Plant Circular RNA Database

Detail information of Solyc04g079120.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc04g079120.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_001554
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 63707118-63710069  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc04g079120.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						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  
						
							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
						Solyc04g079120.2.1:5

General Information
CircRNA Name	Solyc04g079120.2_circ_g.1
ID in PlantcircBase	sly_circ_001554
Alias	NA
Organism	Solanum lycopersicum
Position	chr4: 63707118-63710069 JBrowse»
Reference genome	SL2.50.38
Type	ue-circRNA
Identification method	CIRI
Parent gene	Solyc04g079120.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	NA
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	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	Solyc04g079120.2.1:5

			
						 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  
						
							CACAACAAAACTATATCTTCTTCTCCAAAAAAAAAAGAATACAACTAATCCTCTTTCATTGGCT
GTTAACCCAATCAGTCAACGCAAATCCAACAATTACctttacttgcttcacatagggtacagga
actatatattcgccaacatccatatctccaatggatctcgagaggcagagtccaccaggccaac
atctcaaa

									
								

					

						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: 816
Transcript exons: 63707118-63707225,63707414-63707477,63707564-63707717,63
708567-63708738,63709752-63710069
CTTTACTTGCTTCACATAGGGTACAGGAACTATATATTCGCCAACATCCATATCTCCAATGGAT
CTCGAGAGGCAGAGTCCACCAGGCCAACATCTCAAAGGACCAATCTCTGTACCGCCACCAGCAT
TAAGCCGACCAACTTCTCCACCACAAGCTGTTATACGTTCCCTCTCCTCTTCATTGCAATCAAG
CCTATGATCAGCTGATAGATAATAAATTCCGCCTTCAGCAGATTCAAGTATGCATCGAGAATCG
CCAACTGATGCAACTGTTACAACCCATCCTTCAATTATGACAAACGTGACTGTTGTCCCTGAGG
TTTTTGCTTTTTCTTGGAAATCTTTATCCGTTTTGACAAATCCTGCAACCAATGCTCTAGGAAG
TGCTGCAACCCATTCATCTCTACTAAGATCAGGAGGAATAGCACTCAAGACATTCTGCAAGAGA
TTTTCTTTAGAATATATTGCAGCCGCTGACCCATTGTGCCCATCAAATAATCCAAAAACAGAAT
ATGTAGCTACTCCATCACCCAAAACTCTTTGGCATTCCGTCTTGACAAACGTAAAATCTTCTCC
TTTTTTGCTCTGACTAGCTTGACCATGAGAAAGCTCCGGACTTTCAATCTTCTCATTAGCCAAT
TCACGCTTCAACAACACAGATAGTGGGACCGTTTGATGTTCACCCTTAGACAACATAATTCGGT
CCCTTTCCAAATCACAACAAAACTATATCTTCTTCTCCAAAAAAAAAAGAATACAACTAATCCT
CTTTCATTGGCTGTTAACCCAATCAGTCAACGCAAATCCAACAATTAC
						
					

