sly_circ_000953
Alias	NA
Organism	Solanum lycopersicum
Position	chr3: 5077212-5078880 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc03g033540.2
Parent gene annotation	Calcium-dependent protein kinase
Parent gene strand	-
Alternative splicing	Solyc03g033540.2_circ_g.1
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	CT-AC 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	Solyc03g033540.2.1:4

			
						 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  
						
							TTTAGACGACTGTATTTGACAAATTGCCGCATGTTGGATAAAACAGAAATGTCCAGTGGAATCT
CAGATGCATCCCCTCCTTCTCGGACCCATGGATGTGcattttaagttcttctggagtaatgaat
ccatctttatcaacatcaaatttctcaaaagcagcttgtgatctttgctgccactttgtagaat
tatgctcc

									
								

					

						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: 461
Transcript exons: 5077212-5077385,5078306-5078368,5078561-5078668,5078765-
5078880
CATTTTAAGTTCTTCTGGAGTAATGAATCCATCTTTATCAACATCAAATTTCTCAAAAGCAGCT
TGTGATCTTTGCTGCCACTTTGTAGAATTATGCTCCTCCAACTGATGGACATGTAGAGTGGCAG
CCACAAACTCCGGGAAATCAACAAGCCCATCCGTGTTACTGTCAATCGCTTGAAGAATCTCAAG
AACTCGTGATTCTTTCATTTTCCATGGGAGATCCTTTGCAAGGGCCTGTCTCATTTCTTCGAGA
CTGATGACACCATTCTTATCCACATCAATTGCAGAAAATTGATCCCGCAGATCAGCGATCTCCT
CCTCATCAAGTGTGCTAGCTAACGCACGTAAAGCAAACTGTTTTAGACGACTGTATTTGACAAA
TTGCCGCATGTTGGATAAAACAGAAATGTCCAGTGGAATCTCAGATGCATCCCCTCCTTCTCGG
ACCCATGGATGTG
						
					

						Genomic sequence
						
							CATTTTAAGTTCTTCTGGAGTAATGAATCCATCTTTATCAACATCAAATTTCTCAAAAGCAGCT
TGTGATCTTTGCTGCCACTTTGTAGAATTATGCTCCTCCAACTGATGGACATGTAGAGTGGCAG
CCACAAACTCCGGGAAATCAACAAGCCCATCCGTGTTACTGTCAATCTGCCAAGCAATGAACAA
AATACTTTAGGTCCCGGAACTGCAGAAGAGACCATATAGTAGAAAGTAATGAACATGCATATGA
TGAAAACTATAAAGATTATTATATTAGTTGGCACTTGGCAGCAATATTAGCATTGACAATTGAG
TAAAGTTTGTAACAAGGATTATGGTGCAGGAAAAATTTGGAATATACAATCTGACACAAAGAAA
TCCCCAAATATTTGGTCACCAATTTAAAAATGGTGTAGTACAAGCTTGCACACACATTAACTAT
TCCATCGAGTGTCTCTAACTCCCACCATCGCAAGTACCAAGTAATTTTGCCTCAATAAGGCTCA
AGCAGATGGGAAGAAGTCAGTCAACGTGTTCTGTCACTTACTGGATTTGAACTCTAGTCTTTCA
TGATTTTCATCCCACTTCGTTAACATCTAGGTAACACTCTTGGGTGCATTTGATAACCAATTTC
TTCTAAGGAACTTGCACTTATGAGCTATCCTTTGCTATGATCTTCTTGCACACACCTCAACTAT
TTCATTGAATATCTCCATCTACCACCATCACAAGTACCGGGTAACTTCGCCCCAATAATGCTCA
GACAGAGAGGAAGAAATCACCTAACATGTTTGGCCTCTTACCGGATATGAACTCTAGTCTTTCA
TGGTTTTCATTCCACTTCACTGACTGCTACACAACACTGTTGGGTGCATTTGATAACCAATTCT
TCAAAGGAACTTGCTTCCTAATCCTTGCTATTATCTTCCTTTTTTTGAATATGCTTCTTTTTTT
ATATTATTAAAGTAGTTTCAAACATGCAACAGCCTAAGGCAACAAAAGCGTTTTATACTTGGTA
ATAATTATCTTATTATTTATTAGATGTCATGTTCTGCTCTGATGCTTCATTACTAGATAAATAA
GTTTACCGCTTGAAGAATCTCAAGAACTCGTGATTCTTTCATTTTCCATGGGAGATCCTTTGCA
AGGGCCTGCATTGGAAATGAACGTGGTAAGTCACCAAAAATATGACGACCATATGCATACACAA
TGTTTTTGATCAAGGCATATATACAATTTTTTTGCATCAAGATAACACAAAATAGAGATGTCTC
CAATGTTTGCCAATGGCCATTGAGAGTTGTAAGTACGAAACTAGCTCCAACTCGAAAGATGAGC
AATACCTGTCTCATTTCTTCGAGACTGATGACACCATTCTTATCCACATCAATTGCAGAAAATT
GATCCCGCAGATCAGCGATCTCCTCCTCATCAAGTGTGCTAGCTAACGCCTGCAAGTAGTGGAA
CAGCATCCAGAAATTTATGTTTTGTATACTGAAGTTACCTTATCACAAAAGGTTTAAGAAATAA
GAAAGCAATGAGCTTACACGTAAAGCAAACTGTTTTAGACGACTGTATTTGACAAATTGCCGCA
TGTTGGATAAAACAGAAATGTCCAGTGGAATCTCAGATGCATCCCCTCCTTCTCGGACCCATGG
ATGTG
						
