Plant Circular RNA Database

Detail information of Solyc07g048030.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc07g048030.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_002358
					
						Alias
						7:56541879|56543589
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr7: 59218379-59220089  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc07g048030.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						5/11
					
						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
						Solyc07g048030.2.1:2

General Information
CircRNA Name	Solyc07g048030.2_circ_g.1
ID in PlantcircBase	sly_circ_002358
Alias	7:56541879\|56543589
Organism	Solanum lycopersicum
Position	chr7: 59218379-59220089 JBrowse»
Reference genome	SL2.50.38
Type	ue-circRNA
Identification method	CIRI
Parent gene	Solyc07g048030.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	NA
Support reads	5/11
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	Solyc07g048030.2.1:2

			
						 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  
						
							ATTGGTTATGGACTCGGCAATGCACCCTCAGACATGCCACCTAAAAATTCTGCTAGTTATGTTG
GCAGTTATGGTGTTGGTAAAAGACAGTCAAACAGCGgaaaatgcaatctgatcttgggaagtta
ttcattggtggaatttcatgggacacaaatgaagagcgtctgaaggagtattttagtacttatg
gggaggtt

									
								

					

						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: 1409
Transcript exons: 59218379-59218604,59218907-59220089
GAAAATGCAATCTGATCTTGGGAAGTTATTCATTGGTGGAATTTCATGGGACACAAATGAAGAG
CGTCTGAAGGAGTATTTTAGTACTTATGGGGAGGTTTTAGAGGCTGTAATTATGAAGGATAGGA
CTACTGGACGTGCCCGTGGTTTTGGTTTTATTGTCTTTGCTGATCCTGCTGTTGCTGATAGGGT
AATCAAGGAGAAACACAACATTGATGGCAGGATGGTTGAAGCAAAGAAGGCTGTTCCTAGGGAT
GACCAGAGCACAATAAGTAGAAGCAGTCCTAGCATTCAGGGTTCTCCTGGTCCAGGACGTACAA
GAAAAATATTTGTTGGAGGTTTAGCATCCACAGTAACTGAGACTGACTTTAAGGAGTACTTTGA
GCAATTTGGAACAATCACAGATGTAGTAGTTATGTACGACCATAACACTCAGAGACCAAGAGGC
TTTGGGTTCATAACTTATGATTCAGAGGATGCAGTGGATAAAGTATTGCTTAAGCCCTTCCATG
AACTGAATGGTAAAATGGTCGAGGTCAAACGTGCAGTCCCCAAAGAGTTATCACCAGGTCCAAG
ACTTGGCGGGTTCAACCATCCATTAAGTAGGATCAATAACTTCCTTAATGGATACACACAAGGA
TACTCTCCGAATACAGTTGCAGGATATGGAGTCAGGATGGATGGTAGATTTAGCCCCATTGCTG
GAGGTAGGAGTGGTTTTGCTCCATTTGGTTCTGGTTATGGAATGGGGCTTAACTTTGAACCAGG
GTTAAGCCCAGGATATGGGGGAAGTGCAAACTTTAACAGCAACTTGAGCTATGGAAGGGGACTG
AACCCTTATTATGTTAATAGTTCAAACAGAGTTGGTGGTCCTATTGGGTTTGATGGAGTAAATG
GAGGAAGTAGTTCATTCTTCAGCTCAGCAACTCGGAATTTGTGGGGAAGTGGGGGTTTGGGTTA
TGGAACGAACTCCACAAGCTCTAGCACCTTTGCAGTAGCTGGAAATGGGAACACCGGGGCAGGA
AACTTTAGCAACACTGGAGTTTGGGGTTCATCTTCAATTTCCCCTCAAGGTAGAGGAAATGTTT
CTAACCAAAGTGGAAATCTTGGTTATGGGGGTGATGATAGTTTATATGGGTTGACTGGAGGCTA
TGGAAGAAATGTTACATCAAGTGGGGCTCCTACCTCATCATATCCTGCATCTAATGGTAGCTAT
GATGGTCCTTTAGCTGATTTTTACAGTGGTGGTTTGGGATATAGTGATTCCACTTGGCGCTCGG
CAAATTCTGAGCGAGATGGATCTGGTTCAATTGGTTATGGACTCGGCAATGCACCCTCAGACAT
GCCACCTAAAAATTCTGCTAGTTATGTTGGCAGTTATGGTGTTGGTAAAAGACAGTCAAACAGC
G
						
					

