Plant Circular RNA Database

Detail information of Solyc01g106740.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc01g106740.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_000483
					
						Alias
						1:86245183|86247846, Slcirc029
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr1: 94484383-94487046  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc01g106740.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc01g106740.2_circ_g.1 						
					
						Support reads
						15/10
					
						Tissues
						fruit/leaf
					
						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
						Solyc01g106740.2.1:5

General Information
CircRNA Name	Solyc01g106740.2_circ_g.2
ID in PlantcircBase	sly_circ_000483
Alias	1:86245183\|86247846, Slcirc029
Organism	Solanum lycopersicum
Position	chr1: 94484383-94487046 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc01g106740.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc01g106740.2_circ_g.1
Support reads	15/10
Tissues	fruit/leaf
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	Solyc01g106740.2.1:5

			
						 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  
						
							TTTCTTCTTTAGATGAATCTTTTGCATCATCTGCTGTTGTTACCAAGAAGGGCAACTTCAATCT
TACTGCATTCAACACCTGCACATCCTCTGCAGCAACctttctaatcaaatcctcattgagcttc
agcatgtcctccatagaagtgaaagccatttccatatctagctgtgtaaactcgggttgtctgt
cggctctc

									
								

					

						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: 507
Transcript exons: 94484383-94484503,94484747-94484838,94485214-94485285,94
485456-94485567,94486937-94487046
CTTTCTAATCAAATCCTCATTGAGCTTCAGCATGTCCTCCATAGAAGTGAAAGCCATTTCCATA
TCTAGCTGTGTAAACTCGGGTTGTCTGTCGGCTCTCAAATCTTCATCCCTAAAGCACCTTGCTA
TTTGATAGTATTTATCAAATCCGGAGACCATCAGCATTTGCTTGAACAGCTGTGGACTCTGGGG
TAGTGCATAAAATGTTCCTGGCTGGACTCTTGAAGGAACCAAATAATCACGAGCACCTTCAGGA
GTAGATCTAGATAGTATTGGTGTCTCAATCTCAACAAAATCATGCACATCTTCTAGGTATCTTC
GAAGAAGCTTCACTACTCTATGTCGCAAGATTATATTTGAGCTCATCTGCGGACGGCGTAAATC
AAGGCATCGATACCGCAATCTGATTTCTTCTTTAGATGAATCTTTTGCATCATCTGCTGTTGTT
ACCAAGAAGGGCAACTTCAATCTTACTGCATTCAACACCTGCACATCCTCTGCAGCAAC
						
					