					

			
		

Sequences
Splice junction sequence	TTTAGACGACTGTATTTGACAAATTGCCGCATGTTGGATAAAACAGAAATGTCCAGTGGAATCT CAGATGCATCCCCTCCTTCTCGGACCCATGGATGTGcattttaagttcttctggagtaatgaat ccatctttatcaacatcaaatttctcaaaagcagcttgtgatctttgctgccactttgtagaat tatgctcc
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: 461 Transcript exons: 5077212-5077385,5078306-5078368,5078561-5078668,5078765- 5078880 CATTTTAAGTTCTTCTGGAGTAATGAATCCATCTTTATCAACATCAAATTTCTCAAAAGCAGCT TGTGATCTTTGCTGCCACTTTGTAGAATTATGCTCCTCCAACTGATGGACATGTAGAGTGGCAG CCACAAACTCCGGGAAATCAACAAGCCCATCCGTGTTACTGTCAATCGCTTGAAGAATCTCAAG AACTCGTGATTCTTTCATTTTCCATGGGAGATCCTTTGCAAGGGCCTGTCTCATTTCTTCGAGA CTGATGACACCATTCTTATCCACATCAATTGCAGAAAATTGATCCCGCAGATCAGCGATCTCCT CCTCATCAAGTGTGCTAGCTAACGCACGTAAAGCAAACTGTTTTAGACGACTGTATTTGACAAA TTGCCGCATGTTGGATAAAACAGAAATGTCCAGTGGAATCTCAGATGCATCCCCTCCTTCTCGG ACCCATGGATGTG
Genomic sequence	CATTTTAAGTTCTTCTGGAGTAATGAATCCATCTTTATCAACATCAAATTTCTCAAAAGCAGCT TGTGATCTTTGCTGCCACTTTGTAGAATTATGCTCCTCCAACTGATGGACATGTAGAGTGGCAG CCACAAACTCCGGGAAATCAACAAGCCCATCCGTGTTACTGTCAATCTGCCAAGCAATGAACAA AATACTTTAGGTCCCGGAACTGCAGAAGAGACCATATAGTAGAAAGTAATGAACATGCATATGA TGAAAACTATAAAGATTATTATATTAGTTGGCACTTGGCAGCAATATTAGCATTGACAATTGAG TAAAGTTTGTAACAAGGATTATGGTGCAGGAAAAATTTGGAATATACAATCTGACACAAAGAAA TCCCCAAATATTTGGTCACCAATTTAAAAATGGTGTAGTACAAGCTTGCACACACATTAACTAT TCCATCGAGTGTCTCTAACTCCCACCATCGCAAGTACCAAGTAATTTTGCCTCAATAAGGCTCA AGCAGATGGGAAGAAGTCAGTCAACGTGTTCTGTCACTTACTGGATTTGAACTCTAGTCTTTCA TGATTTTCATCCCACTTCGTTAACATCTAGGTAACACTCTTGGGTGCATTTGATAACCAATTTC TTCTAAGGAACTTGCACTTATGAGCTATCCTTTGCTATGATCTTCTTGCACACACCTCAACTAT TTCATTGAATATCTCCATCTACCACCATCACAAGTACCGGGTAACTTCGCCCCAATAATGCTCA GACAGAGAGGAAGAAATCACCTAACATGTTTGGCCTCTTACCGGATATGAACTCTAGTCTTTCA TGGTTTTCATTCCACTTCACTGACTGCTACACAACACTGTTGGGTGCATTTGATAACCAATTCT TCAAAGGAACTTGCTTCCTAATCCTTGCTATTATCTTCCTTTTTTTGAATATGCTTCTTTTTTT ATATTATTAAAGTAGTTTCAAACATGCAACAGCCTAAGGCAACAAAAGCGTTTTATACTTGGTA ATAATTATCTTATTATTTATTAGATGTCATGTTCTGCTCTGATGCTTCATTACTAGATAAATAA GTTTACCGCTTGAAGAATCTCAAGAACTCGTGATTCTTTCATTTTCCATGGGAGATCCTTTGCA AGGGCCTGCATTGGAAATGAACGTGGTAAGTCACCAAAAATATGACGACCATATGCATACACAA TGTTTTTGATCAAGGCATATATACAATTTTTTTGCATCAAGATAACACAAAATAGAGATGTCTC CAATGTTTGCCAATGGCCATTGAGAGTTGTAAGTACGAAACTAGCTCCAACTCGAAAGATGAGC AATACCTGTCTCATTTCTTCGAGACTGATGACACCATTCTTATCCACATCAATTGCAGAAAATT GATCCCGCAGATCAGCGATCTCCTCCTCATCAAGTGTGCTAGCTAACGCCTGCAAGTAGTGGAA CAGCATCCAGAAATTTATGTTTTGTATACTGAAGTTACCTTATCACAAAAGGTTTAAGAAATAA GAAAGCAATGAGCTTACACGTAAAGCAAACTGTTTTAGACGACTGTATTTGACAAATTGCCGCA TGTTGGATAAAACAGAAATGTCCAGTGGAATCTCAGATGCATCCCCTCCTTCTCGGACCCATGG ATGTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.373454571

