Plant Circular RNA Database

Detail information of Solyc01g090200.2_circ_g.6

			
						 General Information
					
						CircRNA Name
						Solyc01g090200.2_circ_g.6
					
						ID in PlantcircBase
						sly_circ_000265
					
						Alias
						1:75607190|75609708
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr1: 83846390-83848908  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc01g090200.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc01g090200.2_circ_g.2 Solyc01g090200.2_circ_g.3 Solyc01g090200.2_circ_g.4 Solyc01g090200.2_circ_g.5 						
					
						Support reads
						6
					
						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
						Solyc01g090200.2.1:7

General Information
CircRNA Name	Solyc01g090200.2_circ_g.6
ID in PlantcircBase	sly_circ_000265
Alias	1:75607190\|75609708
Organism	Solanum lycopersicum
Position	chr1: 83846390-83848908 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc01g090200.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc01g090200.2_circ_g.2 Solyc01g090200.2_circ_g.3 Solyc01g090200.2_circ_g.4 Solyc01g090200.2_circ_g.5
Support reads	6
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	Solyc01g090200.2.1:7

			
						 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  
						
							AGCCATGGCGGATCTTGCAACTGCAGTTGTTACAGAGTTCACTTCTCTTTCAGGGACAATGGCA
CGCCACTATGCACTTAGAGATGGCTATTCAACGGAGatattggatgcagaagcctatgcaaatg
taatgcaggatgctgggattcttgctgatgtcgaggtaatgcaagttctgcataaacttccatt
tgtactta

									
								

					

						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: 684
Transcript exons: 83846390-83846452,83846545-83846634,83846711-83846797,83
847454-83847525,83847617-83847675,83847829-83847922,8384
8690-83848908
ATATTGGATGCAGAAGCCTATGCAAATGTAATGCAGGATGCTGGGATTCTTGCTGATGTCGAGC
ATCGCAAGAAAACAATTACAGAGAAATCAAATGATTTAGCAAAAAGTGTACATGGACATATTGT
AATGAAGAGTGATTTGCTTGATGAGGTTGTGAATCTTGTTGAGGCACCACTCCCTGTACTTGGC
AAATTCAATGAGTCCTTCTTAGAGCTTCCAAAGGAGCTACTTATAATGGTGATGCAGAAGCATC
AGAAATACTTCGCCATGACTGATGAGAATGGGTTACTGTTGCCATACTTTGTCACAGTTGCAAA
TGGATCAATTGATAACAAGGTAGTTAGAAAAGGAAATGAAGCTGTGCTAAGAGCTCGATTTGAA
GATGCAAAATTTTTCTATGCAATGGACACAAATAGAAAATTTTCTGAATTTCGTACGCAACTGA
AAGGGATTCTTTTCCATGAGAAGCTTGGGACTATGTTAGATAAGATGACACGAGTTCAGAATTT
GGCTAGTGAAGTTGGATTGTCTCTTGGAATAAGTGAAGACAAACTCGAAGTCATCCAAGATGCA
GCCTCATTAGCCATGGCGGATCTTGCAACTGCAGTTGTTACAGAGTTCACTTCTCTTTCAGGGA
CAATGGCACGCCACTATGCACTTAGAGATGGCTATTCAACGGAG
						
					