						Genomic sequence
						
							CTTTCTAATCAAATCCTCATTGAGCTTCAGCATGTCCTCCATAGAAGTGAAAGCCATTTCCATA
TCTAGCTGTGTAAACTCGGGTTGTCTGTCGGCTCTCAAATCTTCATCCCTAAAGCACCTGAAAA
TTACACAATACAGACCAACGTGAGTAGTAGCTTATGGGGGGTACATGCTCATGAGCACATTTCT
TTTCTTTATTTTAAGAATAAGATAACTACTCTTATGTGTCAATAAGACTATATTGTTTCACCTA
GTTTTAAGGGTGGGTAAGCCTGAGCTTTAACTCTGGATCACCATGAACTTTGTATGCAAGAGAT
TTGAAGTAGAAATATCTTAAGTTGCTACTATACAAACGAATTACCTTGCTATTTGATAGTATTT
ATCAAATCCGGAGACCATCAGCATTTGCTTGAACAGCTGTGGACTCTGGGGTAGTGCATAAAAT
GTTCCTGGCTTTATAACACAACCACAAAATAAATTTAATGTCATGGAGAATTAACTAGAGAGAG
CCTTCGTTCAATTAGTATGTCTATCATAAAAATATAACAGTAAGTTCAACAATTTTCTAGACAT
CCCATGGATAATAATTTTGGACAAACTCTTCTTTTGTCGATTTGTTAAGCACATTTCTCCTTGT
TCTCCATAAGCGTATTTAAATTCAAATGTAAAATTAGAATGAAGAATAAATCAAAGATCTGGGG
GAACAAATACTGTAATTTTCGAGAAGACTCGCTACTTTTGTACCAACAGTCTTCCTGAAGAATA
ACAGGAAATAGAGGGAGTGAATTAGCAATAAAAGTAGCAAAACAGAAGATAAGTAAAGAATACC
TGGACTCTTGAAGGAACCAAATAATCACGAGCACCTTCAGGAGTAGATCTAGATAGTATTGGTG
TCTCAATCTACCTTGTAACCATGAGAATGTTGGGGTCAACACTAACAACAGAAGCCACACAACA
AATAAAAGAAAATAAAAAGGCAACAATTTCATCAAGACCAGATAACCAAACTACTTATTCACAA
CAGGAAAAAAGAAGAATATTATAATACAATTAGAGGGCAAACATATTACCTCAACAAAATCATG
CACATCTTCTAGGTATCTTCGAAGAAGCTTCACTACTCTATGTCGCAAGATTATATTTGAGCTC
ATCTGCGGACGGCGTAAATCAAGGCATCGATACCTAAAAATGTGTACAAATTAGTTTCTAGCAA
GAAGCACTGTGTCAATATAAGAAATGGGTACAAAGTTTTAAGGAAACAGGAATTGTTTCTGCAA
TGAAAAAAAAGGATTGTATTCGCAGAATATATACATATAACAAGAAAAACGACAAGCCGCAACA
AATCAAAGCTGATATTTGATATGTGCAAGAGAGCTGGATTATGCCCTTGCTATTTAATTAATAG
TTTGAAAGGTAAATAAGCTGGACTATGCCCTTATCACATCAATAGAAAAGCACTGGTAGAAAAA
GAAGCAAAAAATGACAAAACGCTTATCTAGAAAAATATAAAACCATTTTGAGTGCTTGAGTTCA
TTCATTTTTTTCTACTCTCGAGATTCCAAATAAAGTTCCAAAAGATCAAATGGATCAATTAAAA
ATTTCATTACTAAGAACAAAATTGGGGGAGGCCTAAGCACTTCAATACAAGAACAGAGACAGTC
TCTAGAGACGACAGAGATTGCTCAGAAGACAACTTTTAGCACCTACATAGAAACCAATAATTTC
TAAATGCAACTTCTATCCTGGATCTTTTTTCCTGAATTGGAATTAAACATGCACGGATTCCACC
AGAAAAATAAATGTTCACGAGGTAGGGGTAAGGTTGCGCACACATGACCCTCCTCAGACCCACT
TGTGGGATTAGCATTGGTGGTTCCATTCCACCAGAAAATATAGAGCAAATAAAAAATCCCGCGT
ATTGCAAATAGGGAAGCAAGTTACCAGCAAAGATATTCAAGAAGAAATCTAGAGCACAAAGCCT
TATAAAGTTCAATTACTTCCAACGTGATCCCCCCCCCCCCCAAAAAAAAGAAAAAACTCTCTTG
TGTCGTTACAGAGAAAAGGCACTAATGTTTATTTCTTTTTCAATAAGTACAGACAAATGCCACT
GTTTGCTGATTTTCAAGTCTACAATTAGGTCTCAAAGAACCAATACTGCTAGTAAAATTCAAGA
CACTTATCTAAGAAAAGAGAAAAGAAATGCAAGAACTTCTTGGTTTTGACCCCTAACCAGAAAG
GGAGGAGAATAACAATTAAGATCACCCTTCCAGACCATATTAAGAATTGGTGTAAAGCACCAGC
AACATATTCGTCAAAAAATAAAAGGGTTTAGCAGCTAATAGTTACGTCATTGACTTTGATATCG
TCAAAATATAAATTACTTCAAGTCGCAAAACTATCTAATTAGACAAATACTGCTATCGTATTTA
CAACAACAGCAAACATACCCAACACCAATCCCACAAGTGGGGTCTGACAGGGGGGTCTAACACG
AAACAGAGAAGAAAGAGAAAAAGATTCAGCAAACAGCTATAGAAATTTCATAAGTTACCGCAAT
CTGATTTCTTCTTTAGATGAATCTTTTGCATCATCTGCTGTTGTTACCAAGAAGGGCAACTTCA
ATCTTACTGCATTCAACACCTGCACATCCTCTGCAGCAAC
						