						Genomic sequence
						
							CTTTACTTGCTTCACATAGGGTACAGGAACTATATATTCGCCAACATCCATATCTCCAATGGAT
CTCGAGAGGCAGAGTCCACCAGGCCAACATCTCAAAGGACCAATCTGAAATAAGTTGAAATCAC
TGGTAAGATATAAAGAACAAAGCTAATCTACTTTCTGAAACTTCTTCCCGAAGAAGGAAGTTGG
AGAAATAAAAACGAAAAAGACAACCAGAATGTATGTGTGAGGGGTGGGGTGGGGTAGGGTGCAG
TAATGTTTCAAAACCAGAGATCATATGACCACCAACATACCTCTGTACCGCCACCAGCATTAAG
CCGACCAACTTCTCCACCACAAGCTGTTATACGTTCCCTCCTATTCAATTAAAAACAAAAACAA
TCAATACCTTAATGCAAGAGGTGAAAGCATGCTAATTAATTGGCTAAAGGCATTAATCTTACTC
CTCTTCATTGCAATCAAGCCTATGATCAGCTGATAGATAATAAATTCCGCCTTCAGCAGATTCA
AGTATGCATCGAGAATCGCCAACTGATGCAACTGTTACAACCCATCCTTCAATTATGACAAACG
TGACTGTTGTCCCTGAGGTTTTTGCTGCAGTTTAACACAATACAATGTCAGGAAATGCATAGTA
TAGTAGCAGACAATTAGATTGTTTCTTCTTTGAGAAAAGTCAACTATACCGGAGATATTAGTAT
TAGAAGCCAAGCCAGAAGGGAAGAAAACATACAGCAAGAGGCCAAGAGCTGAAGGAAATATGTA
TAATATCATCGGAAGCAAATACAAATTCAGAAGCCCCGAAATAATAACAAGTCTTGCATCAAGA
AATGGAATATCACATGCCTTATGAGCCATGTTTGATCAATCAGGCGTAATACCAGCACAAAACA
AAAACTACAAGGTTTCCTTGATTATCTACATCTTATAGCATATTAATGTTAGGCTGTCAAAAGC
ATTTCCGCTGCAGCATTCAATGAGCTCAAGCTAAGTTGATCGGACTCAAGTGATGATATAAAGC
TCGGATCCTTCATGATCTAAATTTTAAGACTCAGGGATACAGATCTAGATACAGATACAGGTGC
GGGAATTCGGAAAATAATTCAAAATATCTATTAGAGTTAATGTCTAAATTATGAGGAAACTTTA
CAAGGTATTCCGTGGAGAAAATATTGATCAAGAGGAGATTCCCAGGAGGTGATATAAGGAAATG
TACCCAAAACCGGTTGAACAAATCCAGTAAGTATCCCATACCCACACCCATGGGTGTGACACCA
AAAGTGAAGGATCCGGGCAACTTGGGGTTCAGGTAATTCACAACAAAAAGTCAACAGGGGCATC
AGGAATTACTACTCCACTTTGACTGTAATTCACTCACTGGCTCTCGTCATACACACCAAATTGC
AACATCTTGTTTCCAGAAATTAATGAAGAAACCACTCGTACCTTTTTCTTGGAAATCTTTATCC
GTTTTGACAAATCCTGCAACCAATGCTCTAGGAAGTGCTGCAACCCATTCATCTCTACTAAGAT
CAGGAGGAATAGCACTCAAGACATTCTGCAAGAGATTTTCTTTAGAATATATTGCAGCCGCTGA
CCCATTGTGCCCATCAAATAACTGCAAAGATGGGAGATCACAAATATTAGACGGACGTTATTTA
AAAAAGGAAATGGTTAGTGCGGTTATTGAAATTTAAAATCTTAAACAGAATTTCCAGGTCAACA
GAGATGTTAGGTAGTGTTCAACACAGAAATTCTTTATTTGGAAAAAACAATAAAGTTGAAGAAA
TGAAAATGAGAAAAGGAAAAAGACAAAACTTAAAAGATAATGCTGCATAGAGTAGAAAATATGA
CAATGTGATTACGGAAGGATCCAAAGACCAACAACTTATAAAAGCAAAGATGGAAACTATATCT
TATAAGTTCGACAAGTCAAAAACATAACTAATGGCACAGATCGAACAATCAGAGATGCCGTTAT
ACTTCAACAAGTCGACTAAATTCACAAGACATCCAATCCTAGAGAACAAACAGCAGGTTAGCCT
GTAATCAGAGTTGCGTCACTGCTACATAATGTCGTATTAGCTAGTTTCGAATAACAAAAACTAG
AGAATCTCCGCAAAAACATGATTCAATGAAGGACACTCAATCAGCTATACCACCAGGACCTCAT
GGGTGCACAAAAATGAAACTAAAGATAAACAATTATTCCTTTAGATTTATAAAATCATATTTCT
ATCCCTTCAAAGACCTCTCCTATTTCTCTCCTTCAATACAACCCACACAAGAGCTTTAAGTAAA
CCATCCCACACCTTAAGTTCCACTTGTTCCATCGCTCAATAGCTTAAACCAAATGGGGCCATCA
AACTTTTGCAATGAAACAACCTCAATACACACCTCTACTTACTAGATGTTGCATTTGAACAAAT
GAATTAGCAGTTGATAATCGGAACAAACAAAGAGTTCTCGACTTGCATCTTACACAATCCATCT
AAGACAACAAAGTCAGAAGCTATCCTTGTCAAACAATAAATCTATCTAATAATCCAACAATAAC
AAATAGCAAACACATATACAAGCATTAATAACAACATTAGCATATAAATGAAACATTTTTCTGA
AAAATCTTACTCCAAAAACAGAATATGTAGCTACTCCATCACCCAAAACTCTTTGGCATTCCGT
CTTGACAAACGTAAAATCTTCTCCTTTTTTGCTCTGACTAGCTTGACCATGAGAAAGCTCCGGA
CTTTCAATCTTCTCATTAGCCAATTCACGCTTCAACAACACAGATAGTGGGACCGTTTGATGTT
CACCCTTAGACAACATAATTCGGTCCCTTTCCAAATCACAACAAAACTATATCTTCTTCTCCAA
AAAAAAAAGAATACAACTAATCCTCTTTCATTGGCTGTTAACCCAATCAGTCAACGCAAATCCA
ACAATTAC
						
