Plant Circular RNA Database

Detail information of Solyc01g097320.2_circ_g.4

			
						 General Information
					
						CircRNA Name
						Solyc01g097320.2_circ_g.4
					
						ID in PlantcircBase
						sly_circ_000344
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr1: 88219309-88220388  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc01g097320.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc01g097320.2_circ_g.1 Solyc01g097320.2_circ_g.2 Solyc01g097320.2_circ_g.3 						
					
						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
						Solyc01g097320.2.1:1

General Information
CircRNA Name	Solyc01g097320.2_circ_g.4
ID in PlantcircBase	sly_circ_000344
Alias	NA
Organism	Solanum lycopersicum
Position	chr1: 88219309-88220388 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc01g097320.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc01g097320.2_circ_g.1 Solyc01g097320.2_circ_g.2 Solyc01g097320.2_circ_g.3
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	Solyc01g097320.2.1:1

			
						 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  
						
							CTTCATGCATAAAAAACAACGAGTCGGCAGCTTGGGTGAAACATGTATCATGACTAGATAAAGT
GGATGCAAGCTGCTGACTGTATTGTATCAACGGGACcttgcgagaatcgccaagcatttcttct
acatggcattgaagctgaatatcgctgggaactctgcagatctgactatttttctcaagttctt
taagaatc

									
								

					

						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: 1080
Transcript exons: 88219309-88220388
CTTGCGAGAATCGCCAAGCATTTCTTCTACATGGCATTGAAGCTGAATATCGCTGGGAACTCTG
CAGATCTGACTATTTTTCTCAAGTTCTTTAAGAATCTCTAGCAAACGAGTATAGCGATTACAGC
ATATCACCCTTAGCAGCAACTTCTCAATGTCAATACAACTCTGGTCAAGGGAAAATTCTGCTTC
TTTTCCCGTTAGAGGATCAATAACAAATGTGCTATGAAGACACTTAATTCGCAGATCTGGTCCA
GGTTCAATTTTTATAAATGGGCATGTTCCAATTTCGGATGTTCCAGAGTTCTTATCCAAATCCA
ACCAATACAAAATCTTCAGCCCAGGAGTACGCAAACTAGCAGAGTCAGACTCCCCGTCTTGTGA
TGTTTGTGTGGAGCCAGCACTGCCAGCCTGTCCAGTACTGACATCAGTTATGAGCTCAAAACGA
ATAGCATCTTTCCACCTTCCTTGACGAAGTGTTTGCACTTGCCTTATGACTGTGTCCATAACAA
GTGCCACACAAAGCTCATGCAAGATAGAGTATAAGGTCATAAATGGATGGTCTGCAGCAGCCAT
TCTTCGTTCTAAATCATCACCAAGAGCATGCCGCCGAAAGTCATCCAGCTTCATAGGACCACTT
CTCTCACCAACAAGCAGCTCCATATGTAATATCCTCCACATTGACAAGTGTCCTCTGTAACCGA
GGGTAACTAGAACTTTAAATTCTCCTTCCACACGAAGCAGAACAGTACCATCAGAAACTTTGAC
TTCAGTAATGTCCTTAGGAAGCGAAACTTCAAGGAGTTTCGACCTAACCAGTGTGTCTAATTTC
TTTAATGCTGGTTTTTGCTGGTCATCATTTAATGTGCTCTGCAAGCCTACATCTTCTATACATT
TTGGCAAACGATCATAACTTCCGGTAAGAAGAACTTCAACAGCTGAAGGAACATCATAGATGGG
AGCACGGGCTTGTTGTAGTCCTTCATGCATAAAAAACAACGAGTCGGCAGCTTGGGTGAAACAT
GTATCATGACTAGATAAAGTGGATGCAAGCTGCTGACTGTATTGTATCAACGGGAC
						
					