Conservation Information
Conserved circRNAs	NA
PMCS	0.373454571

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5078877-5077317(+)
5078812-5077216(+)
5078849-5077277(+)
5077371-5078846(-)
5078814-5078784(-)
						
						Potential amino acid sequence
						
							MCILSSSGVMNPSLSTSNFSKAACDLCCHFVELCSSN*(+)
MLDKTEMSSGISDASPPSRTHGCAF*(+)
MHPLLLGPMDVHFKFFWSNESIFINIKFLKSSL*(+)
MGLLISRSLWLPLYMSISWRSIILQSGSKDHKLLLRNLMLIKMDSLLQKNLKCTSMGPRRRGCI
*(-)
MRQFVKYSRLKQFALRALASTLDEEEIADLRDQFSAIDVDKNGVISLEEMRQALAKDLPWKMKE
SRVLEILQAIDSNTDGLVDFPEFVAATLHVHQLEEHNSTKWQQRSQAAFEKFDVDKDGFITPEE
LKMHIHGSEKEGMHLRFHWTFLFYPTCGNLSNTVV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5078877-5077317(+) 5078812-5077216(+) 5078849-5077277(+) 5077371-5078846(-) 5078814-5078784(-)
Potential amino acid sequence	MCILSSSGVMNPSLSTSNFSKAACDLCCHFVELCSSN(+) MLDKTEMSSGISDASPPSRTHGCAF(+) MHPLLLGPMDVHFKFFWSNESIFINIKFLKSSL(+) MGLLISRSLWLPLYMSISWRSIILQSGSKDHKLLLRNLMLIKMDSLLQKNLKCTSMGPRRRGCI (-) MRQFVKYSRLKQFALRALASTLDEEEIADLRDQFSAIDVDKNGVISLEEMRQALAKDLPWKMKE SRVLEILQAIDSNTDGLVDFPEFVAATLHVHQLEEHNSTKWQQRSQAAFEKFDVDKDGFITPEE LKMHIHGSEKEGMHLRFHWTFLFYPTCGNLSNTVV*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc03g033540.2_circ_g.2

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