					

			
		

Sequences
Splice junction sequence	CACAACAAAACTATATCTTCTTCTCCAAAAAAAAAAGAATACAACTAATCCTCTTTCATTGGCT GTTAACCCAATCAGTCAACGCAAATCCAACAATTACctttacttgcttcacatagggtacagga actatatattcgccaacatccatatctccaatggatctcgagaggcagagtccaccaggccaac atctcaaa
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: 816 Transcript exons: 63707118-63707225,63707414-63707477,63707564-63707717,63 708567-63708738,63709752-63710069 CTTTACTTGCTTCACATAGGGTACAGGAACTATATATTCGCCAACATCCATATCTCCAATGGAT CTCGAGAGGCAGAGTCCACCAGGCCAACATCTCAAAGGACCAATCTCTGTACCGCCACCAGCAT TAAGCCGACCAACTTCTCCACCACAAGCTGTTATACGTTCCCTCTCCTCTTCATTGCAATCAAG CCTATGATCAGCTGATAGATAATAAATTCCGCCTTCAGCAGATTCAAGTATGCATCGAGAATCG CCAACTGATGCAACTGTTACAACCCATCCTTCAATTATGACAAACGTGACTGTTGTCCCTGAGG TTTTTGCTTTTTCTTGGAAATCTTTATCCGTTTTGACAAATCCTGCAACCAATGCTCTAGGAAG TGCTGCAACCCATTCATCTCTACTAAGATCAGGAGGAATAGCACTCAAGACATTCTGCAAGAGA TTTTCTTTAGAATATATTGCAGCCGCTGACCCATTGTGCCCATCAAATAATCCAAAAACAGAAT ATGTAGCTACTCCATCACCCAAAACTCTTTGGCATTCCGTCTTGACAAACGTAAAATCTTCTCC TTTTTTGCTCTGACTAGCTTGACCATGAGAAAGCTCCGGACTTTCAATCTTCTCATTAGCCAAT TCACGCTTCAACAACACAGATAGTGGGACCGTTTGATGTTCACCCTTAGACAACATAATTCGGT CCCTTTCCAAATCACAACAAAACTATATCTTCTTCTCCAAAAAAAAAAGAATACAACTAATCCT CTTTCATTGGCTGTTAACCCAATCAGTCAACGCAAATCCAACAATTAC
Genomic sequence	CTTTACTTGCTTCACATAGGGTACAGGAACTATATATTCGCCAACATCCATATCTCCAATGGAT CTCGAGAGGCAGAGTCCACCAGGCCAACATCTCAAAGGACCAATCTGAAATAAGTTGAAATCAC TGGTAAGATATAAAGAACAAAGCTAATCTACTTTCTGAAACTTCTTCCCGAAGAAGGAAGTTGG AGAAATAAAAACGAAAAAGACAACCAGAATGTATGTGTGAGGGGTGGGGTGGGGTAGGGTGCAG TAATGTTTCAAAACCAGAGATCATATGACCACCAACATACCTCTGTACCGCCACCAGCATTAAG CCGACCAACTTCTCCACCACAAGCTGTTATACGTTCCCTCCTATTCAATTAAAAACAAAAACAA TCAATACCTTAATGCAAGAGGTGAAAGCATGCTAATTAATTGGCTAAAGGCATTAATCTTACTC CTCTTCATTGCAATCAAGCCTATGATCAGCTGATAGATAATAAATTCCGCCTTCAGCAGATTCA AGTATGCATCGAGAATCGCCAACTGATGCAACTGTTACAACCCATCCTTCAATTATGACAAACG TGACTGTTGTCCCTGAGGTTTTTGCTGCAGTTTAACACAATACAATGTCAGGAAATGCATAGTA TAGTAGCAGACAATTAGATTGTTTCTTCTTTGAGAAAAGTCAACTATACCGGAGATATTAGTAT TAGAAGCCAAGCCAGAAGGGAAGAAAACATACAGCAAGAGGCCAAGAGCTGAAGGAAATATGTA TAATATCATCGGAAGCAAATACAAATTCAGAAGCCCCGAAATAATAACAAGTCTTGCATCAAGA AATGGAATATCACATGCCTTATGAGCCATGTTTGATCAATCAGGCGTAATACCAGCACAAAACA