						Genomic sequence
						
							CTTGCGAGAATCGCCAAGCATTTCTTCTACATGGCATTGAAGCTGAATATCGCTGGGAACTCTG
CAGATCTGACTATTTTTCTCAAGTTCTTTAAGAATCTCTAGCAAACGAGTATAGCGATTACAGC
ATATCACCCTTAGCAGCAACTTCTCAATGTCAATACAACTCTGGTCAAGGGAAAATTCTGCTTC
TTTTCCCGTTAGAGGATCAATAACAAATGTGCTATGAAGACACTTAATTCGCAGATCTGGTCCA
GGTTCAATTTTTATAAATGGGCATGTTCCAATTTCGGATGTTCCAGAGTTCTTATCCAAATCCA
ACCAATACAAAATCTTCAGCCCAGGAGTACGCAAACTAGCAGAGTCAGACTCCCCGTCTTGTGA
TGTTTGTGTGGAGCCAGCACTGCCAGCCTGTCCAGTACTGACATCAGTTATGAGCTCAAAACGA
ATAGCATCTTTCCACCTTCCTTGACGAAGTGTTTGCACTTGCCTTATGACTGTGTCCATAACAA
GTGCCACACAAAGCTCATGCAAGATAGAGTATAAGGTCATAAATGGATGGTCTGCAGCAGCCAT
TCTTCGTTCTAAATCATCACCAAGAGCATGCCGCCGAAAGTCATCCAGCTTCATAGGACCACTT
CTCTCACCAACAAGCAGCTCCATATGTAATATCCTCCACATTGACAAGTGTCCTCTGTAACCGA
GGGTAACTAGAACTTTAAATTCTCCTTCCACACGAAGCAGAACAGTACCATCAGAAACTTTGAC
TTCAGTAATGTCCTTAGGAAGCGAAACTTCAAGGAGTTTCGACCTAACCAGTGTGTCTAATTTC
TTTAATGCTGGTTTTTGCTGGTCATCATTTAATGTGCTCTGCAAGCCTACATCTTCTATACATT
TTGGCAAACGATCATAACTTCCGGTAAGAAGAACTTCAACAGCTGAAGGAACATCATAGATGGG
AGCACGGGCTTGTTGTAGTCCTTCATGCATAAAAAACAACGAGTCGGCAGCTTGGGTGAAACAT
GTATCATGACTAGATAAAGTGGATGCAAGCTGCTGACTGTATTGTATCAACGGGAC
						
					

			
		

Sequences
Splice junction sequence	CTTCATGCATAAAAAACAACGAGTCGGCAGCTTGGGTGAAACATGTATCATGACTAGATAAAGT GGATGCAAGCTGCTGACTGTATTGTATCAACGGGACcttgcgagaatcgccaagcatttcttct acatggcattgaagctgaatatcgctgggaactctgcagatctgactatttttctcaagttctt taagaatc
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: 1080 Transcript exons: 88219309-88220388 CTTGCGAGAATCGCCAAGCATTTCTTCTACATGGCATTGAAGCTGAATATCGCTGGGAACTCTG CAGATCTGACTATTTTTCTCAAGTTCTTTAAGAATCTCTAGCAAACGAGTATAGCGATTACAGC ATATCACCCTTAGCAGCAACTTCTCAATGTCAATACAACTCTGGTCAAGGGAAAATTCTGCTTC TTTTCCCGTTAGAGGATCAATAACAAATGTGCTATGAAGACACTTAATTCGCAGATCTGGTCCA GGTTCAATTTTTATAAATGGGCATGTTCCAATTTCGGATGTTCCAGAGTTCTTATCCAAATCCA ACCAATACAAAATCTTCAGCCCAGGAGTACGCAAACTAGCAGAGTCAGACTCCCCGTCTTGTGA