						Genomic sequence
						
							ATATTGGATGCAGAAGCCTATGCAAATGTAATGCAGGATGCTGGGATTCTTGCTGATGTCGAGG
TAATGCAAGTTCTGCATAAACTTCCATTTGTACTTACTATTACTATACTTGTTGATGATCTTTT
TGACGTTTAACCATCATAAAATATCAGCATCGCAAGAAAACAATTACAGAGAAATCAAATGATT
TAGCAAAAAGTGTACATGGACATATTGTAATGAAGAGTGATTTGCTTGATGAGGTAATGCTTGA
TGTTCCACACTTTTTTAGCCAATTGTCAGACTGAACAGTATTTAAGCATTTTCCTCTATGTTTA
GGTTGTGAATCTTGTTGAGGCACCACTCCCTGTACTTGGCAAATTCAATGAGTCCTTCTTAGAG
CTTCCAAAGGAGCTACTTATAATGGTAAACTCTATTATTATTTGGAACTTCAATTGTTTTTTTC
TTCTGTATTCATTTGTGATATTATAAGGTTGAGCAAAAGATGCTACTGTCTTTGGGTGAAGGAA
ATAAGCATGGATATTCTACTTGTTTACTATGTCTTTTTAACCCATCTCTCTCTCTCTCTCAATC
AGAAATTTAGATGTTTACAGTTTCTGGGAGTAACGTTATCCTTCTGGTACTGTAGGCTTAAATG
CTATACAAACTTTTTCTTTAAGGGGCTAGACACTATTTGTGTCTACTTCCTTTTCTTGGCCAAA
ATAATATCCTACTATTTCTCTTTCTTTTGGTTATCTGAAAACCAATTTCATAATTCCTATAAAA
CTTCTTACCATTGCAATACGTGGAGGAATATAAATGGACTATCATGGATCCATTCATATTGGTT
ATCATCAGTGACTGTCAAGCATGGCCTTGATTGCTGGGTCGTTGAAGGGTGCTGGTTAAGCATA
ATGTCCTCTTTGTCATTTTCCTTGTGTTACATGTCATTTATATGTATTTCTGAAGCCCTCATTA
TGTTAAAAGAAAGGAGGCAGCCCAGTGCACTAAAAGCTCCCTCTATGTGCAGGGAAGCTCTTTA
TTATGTTAGAGTTGGTAAATTTTTCTTTTGCGTTATGCAGGTGATGCAGAAGCATCAGAAATAC
TTCGCCATGACTGATGAGAATGGGTTACTGTTGCCATACTTTGTCACAGTGAGTTGTTTCTGTG
GCAAACTCTTACCTGCTTAGCTTAAAGTGAGATGTTAGCTTGTAATGGTAACTTGATATGGATT
TAACTTTTCAGGTTGCAAATGGATCAATTGATAACAAGGTAGTTAGAAAAGGAAATGAAGCTGT
GCTAAGGTTACTTTCCTTTAGTTAGTCTCTTTCCTTCATATTTCTAAAGTTTTGGATCTAGGTG
CTACTTGCACTTTTTATATTTTACTTGATTCCTTATCAGCTTACTTTATGATAACTGGTATATC
CTTAAAGATGTGAACTGCATACACATTGCAGAGCTCGATTTGAAGATGCAAAATTTTTCTATGC
AATGGACACAAATAGAAAATTTTCTGAATTTCGTACGCAACTGAAAGGGATTCTTTTCCATGTA
AGTCTTAGAATTCCATCTTGATTGCCCTCTTTTTTCCTGTTATGCTTTGACACTTCAAATTTCT
ATAATACTTTAGTTCTCGTTGGCGTCTCTAATTGGGGAATTGTTATCTATAGCTAAATTTAATT
TCAAGTTGAAGTATTGAAATCCTTATTCTGTTTGTAAGTCTTTACTGAATTGATTGTTATCTAA
TCTAAAATTAGTCTTTTTGATGTACATACAAGCTTTGTGCAATCAGTGAAATTTTACTTTTATT
TAAAATATATCAATTATGAAATTGTTATCTCATAAGGTATATTTGACTAGTGCGTCAATCAAAA
TTTCTATAAATGGACCTTGAGCCTAACTCAACCTCAAAAGATAGCTCTAGAGGTGAGGGATTGC
CTAAGCCATATAAAGAGACCATCCACTCCATAATTGGGCGATGTAGGGCTCTTCAACACTCCCT
GGCACGCCTACGACTGACATAAATCAGAGCGTGGACAAAATTTTTTGGGAGCCCTACTTCGGAA
AACCAAGAATTGGCCCTGCTCTGAACACCATGTAAAGAAATGGACCTTTGACCTAACTTAACCT
CAAAAGCTATTTCAAGAGGTGTGGATAGCCTAAACCATACAAAGAGACCTTCTCTCCCATAAGA
GCCCAATGTGACACTCTTCAACAACAATAATAATTTCTCTAATTCTTGCAAATTTGTTAGTTCT
TAGCCCATAATTTCTGCTGATCTGTAGTAGTTTTCGCTAAACGATAACGCCTCTGTACAGGAGA
AGCTTGGGACTATGTTAGATAAGATGACACGAGTTCAGAATTTGGCTAGTGAAGTTGGATTGTC
TCTTGGAATAAGTGAAGACAAACTCGAAGTCATCCAAGATGCAGCCTCATTAGCCATGGCGGAT
CTTGCAACTGCAGTTGTTACAGAGTTCACTTCTCTTTCAGGGACAATGGCACGCCACTATGCAC
TTAGAGATGGCTATTCAACGGAG
						