AAAACTACAAGGTTTCCTTGATTATCTACATCTTATAGCATATTAATGTTAGGCTGTCAAAAGC ATTTCCGCTGCAGCATTCAATGAGCTCAAGCTAAGTTGATCGGACTCAAGTGATGATATAAAGC TCGGATCCTTCATGATCTAAATTTTAAGACTCAGGGATACAGATCTAGATACAGATACAGGTGC GGGAATTCGGAAAATAATTCAAAATATCTATTAGAGTTAATGTCTAAATTATGAGGAAACTTTA CAAGGTATTCCGTGGAGAAAATATTGATCAAGAGGAGATTCCCAGGAGGTGATATAAGGAAATG TACCCAAAACCGGTTGAACAAATCCAGTAAGTATCCCATACCCACACCCATGGGTGTGACACCA AAAGTGAAGGATCCGGGCAACTTGGGGTTCAGGTAATTCACAACAAAAAGTCAACAGGGGCATC AGGAATTACTACTCCACTTTGACTGTAATTCACTCACTGGCTCTCGTCATACACACCAAATTGC AACATCTTGTTTCCAGAAATTAATGAAGAAACCACTCGTACCTTTTTCTTGGAAATCTTTATCC GTTTTGACAAATCCTGCAACCAATGCTCTAGGAAGTGCTGCAACCCATTCATCTCTACTAAGAT CAGGAGGAATAGCACTCAAGACATTCTGCAAGAGATTTTCTTTAGAATATATTGCAGCCGCTGA CCCATTGTGCCCATCAAATAACTGCAAAGATGGGAGATCACAAATATTAGACGGACGTTATTTA AAAAAGGAAATGGTTAGTGCGGTTATTGAAATTTAAAATCTTAAACAGAATTTCCAGGTCAACA GAGATGTTAGGTAGTGTTCAACACAGAAATTCTTTATTTGGAAAAAACAATAAAGTTGAAGAAA TGAAAATGAGAAAAGGAAAAAGACAAAACTTAAAAGATAATGCTGCATAGAGTAGAAAATATGA CAATGTGATTACGGAAGGATCCAAAGACCAACAACTTATAAAAGCAAAGATGGAAACTATATCT TATAAGTTCGACAAGTCAAAAACATAACTAATGGCACAGATCGAACAATCAGAGATGCCGTTAT ACTTCAACAAGTCGACTAAATTCACAAGACATCCAATCCTAGAGAACAAACAGCAGGTTAGCCT GTAATCAGAGTTGCGTCACTGCTACATAATGTCGTATTAGCTAGTTTCGAATAACAAAAACTAG AGAATCTCCGCAAAAACATGATTCAATGAAGGACACTCAATCAGCTATACCACCAGGACCTCAT GGGTGCACAAAAATGAAACTAAAGATAAACAATTATTCCTTTAGATTTATAAAATCATATTTCT ATCCCTTCAAAGACCTCTCCTATTTCTCTCCTTCAATACAACCCACACAAGAGCTTTAAGTAAA CCATCCCACACCTTAAGTTCCACTTGTTCCATCGCTCAATAGCTTAAACCAAATGGGGCCATCA AACTTTTGCAATGAAACAACCTCAATACACACCTCTACTTACTAGATGTTGCATTTGAACAAAT GAATTAGCAGTTGATAATCGGAACAAACAAAGAGTTCTCGACTTGCATCTTACACAATCCATCT AAGACAACAAAGTCAGAAGCTATCCTTGTCAAACAATAAATCTATCTAATAATCCAACAATAAC AAATAGCAAACACATATACAAGCATTAATAACAACATTAGCATATAAATGAAACATTTTTCTGA AAAATCTTACTCCAAAAACAGAATATGTAGCTACTCCATCACCCAAAACTCTTTGGCATTCCGT CTTGACAAACGTAAAATCTTCTCCTTTTTTGCTCTGACTAGCTTGACCATGAGAAAGCTCCGGA CTTTCAATCTTCTCATTAGCCAATTCACGCTTCAACAACACAGATAGTGGGACCGTTTGATGTT CACCCTTAGACAACATAATTCGGTCCCTTTCCAAATCACAACAAAACTATATCTTCTTCTCCAA AAAAAAAAGAATACAACTAATCCTCTTTCATTGGCTGTTAACCCAATCAGTCAACGCAAATCCA ACAATTAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.3221312