TGTTTGTGTGGAGCCAGCACTGCCAGCCTGTCCAGTACTGACATCAGTTATGAGCTCAAAACGA ATAGCATCTTTCCACCTTCCTTGACGAAGTGTTTGCACTTGCCTTATGACTGTGTCCATAACAA GTGCCACACAAAGCTCATGCAAGATAGAGTATAAGGTCATAAATGGATGGTCTGCAGCAGCCAT TCTTCGTTCTAAATCATCACCAAGAGCATGCCGCCGAAAGTCATCCAGCTTCATAGGACCACTT CTCTCACCAACAAGCAGCTCCATATGTAATATCCTCCACATTGACAAGTGTCCTCTGTAACCGA GGGTAACTAGAACTTTAAATTCTCCTTCCACACGAAGCAGAACAGTACCATCAGAAACTTTGAC TTCAGTAATGTCCTTAGGAAGCGAAACTTCAAGGAGTTTCGACCTAACCAGTGTGTCTAATTTC TTTAATGCTGGTTTTTGCTGGTCATCATTTAATGTGCTCTGCAAGCCTACATCTTCTATACATT TTGGCAAACGATCATAACTTCCGGTAAGAAGAACTTCAACAGCTGAAGGAACATCATAGATGGG AGCACGGGCTTGTTGTAGTCCTTCATGCATAAAAAACAACGAGTCGGCAGCTTGGGTGAAACAT GTATCATGACTAGATAAAGTGGATGCAAGCTGCTGACTGTATTGTATCAACGGGAC
Genomic sequence	CTTGCGAGAATCGCCAAGCATTTCTTCTACATGGCATTGAAGCTGAATATCGCTGGGAACTCTG CAGATCTGACTATTTTTCTCAAGTTCTTTAAGAATCTCTAGCAAACGAGTATAGCGATTACAGC ATATCACCCTTAGCAGCAACTTCTCAATGTCAATACAACTCTGGTCAAGGGAAAATTCTGCTTC TTTTCCCGTTAGAGGATCAATAACAAATGTGCTATGAAGACACTTAATTCGCAGATCTGGTCCA GGTTCAATTTTTATAAATGGGCATGTTCCAATTTCGGATGTTCCAGAGTTCTTATCCAAATCCA ACCAATACAAAATCTTCAGCCCAGGAGTACGCAAACTAGCAGAGTCAGACTCCCCGTCTTGTGA TGTTTGTGTGGAGCCAGCACTGCCAGCCTGTCCAGTACTGACATCAGTTATGAGCTCAAAACGA ATAGCATCTTTCCACCTTCCTTGACGAAGTGTTTGCACTTGCCTTATGACTGTGTCCATAACAA GTGCCACACAAAGCTCATGCAAGATAGAGTATAAGGTCATAAATGGATGGTCTGCAGCAGCCAT TCTTCGTTCTAAATCATCACCAAGAGCATGCCGCCGAAAGTCATCCAGCTTCATAGGACCACTT CTCTCACCAACAAGCAGCTCCATATGTAATATCCTCCACATTGACAAGTGTCCTCTGTAACCGA GGGTAACTAGAACTTTAAATTCTCCTTCCACACGAAGCAGAACAGTACCATCAGAAACTTTGAC TTCAGTAATGTCCTTAGGAAGCGAAACTTCAAGGAGTTTCGACCTAACCAGTGTGTCTAATTTC TTTAATGCTGGTTTTTGCTGGTCATCATTTAATGTGCTCTGCAAGCCTACATCTTCTATACATT TTGGCAAACGATCATAACTTCCGGTAAGAAGAACTTCAACAGCTGAAGGAACATCATAGATGGG AGCACGGGCTTGTTGTAGTCCTTCATGCATAAAAAACAACGAGTCGGCAGCTTGGGTGAAACAT GTATCATGACTAGATAAAGTGGATGCAAGCTGCTGACTGTATTGTATCAACGGGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.933453223