					

			
		

Sequences
Splice junction sequence	AGCCATGGCGGATCTTGCAACTGCAGTTGTTACAGAGTTCACTTCTCTTTCAGGGACAATGGCA CGCCACTATGCACTTAGAGATGGCTATTCAACGGAGatattggatgcagaagcctatgcaaatg taatgcaggatgctgggattcttgctgatgtcgaggtaatgcaagttctgcataaacttccatt tgtactta
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: 684 Transcript exons: 83846390-83846452,83846545-83846634,83846711-83846797,83 847454-83847525,83847617-83847675,83847829-83847922,8384 8690-83848908 ATATTGGATGCAGAAGCCTATGCAAATGTAATGCAGGATGCTGGGATTCTTGCTGATGTCGAGC ATCGCAAGAAAACAATTACAGAGAAATCAAATGATTTAGCAAAAAGTGTACATGGACATATTGT AATGAAGAGTGATTTGCTTGATGAGGTTGTGAATCTTGTTGAGGCACCACTCCCTGTACTTGGC AAATTCAATGAGTCCTTCTTAGAGCTTCCAAAGGAGCTACTTATAATGGTGATGCAGAAGCATC AGAAATACTTCGCCATGACTGATGAGAATGGGTTACTGTTGCCATACTTTGTCACAGTTGCAAA TGGATCAATTGATAACAAGGTAGTTAGAAAAGGAAATGAAGCTGTGCTAAGAGCTCGATTTGAA GATGCAAAATTTTTCTATGCAATGGACACAAATAGAAAATTTTCTGAATTTCGTACGCAACTGA AAGGGATTCTTTTCCATGAGAAGCTTGGGACTATGTTAGATAAGATGACACGAGTTCAGAATTT GGCTAGTGAAGTTGGATTGTCTCTTGGAATAAGTGAAGACAAACTCGAAGTCATCCAAGATGCA GCCTCATTAGCCATGGCGGATCTTGCAACTGCAGTTGTTACAGAGTTCACTTCTCTTTCAGGGA CAATGGCACGCCACTATGCACTTAGAGATGGCTATTCAACGGAG
Genomic sequence	ATATTGGATGCAGAAGCCTATGCAAATGTAATGCAGGATGCTGGGATTCTTGCTGATGTCGAGG TAATGCAAGTTCTGCATAAACTTCCATTTGTACTTACTATTACTATACTTGTTGATGATCTTTT TGACGTTTAACCATCATAAAATATCAGCATCGCAAGAAAACAATTACAGAGAAATCAAATGATT TAGCAAAAAGTGTACATGGACATATTGTAATGAAGAGTGATTTGCTTGATGAGGTAATGCTTGA TGTTCCACACTTTTTTAGCCAATTGTCAGACTGAACAGTATTTAAGCATTTTCCTCTATGTTTA GGTTGTGAATCTTGTTGAGGCACCACTCCCTGTACTTGGCAAATTCAATGAGTCCTTCTTAGAG CTTCCAAAGGAGCTACTTATAATGGTAAACTCTATTATTATTTGGAACTTCAATTGTTTTTTTC TTCTGTATTCATTTGTGATATTATAAGGTTGAGCAAAAGATGCTACTGTCTTTGGGTGAAGGAA ATAAGCATGGATATTCTACTTGTTTACTATGTCTTTTTAACCCATCTCTCTCTCTCTCTCAATC AGAAATTTAGATGTTTACAGTTTCTGGGAGTAACGTTATCCTTCTGGTACTGTAGGCTTAAATG CTATACAAACTTTTTCTTTAAGGGGCTAGACACTATTTGTGTCTACTTCCTTTTCTTGGCCAAA ATAATATCCTACTATTTCTCTTTCTTTTGGTTATCTGAAAACCAATTTCATAATTCCTATAAAA