						Genomic sequence
						
							GAAAATGCAATCTGATCTTGGGAAGTTATTCATTGGTGGAATTTCATGGGACACAAATGAAGAG
CGTCTGAAGGAGTATTTTAGTACTTATGGGGAGGTTTTAGAGGCTGTAATTATGAAGGATAGGA
CTACTGGACGTGCCCGTGGTTTTGGTTTTATTGTCTTTGCTGATCCTGCTGTTGCTGATAGGGT
AATCAAGGAGAAACACAACATTGATGGCAGGATGGTAAGCTGTTCTAGTTTGCAAATTGGTTCC
TTTTGATTTGTTGAACAAGGAGCATATAAGGTTGTCGTTTGAACTTCTGATGAGATTATACTCT
TGGATGACACCTAAAATCAATGGGAAATGTGGCACTGTAATGGAGAGTTAGCTTTATAAATCTA
TGTTTTTTTGGTACAAATGGTGTTCTACCCTGCACTAAACTGGCACATTGTTCCTATTCTTATG
GCATATCACATCTGGAAGAGTGGTTATAATTAACTCTCAAATCTCTTCTTTTTACTCATCATGG
TCTACTTATATTTCAGGTTGAAGCAAAGAAGGCTGTTCCTAGGGATGACCAGAGCACAATAAGT
AGAAGCAGTCCTAGCATTCAGGGTTCTCCTGGTCCAGGACGTACAAGAAAAATATTTGTTGGAG
GTTTAGCATCCACAGTAACTGAGACTGACTTTAAGGAGTACTTTGAGCAATTTGGAACAATCAC
AGATGTAGTAGTTATGTACGACCATAACACTCAGAGACCAAGAGGCTTTGGGTTCATAACTTAT
GATTCAGAGGATGCAGTGGATAAAGTATTGCTTAAGCCCTTCCATGAACTGAATGGTAAAATGG
TCGAGGTCAAACGTGCAGTCCCCAAAGAGTTATCACCAGGTCCAAGACTTGGCGGGTTCAACCA
TCCATTAAGTAGGATCAATAACTTCCTTAATGGATACACACAAGGATACTCTCCGAATACAGTT
GCAGGATATGGAGTCAGGATGGATGGTAGATTTAGCCCCATTGCTGGAGGTAGGAGTGGTTTTG
CTCCATTTGGTTCTGGTTATGGAATGGGGCTTAACTTTGAACCAGGGTTAAGCCCAGGATATGG
GGGAAGTGCAAACTTTAACAGCAACTTGAGCTATGGAAGGGGACTGAACCCTTATTATGTTAAT
AGTTCAAACAGAGTTGGTGGTCCTATTGGGTTTGATGGAGTAAATGGAGGAAGTAGTTCATTCT
TCAGCTCAGCAACTCGGAATTTGTGGGGAAGTGGGGGTTTGGGTTATGGAACGAACTCCACAAG
CTCTAGCACCTTTGCAGTAGCTGGAAATGGGAACACCGGGGCAGGAAACTTTAGCAACACTGGA
GTTTGGGGTTCATCTTCAATTTCCCCTCAAGGTAGAGGAAATGTTTCTAACCAAAGTGGAAATC
TTGGTTATGGGGGTGATGATAGTTTATATGGGTTGACTGGAGGCTATGGAAGAAATGTTACATC
AAGTGGGGCTCCTACCTCATCATATCCTGCATCTAATGGTAGCTATGATGGTCCTTTAGCTGAT
TTTTACAGTGGTGGTTTGGGATATAGTGATTCCACTTGGCGCTCGGCAAATTCTGAGCGAGATG
GATCTGGTTCAATTGGTTATGGACTCGGCAATGCACCCTCAGACATGCCACCTAAAAATTCTGC
TAGTTATGTTGGCAGTTATGGTGTTGGTAAAAGACAGTCAAACAGCG
						
					

			
		