					

			
		

Sequences
Splice junction sequence	TTTCTTCTTTAGATGAATCTTTTGCATCATCTGCTGTTGTTACCAAGAAGGGCAACTTCAATCT TACTGCATTCAACACCTGCACATCCTCTGCAGCAACctttctaatcaaatcctcattgagcttc agcatgtcctccatagaagtgaaagccatttccatatctagctgtgtaaactcgggttgtctgt cggctctc
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: 507 Transcript exons: 94484383-94484503,94484747-94484838,94485214-94485285,94 485456-94485567,94486937-94487046 CTTTCTAATCAAATCCTCATTGAGCTTCAGCATGTCCTCCATAGAAGTGAAAGCCATTTCCATA TCTAGCTGTGTAAACTCGGGTTGTCTGTCGGCTCTCAAATCTTCATCCCTAAAGCACCTTGCTA TTTGATAGTATTTATCAAATCCGGAGACCATCAGCATTTGCTTGAACAGCTGTGGACTCTGGGG TAGTGCATAAAATGTTCCTGGCTGGACTCTTGAAGGAACCAAATAATCACGAGCACCTTCAGGA GTAGATCTAGATAGTATTGGTGTCTCAATCTCAACAAAATCATGCACATCTTCTAGGTATCTTC GAAGAAGCTTCACTACTCTATGTCGCAAGATTATATTTGAGCTCATCTGCGGACGGCGTAAATC AAGGCATCGATACCGCAATCTGATTTCTTCTTTAGATGAATCTTTTGCATCATCTGCTGTTGTT ACCAAGAAGGGCAACTTCAATCTTACTGCATTCAACACCTGCACATCCTCTGCAGCAAC
Genomic sequence	CTTTCTAATCAAATCCTCATTGAGCTTCAGCATGTCCTCCATAGAAGTGAAAGCCATTTCCATA TCTAGCTGTGTAAACTCGGGTTGTCTGTCGGCTCTCAAATCTTCATCCCTAAAGCACCTGAAAA TTACACAATACAGACCAACGTGAGTAGTAGCTTATGGGGGGTACATGCTCATGAGCACATTTCT TTTCTTTATTTTAAGAATAAGATAACTACTCTTATGTGTCAATAAGACTATATTGTTTCACCTA GTTTTAAGGGTGGGTAAGCCTGAGCTTTAACTCTGGATCACCATGAACTTTGTATGCAAGAGAT TTGAAGTAGAAATATCTTAAGTTGCTACTATACAAACGAATTACCTTGCTATTTGATAGTATTT ATCAAATCCGGAGACCATCAGCATTTGCTTGAACAGCTGTGGACTCTGGGGTAGTGCATAAAAT GTTCCTGGCTTTATAACACAACCACAAAATAAATTTAATGTCATGGAGAATTAACTAGAGAGAG CCTTCGTTCAATTAGTATGTCTATCATAAAAATATAACAGTAAGTTCAACAATTTTCTAGACAT CCCATGGATAATAATTTTGGACAAACTCTTCTTTTGTCGATTTGTTAAGCACATTTCTCCTTGT TCTCCATAAGCGTATTTAAATTCAAATGTAAAATTAGAATGAAGAATAAATCAAAGATCTGGGG GAACAAATACTGTAATTTTCGAGAAGACTCGCTACTTTTGTACCAACAGTCTTCCTGAAGAATA ACAGGAAATAGAGGGAGTGAATTAGCAATAAAAGTAGCAAAACAGAAGATAAGTAAAGAATACC TGGACTCTTGAAGGAACCAAATAATCACGAGCACCTTCAGGAGTAGATCTAGATAGTATTGGTG