Conservation Information
Conserved circRNAs	NA
PMCS	0.3221312

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							63709930-63707595(+)
63709951-63710027(-)
63707213-63710046(-)
						
						Potential amino acid sequence
						
							MFTLRQHNSVPFQITTKLYLLLQKKKNTTNPLSLAVNPISQRKSNNYLYLLHIGYRNYIFANIH
ISNGSREAESTRPTSQRTNLCTATSIKPTNFSTTSCYTFPLLFIAIKPMIS*(+)
MLSKGEHQTVPLSVLLKRELANEKIESPELSHGQASQSKKGEDFTFVKTECQRVLGDGVATYSV
FGLFDGHNGSAAAIYSKENLLQNVLSAIPPDLSRDEWVAALPRALVAGFVKTDKDFQEKAKTSG
TTVTFVIIEGWVVTVASVGDSRCILESAEGGIYYLSADHRLDCNEEERERITACGGEVGRLNAG
GGTEIGPLRCWPGGLCLSRSIGDMDVGEYIVPVPYVKQVKVIVGFALTDWVNSQ*(-)
MLAWWTLPLEIHWRYGCWRIYSSCTLCEASKGNCWICVD*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	63709930-63707595(+) 63709951-63710027(-) 63707213-63710046(-)
Potential amino acid sequence	MFTLRQHNSVPFQITTKLYLLLQKKKNTTNPLSLAVNPISQRKSNNYLYLLHIGYRNYIFANIH ISNGSREAESTRPTSQRTNLCTATSIKPTNFSTTSCYTFPLLFIAIKPMIS(+) MLSKGEHQTVPLSVLLKRELANEKIESPELSHGQASQSKKGEDFTFVKTECQRVLGDGVATYSV FGLFDGHNGSAAAIYSKENLLQNVLSAIPPDLSRDEWVAALPRALVAGFVKTDKDFQEKAKTSG TTVTFVIIEGWVVTVASVGDSRCILESAEGGIYYLSADHRLDCNEEERERITACGGEVGRLNAG GGTEIGPLRCWPGGLCLSRSIGDMDVGEYIVPVPYVKQVKVIVGFALTDWVNSQ(-) MLAWWTLPLEIHWRYGCWRIYSSCTLCEASKGNCWICVD*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc04g079120.2_circ_g.1

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