Sequences
Splice junction sequence	ATTGGTTATGGACTCGGCAATGCACCCTCAGACATGCCACCTAAAAATTCTGCTAGTTATGTTG GCAGTTATGGTGTTGGTAAAAGACAGTCAAACAGCGgaaaatgcaatctgatcttgggaagtta ttcattggtggaatttcatgggacacaaatgaagagcgtctgaaggagtattttagtacttatg gggaggtt
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: 1409 Transcript exons: 59218379-59218604,59218907-59220089 GAAAATGCAATCTGATCTTGGGAAGTTATTCATTGGTGGAATTTCATGGGACACAAATGAAGAG CGTCTGAAGGAGTATTTTAGTACTTATGGGGAGGTTTTAGAGGCTGTAATTATGAAGGATAGGA CTACTGGACGTGCCCGTGGTTTTGGTTTTATTGTCTTTGCTGATCCTGCTGTTGCTGATAGGGT AATCAAGGAGAAACACAACATTGATGGCAGGATGGTTGAAGCAAAGAAGGCTGTTCCTAGGGAT GACCAGAGCACAATAAGTAGAAGCAGTCCTAGCATTCAGGGTTCTCCTGGTCCAGGACGTACAA GAAAAATATTTGTTGGAGGTTTAGCATCCACAGTAACTGAGACTGACTTTAAGGAGTACTTTGA GCAATTTGGAACAATCACAGATGTAGTAGTTATGTACGACCATAACACTCAGAGACCAAGAGGC TTTGGGTTCATAACTTATGATTCAGAGGATGCAGTGGATAAAGTATTGCTTAAGCCCTTCCATG AACTGAATGGTAAAATGGTCGAGGTCAAACGTGCAGTCCCCAAAGAGTTATCACCAGGTCCAAG ACTTGGCGGGTTCAACCATCCATTAAGTAGGATCAATAACTTCCTTAATGGATACACACAAGGA TACTCTCCGAATACAGTTGCAGGATATGGAGTCAGGATGGATGGTAGATTTAGCCCCATTGCTG GAGGTAGGAGTGGTTTTGCTCCATTTGGTTCTGGTTATGGAATGGGGCTTAACTTTGAACCAGG GTTAAGCCCAGGATATGGGGGAAGTGCAAACTTTAACAGCAACTTGAGCTATGGAAGGGGACTG AACCCTTATTATGTTAATAGTTCAAACAGAGTTGGTGGTCCTATTGGGTTTGATGGAGTAAATG GAGGAAGTAGTTCATTCTTCAGCTCAGCAACTCGGAATTTGTGGGGAAGTGGGGGTTTGGGTTA TGGAACGAACTCCACAAGCTCTAGCACCTTTGCAGTAGCTGGAAATGGGAACACCGGGGCAGGA AACTTTAGCAACACTGGAGTTTGGGGTTCATCTTCAATTTCCCCTCAAGGTAGAGGAAATGTTT CTAACCAAAGTGGAAATCTTGGTTATGGGGGTGATGATAGTTTATATGGGTTGACTGGAGGCTA TGGAAGAAATGTTACATCAAGTGGGGCTCCTACCTCATCATATCCTGCATCTAATGGTAGCTAT GATGGTCCTTTAGCTGATTTTTACAGTGGTGGTTTGGGATATAGTGATTCCACTTGGCGCTCGG CAAATTCTGAGCGAGATGGATCTGGTTCAATTGGTTATGGACTCGGCAATGCACCCTCAGACAT GCCACCTAAAAATTCTGCTAGTTATGTTGGCAGTTATGGTGTTGGTAAAAGACAGTCAAACAGC G
Genomic sequence	GAAAATGCAATCTGATCTTGGGAAGTTATTCATTGGTGGAATTTCATGGGACACAAATGAAGAG CGTCTGAAGGAGTATTTTAGTACTTATGGGGAGGTTTTAGAGGCTGTAATTATGAAGGATAGGA CTACTGGACGTGCCCGTGGTTTTGGTTTTATTGTCTTTGCTGATCCTGCTGTTGCTGATAGGGT AATCAAGGAGAAACACAACATTGATGGCAGGATGGTAAGCTGTTCTAGTTTGCAAATTGGTTCC TTTTGATTTGTTGAACAAGGAGCATATAAGGTTGTCGTTTGAACTTCTGATGAGATTATACTCT TGGATGACACCTAAAATCAATGGGAAATGTGGCACTGTAATGGAGAGTTAGCTTTATAAATCTA TGTTTTTTTGGTACAAATGGTGTTCTACCCTGCACTAAACTGGCACATTGTTCCTATTCTTATG GCATATCACATCTGGAAGAGTGGTTATAATTAACTCTCAAATCTCTTCTTTTTACTCATCATGG TCTACTTATATTTCAGGTTGAAGCAAAGAAGGCTGTTCCTAGGGATGACCAGAGCACAATAAGT AGAAGCAGTCCTAGCATTCAGGGTTCTCCTGGTCCAGGACGTACAAGAAAAATATTTGTTGGAG GTTTAGCATCCACAGTAACTGAGACTGACTTTAAGGAGTACTTTGAGCAATTTGGAACAATCAC AGATGTAGTAGTTATGTACGACCATAACACTCAGAGACCAAGAGGCTTTGGGTTCATAACTTAT GATTCAGAGGATGCAGTGGATAAAGTATTGCTTAAGCCCTTCCATGAACTGAATGGTAAAATGG TCGAGGTCAAACGTGCAGTCCCCAAAGAGTTATCACCAGGTCCAAGACTTGGCGGGTTCAACCA TCCATTAAGTAGGATCAATAACTTCCTTAATGGATACACACAAGGATACTCTCCGAATACAGTT GCAGGATATGGAGTCAGGATGGATGGTAGATTTAGCCCCATTGCTGGAGGTAGGAGTGGTTTTG CTCCATTTGGTTCTGGTTATGGAATGGGGCTTAACTTTGAACCAGGGTTAAGCCCAGGATATGG GGGAAGTGCAAACTTTAACAGCAACTTGAGCTATGGAAGGGGACTGAACCCTTATTATGTTAAT AGTTCAAACAGAGTTGGTGGTCCTATTGGGTTTGATGGAGTAAATGGAGGAAGTAGTTCATTCT TCAGCTCAGCAACTCGGAATTTGTGGGGAAGTGGGGGTTTGGGTTATGGAACGAACTCCACAAG CTCTAGCACCTTTGCAGTAGCTGGAAATGGGAACACCGGGGCAGGAAACTTTAGCAACACTGGA GTTTGGGGTTCATCTTCAATTTCCCCTCAAGGTAGAGGAAATGTTTCTAACCAAAGTGGAAATC TTGGTTATGGGGGTGATGATAGTTTATATGGGTTGACTGGAGGCTATGGAAGAAATGTTACATC AAGTGGGGCTCCTACCTCATCATATCCTGCATCTAATGGTAGCTATGATGGTCCTTTAGCTGAT TTTTACAGTGGTGGTTTGGGATATAGTGATTCCACTTGGCGCTCGGCAAATTCTGAGCGAGATG GATCTGGTTCAATTGGTTATGGACTCGGCAATGCACCCTCAGACATGCCACCTAAAAATTCTGC TAGTTATGTTGGCAGTTATGGTGTTGGTAAAAGACAGTCAAACAGCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.871238547