CTTCTTACCATTGCAATACGTGGAGGAATATAAATGGACTATCATGGATCCATTCATATTGGTT ATCATCAGTGACTGTCAAGCATGGCCTTGATTGCTGGGTCGTTGAAGGGTGCTGGTTAAGCATA ATGTCCTCTTTGTCATTTTCCTTGTGTTACATGTCATTTATATGTATTTCTGAAGCCCTCATTA TGTTAAAAGAAAGGAGGCAGCCCAGTGCACTAAAAGCTCCCTCTATGTGCAGGGAAGCTCTTTA TTATGTTAGAGTTGGTAAATTTTTCTTTTGCGTTATGCAGGTGATGCAGAAGCATCAGAAATAC TTCGCCATGACTGATGAGAATGGGTTACTGTTGCCATACTTTGTCACAGTGAGTTGTTTCTGTG GCAAACTCTTACCTGCTTAGCTTAAAGTGAGATGTTAGCTTGTAATGGTAACTTGATATGGATT TAACTTTTCAGGTTGCAAATGGATCAATTGATAACAAGGTAGTTAGAAAAGGAAATGAAGCTGT GCTAAGGTTACTTTCCTTTAGTTAGTCTCTTTCCTTCATATTTCTAAAGTTTTGGATCTAGGTG CTACTTGCACTTTTTATATTTTACTTGATTCCTTATCAGCTTACTTTATGATAACTGGTATATC CTTAAAGATGTGAACTGCATACACATTGCAGAGCTCGATTTGAAGATGCAAAATTTTTCTATGC AATGGACACAAATAGAAAATTTTCTGAATTTCGTACGCAACTGAAAGGGATTCTTTTCCATGTA AGTCTTAGAATTCCATCTTGATTGCCCTCTTTTTTCCTGTTATGCTTTGACACTTCAAATTTCT ATAATACTTTAGTTCTCGTTGGCGTCTCTAATTGGGGAATTGTTATCTATAGCTAAATTTAATT TCAAGTTGAAGTATTGAAATCCTTATTCTGTTTGTAAGTCTTTACTGAATTGATTGTTATCTAA TCTAAAATTAGTCTTTTTGATGTACATACAAGCTTTGTGCAATCAGTGAAATTTTACTTTTATT TAAAATATATCAATTATGAAATTGTTATCTCATAAGGTATATTTGACTAGTGCGTCAATCAAAA TTTCTATAAATGGACCTTGAGCCTAACTCAACCTCAAAAGATAGCTCTAGAGGTGAGGGATTGC CTAAGCCATATAAAGAGACCATCCACTCCATAATTGGGCGATGTAGGGCTCTTCAACACTCCCT GGCACGCCTACGACTGACATAAATCAGAGCGTGGACAAAATTTTTTGGGAGCCCTACTTCGGAA AACCAAGAATTGGCCCTGCTCTGAACACCATGTAAAGAAATGGACCTTTGACCTAACTTAACCT CAAAAGCTATTTCAAGAGGTGTGGATAGCCTAAACCATACAAAGAGACCTTCTCTCCCATAAGA GCCCAATGTGACACTCTTCAACAACAATAATAATTTCTCTAATTCTTGCAAATTTGTTAGTTCT TAGCCCATAATTTCTGCTGATCTGTAGTAGTTTTCGCTAAACGATAACGCCTCTGTACAGGAGA AGCTTGGGACTATGTTAGATAAGATGACACGAGTTCAGAATTTGGCTAGTGAAGTTGGATTGTC TCTTGGAATAAGTGAAGACAAACTCGAAGTCATCCAAGATGCAGCCTCATTAGCCATGGCGGAT CTTGCAACTGCAGTTGTTACAGAGTTCACTTCTCTTTCAGGGACAATGGCACGCCACTATGCAC TTAGAGATGGCTATTCAACGGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.543484209

Conservation Information
Conserved circRNAs	NA
PMCS	0.543484209

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							83846421-83848905(+)
83846549-83848902(-)
						