Conservation Information
Conserved circRNAs	NA
PMCS	0.933453223

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							88220356-88219400(+)
88220300-88219311(-)
88219347-88220344(-)
						
					

						Potential amino acid sequence
						
							MQAADCIVSTGPCENRQAFLLHGIEAEYRWELCRSDYFSQVL*(+)
MHEGLQQARAPIYDVPSAVEVLLTGSYDRLPKCIEDVGLQSTLNDDQQKPALKKLDTLVRSKLL
EVSLPKDITEVKVSDGTVLLRVEGEFKVLVTLGYRGHLSMWRILHMELLVGERSGPMKLDDFRR
HALGDDLERRMAAADHPFMTLYSILHELCVALVMDTVIRQVQTLRQGRWKDAIRFELITDVSTG
QAGSAGSTQTSQDGESDSASLRTPGLKILYWLDLDKNSGTSEIGTCPFIKIEPGPDLRIKCLHS
TFVIDPLTGKEAEFSLDQSCIDIEKLLLRVICCNRYTRLLEILKELEKNSQICRVPSDIQLQCH
VEEMLGDSRKVPLIQYSQQLASTLSSHDTCFTQAADSLFFMHEGLQQARAPIYDVPSAVEVLLT
GSYDRLPKCIEDVGLQSTLNDDQQKPALKKLDTLVRSKLLEVSLPKDITEVKVSDGTVLLRVEG
EFKVLVTLGYRGHLSMWRILHMELLVGERSGPMKLDDFRRHALGDDLERRMAAADHPFMTLYSI
LHELCVALVMDTVIRQVQTLRQGRWKDAIRFELITDVSTGQAGSAGSTQTSQDGESDSASLRTP
GLKILYWLDLDKNSGTSEIGTCPFIKIEPGPDLRIKCLHSTFVIDPLTGKEAEFSLDQSCIDIE
KLLLRVICCNRYTRLLEILKELEKNSQICRVPSDIQLQCHVEEMLGDSRKVPLIQYSQQLASTL
SSHDTCFTQAADSLFFMHEGLQQARAPIYDVPSAVEVLLTGSYDRLPKCIEDVGLQSTLNDDQQ
KPALKKLDTLVRSKLLEVSLPKDITEVKVSDGTVLLRVEGEFKVLVTLGYRGHLSMWRILHMEL
LVGERSGPMKLDDFRRHALGDDLERRMAAADHPFMTLYSILHELCVALVMDTVIRQVQTLRQGR
WKDAIRFELITDVSTGQAGSAGSTQTSQDGESDSASLRTPGLKILYWLDLDKNSGTSEIGTCPF
IKIEPGPDLRIKCLHSTFVIDPLTGKEAEFSLDQSCIDIEKLLLRVICCNRYTRLLEILKELEK
NSQICRVPSDIQLQCHVEEMLGDSRKVPLIQYSQQLASTLSSHDTCFTQAADSLFFMHEGLQQA
RAPIYDVPSAVEVLLTGSYDRLPKCIEDVGLQSTLNDDQQKPALKKLDTLVRSKLLEVSLPKDI
TEVKVSDGTVLLRVEGEFKVLVTLGYRGHLSMWRILHMELLVGERSGPMKLDDFRRHALGDDLE
RRMAAADHPFMTLYSILHELCVALVMDTVIRQVQTLRQGRWKDAIRFELITDVSTGQAGSAGST
QTSQDGESDSASLRTPGLKILYWLDLDKNSGTSEIGTCPFIKIEPGPDLRIKCLHSTFVIDPLT
GKEAEFSLDQSCIDIEKLLLRVICCNRYTRLLEILKELEKNSQICRVPSDIQLQCHVEEMLGDS
RK(-)
MPCRRNAWRFSQGPVDTIQSAACIHFI*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	88220356-88219400(+) 88220300-88219311(-) 88219347-88220344(-)
Potential amino acid sequence	MQAADCIVSTGPCENRQAFLLHGIEAEYRWELCRSDYFSQVL(+) MHEGLQQARAPIYDVPSAVEVLLTGSYDRLPKCIEDVGLQSTLNDDQQKPALKKLDTLVRSKLL EVSLPKDITEVKVSDGTVLLRVEGEFKVLVTLGYRGHLSMWRILHMELLVGERSGPMKLDDFRR HALGDDLERRMAAADHPFMTLYSILHELCVALVMDTVIRQVQTLRQGRWKDAIRFELITDVSTG QAGSAGSTQTSQDGESDSASLRTPGLKILYWLDLDKNSGTSEIGTCPFIKIEPGPDLRIKCLHS TFVIDPLTGKEAEFSLDQSCIDIEKLLLRVICCNRYTRLLEILKELEKNSQICRVPSDIQLQCH VEEMLGDSRKVPLIQYSQQLASTLSSHDTCFTQAADSLFFMHEGLQQARAPIYDVPSAVEVLLT GSYDRLPKCIEDVGLQSTLNDDQQKPALKKLDTLVRSKLLEVSLPKDITEVKVSDGTVLLRVEG EFKVLVTLGYRGHLSMWRILHMELLVGERSGPMKLDDFRRHALGDDLERRMAAADHPFMTLYSI LHELCVALVMDTVIRQVQTLRQGRWKDAIRFELITDVSTGQAGSAGSTQTSQDGESDSASLRTP GLKILYWLDLDKNSGTSEIGTCPFIKIEPGPDLRIKCLHSTFVIDPLTGKEAEFSLDQSCIDIE KLLLRVICCNRYTRLLEILKELEKNSQICRVPSDIQLQCHVEEMLGDSRKVPLIQYSQQLASTL SSHDTCFTQAADSLFFMHEGLQQARAPIYDVPSAVEVLLTGSYDRLPKCIEDVGLQSTLNDDQQ KPALKKLDTLVRSKLLEVSLPKDITEVKVSDGTVLLRVEGEFKVLVTLGYRGHLSMWRILHMEL LVGERSGPMKLDDFRRHALGDDLERRMAAADHPFMTLYSILHELCVALVMDTVIRQVQTLRQGR WKDAIRFELITDVSTGQAGSAGSTQTSQDGESDSASLRTPGLKILYWLDLDKNSGTSEIGTCPF IKIEPGPDLRIKCLHSTFVIDPLTGKEAEFSLDQSCIDIEKLLLRVICCNRYTRLLEILKELEK NSQICRVPSDIQLQCHVEEMLGDSRKVPLIQYSQQLASTLSSHDTCFTQAADSLFFMHEGLQQA RAPIYDVPSAVEVLLTGSYDRLPKCIEDVGLQSTLNDDQQKPALKKLDTLVRSKLLEVSLPKDI TEVKVSDGTVLLRVEGEFKVLVTLGYRGHLSMWRILHMELLVGERSGPMKLDDFRRHALGDDLE RRMAAADHPFMTLYSILHELCVALVMDTVIRQVQTLRQGRWKDAIRFELITDVSTGQAGSAGST QTSQDGESDSASLRTPGLKILYWLDLDKNSGTSEIGTCPFIKIEPGPDLRIKCLHSTFVIDPLT GKEAEFSLDQSCIDIEKLLLRVICCNRYTRLLEILKELEKNSQICRVPSDIQLQCHVEEMLGDS RK(-) MPCRRNAWRFSQGPVDTIQSAACIHFI(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc01g097320.2_circ_g.4

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