Conservation Information
Conserved circRNAs	NA
PMCS	0.871238547

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							59218384-59218446(+)
59219977-59218390(+)
59218413-59220044(-)
						
						Potential amino acid sequence
						
							MQSDLGKLFIGGISWDTNEERLKEYFSTYGEVLEAVIMKDRTTGRARGFGFIVFADPAVADRVI
KEKHNIDGRMVEAKKAVPRDDQSTISRSSPSIQGSPGPGRTRKIFVGGLASTVTETDFKEYFEQ
FGTITDVVVMYDHNTQRPRGFGFITYDSEDAVDKVLLKPFHELNGKMVEVKRAVPKELSPGPRL
GGFNHPLSRINNFLNGYTQGYSPNTVAGYGVRMDGRFSPIAGGRSGFAPFGSGYGMGLNFEPGL
SPGYGGSANFNSNLSYGRGLNPYYVNSSNRVGGPIGFDGVNGGSSSFFSSATRNLWGSGGLGYG
TNSTSSSTFAVAGNGNTGAGNFSNTGVWGSSSISPQGRGNVSNQSGNLGYGGDDSLYGLTGGYG
RNVTSSGAPTSSYPASNGSYDGPLADFYSGGLGYSDSTWRSANSERDGSGSIGYGLGNAPSDMP
PKNSASYVGSYGVGKRQSNSGKCNLILGSYSLVEFHGTQMKSV*(+)
MDLVQLVMDSAMHPQTCHLKILLVMLAVMVLVKDSQTAENAI*(+)
MNNFPRSDCIFRCLTVFYQHHNCQHN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	59218384-59218446(+) 59219977-59218390(+) 59218413-59220044(-)
Potential amino acid sequence	MQSDLGKLFIGGISWDTNEERLKEYFSTYGEVLEAVIMKDRTTGRARGFGFIVFADPAVADRVI KEKHNIDGRMVEAKKAVPRDDQSTISRSSPSIQGSPGPGRTRKIFVGGLASTVTETDFKEYFEQ FGTITDVVVMYDHNTQRPRGFGFITYDSEDAVDKVLLKPFHELNGKMVEVKRAVPKELSPGPRL GGFNHPLSRINNFLNGYTQGYSPNTVAGYGVRMDGRFSPIAGGRSGFAPFGSGYGMGLNFEPGL SPGYGGSANFNSNLSYGRGLNPYYVNSSNRVGGPIGFDGVNGGSSSFFSSATRNLWGSGGLGYG TNSTSSSTFAVAGNGNTGAGNFSNTGVWGSSSISPQGRGNVSNQSGNLGYGGDDSLYGLTGGYG RNVTSSGAPTSSYPASNGSYDGPLADFYSGGLGYSDSTWRSANSERDGSGSIGYGLGNAPSDMP PKNSASYVGSYGVGKRQSNSGKCNLILGSYSLVEFHGTQMKSV(+) MDLVQLVMDSAMHPQTCHLKILLVMLAVMVLVKDSQTAENAI(+) MNNFPRSDCIFRCLTVFYQHHNCQHN*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

			
						 Other Information
					
						References
						Zuo et al., 2016; Yin et al., 2018

circRNA

Detail information of Solyc07g048030.2_circ_g.1

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