						Potential amino acid sequence
						
							MQDAGILADVEHRKKTITEKSNDLAKSVHGHIVMKSDLLDEVVNLVEAPLPVLGKFNESFLELP
KELLIMVMQKHQKYFAMTDENGLLLPYFVTVANGSIDNKVVRKGNEAVLRARFEDAKFFYAMDT
NRKFSEFRTQLKGILFHEKLGTMLDKMTRVQNLASEVGLSLGISEDKLEVIQDAASLAMADLAT
AVVTEFTSLSGTMARHYALRDGYSTEILDAEAYANVMQDAGILADVEHRKKTITEKSNDLAKSV
HGHIVMKSDLLDEVVNLVEAPLPVLGKFNESFLELPKELLIMVMQKHQKYFAMTDENGLLLPYF
VTVANGSIDNKVVRKGNEAVLRARFEDAKFFYAMDTNRKFSEFRTQLKGILFHEKLGTMLDKMT
RVQNLASEVGLSLGISEDKLEVIQDAASLAMADLATAVVTEFTSLSGTMARHYALRDGYSTEIL
DAEAYANVMQDAGILADVEHRKKTITEKSNDLAKSVHGHIVMKSDLLDEVVNLVEAPLPVLGKF
NESFLELPKELLIMVMQKHQKYFAMTDENGLLLPYFVTVANGSIDNKVVRKGNEAVLRARFEDA
KFFYAMDTNRKFSEFRTQLKGILFHEKLGTMLDKMTRVQNLASEVGLSLGISEDKLEVIQDAAS
LAMADLATAVVTEFTSLSGTMARHYALRDGYSTEILDAEAYANVMQDAGILADVEHRKKTITEK
SNDLAKSVHGHIVMKSDLLDEVVNLVEAPLPVLGKFNESFLELPKELLIMVMQKHQKYFAMTDE
NGLLLPYFVTVANGSIDNKVVRKGNEAVLRARFEDAKFFYAMDTNRKFSEFRTQLKGILFHEKL
GTMLDKMTRVQNLASEVGLSLGISEDKLEVIQDAASLAMADLATAVVTEFTSLSGTMARHYALR
DGYSTE(+)
MLDISKNPSILHYICIGFCIQYLR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	83846421-83848905(+) 83846549-83848902(-)
Potential amino acid sequence	MQDAGILADVEHRKKTITEKSNDLAKSVHGHIVMKSDLLDEVVNLVEAPLPVLGKFNESFLELP KELLIMVMQKHQKYFAMTDENGLLLPYFVTVANGSIDNKVVRKGNEAVLRARFEDAKFFYAMDT NRKFSEFRTQLKGILFHEKLGTMLDKMTRVQNLASEVGLSLGISEDKLEVIQDAASLAMADLAT AVVTEFTSLSGTMARHYALRDGYSTEILDAEAYANVMQDAGILADVEHRKKTITEKSNDLAKSV HGHIVMKSDLLDEVVNLVEAPLPVLGKFNESFLELPKELLIMVMQKHQKYFAMTDENGLLLPYF VTVANGSIDNKVVRKGNEAVLRARFEDAKFFYAMDTNRKFSEFRTQLKGILFHEKLGTMLDKMT RVQNLASEVGLSLGISEDKLEVIQDAASLAMADLATAVVTEFTSLSGTMARHYALRDGYSTEIL DAEAYANVMQDAGILADVEHRKKTITEKSNDLAKSVHGHIVMKSDLLDEVVNLVEAPLPVLGKF NESFLELPKELLIMVMQKHQKYFAMTDENGLLLPYFVTVANGSIDNKVVRKGNEAVLRARFEDA KFFYAMDTNRKFSEFRTQLKGILFHEKLGTMLDKMTRVQNLASEVGLSLGISEDKLEVIQDAAS LAMADLATAVVTEFTSLSGTMARHYALRDGYSTEILDAEAYANVMQDAGILADVEHRKKTITEK SNDLAKSVHGHIVMKSDLLDEVVNLVEAPLPVLGKFNESFLELPKELLIMVMQKHQKYFAMTDE NGLLLPYFVTVANGSIDNKVVRKGNEAVLRARFEDAKFFYAMDTNRKFSEFRTQLKGILFHEKL GTMLDKMTRVQNLASEVGLSLGISEDKLEVIQDAASLAMADLATAVVTEFTSLSGTMARHYALR DGYSTE(+) MLDISKNPSILHYICIGFCIQYLR*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc01g090200.2_circ_g.6

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