TCTCAATCTACCTTGTAACCATGAGAATGTTGGGGTCAACACTAACAACAGAAGCCACACAACA AATAAAAGAAAATAAAAAGGCAACAATTTCATCAAGACCAGATAACCAAACTACTTATTCACAA CAGGAAAAAAGAAGAATATTATAATACAATTAGAGGGCAAACATATTACCTCAACAAAATCATG CACATCTTCTAGGTATCTTCGAAGAAGCTTCACTACTCTATGTCGCAAGATTATATTTGAGCTC ATCTGCGGACGGCGTAAATCAAGGCATCGATACCTAAAAATGTGTACAAATTAGTTTCTAGCAA GAAGCACTGTGTCAATATAAGAAATGGGTACAAAGTTTTAAGGAAACAGGAATTGTTTCTGCAA TGAAAAAAAAGGATTGTATTCGCAGAATATATACATATAACAAGAAAAACGACAAGCCGCAACA AATCAAAGCTGATATTTGATATGTGCAAGAGAGCTGGATTATGCCCTTGCTATTTAATTAATAG TTTGAAAGGTAAATAAGCTGGACTATGCCCTTATCACATCAATAGAAAAGCACTGGTAGAAAAA GAAGCAAAAAATGACAAAACGCTTATCTAGAAAAATATAAAACCATTTTGAGTGCTTGAGTTCA TTCATTTTTTTCTACTCTCGAGATTCCAAATAAAGTTCCAAAAGATCAAATGGATCAATTAAAA ATTTCATTACTAAGAACAAAATTGGGGGAGGCCTAAGCACTTCAATACAAGAACAGAGACAGTC TCTAGAGACGACAGAGATTGCTCAGAAGACAACTTTTAGCACCTACATAGAAACCAATAATTTC TAAATGCAACTTCTATCCTGGATCTTTTTTCCTGAATTGGAATTAAACATGCACGGATTCCACC AGAAAAATAAATGTTCACGAGGTAGGGGTAAGGTTGCGCACACATGACCCTCCTCAGACCCACT TGTGGGATTAGCATTGGTGGTTCCATTCCACCAGAAAATATAGAGCAAATAAAAAATCCCGCGT ATTGCAAATAGGGAAGCAAGTTACCAGCAAAGATATTCAAGAAGAAATCTAGAGCACAAAGCCT TATAAAGTTCAATTACTTCCAACGTGATCCCCCCCCCCCCCAAAAAAAAGAAAAAACTCTCTTG TGTCGTTACAGAGAAAAGGCACTAATGTTTATTTCTTTTTCAATAAGTACAGACAAATGCCACT GTTTGCTGATTTTCAAGTCTACAATTAGGTCTCAAAGAACCAATACTGCTAGTAAAATTCAAGA CACTTATCTAAGAAAAGAGAAAAGAAATGCAAGAACTTCTTGGTTTTGACCCCTAACCAGAAAG GGAGGAGAATAACAATTAAGATCACCCTTCCAGACCATATTAAGAATTGGTGTAAAGCACCAGC AACATATTCGTCAAAAAATAAAAGGGTTTAGCAGCTAATAGTTACGTCATTGACTTTGATATCG TCAAAATATAAATTACTTCAAGTCGCAAAACTATCTAATTAGACAAATACTGCTATCGTATTTA CAACAACAGCAAACATACCCAACACCAATCCCACAAGTGGGGTCTGACAGGGGGGTCTAACACG AAACAGAGAAGAAAGAGAAAAAGATTCAGCAAACAGCTATAGAAATTTCATAAGTTACCGCAAT CTGATTTCTTCTTTAGATGAATCTTTTGCATCATCTGCTGTTGTTACCAAGAAGGGCAACTTCA ATCTTACTGCATTCAACACCTGCACATCCTCTGCAGCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.344270007

Conservation Information
Conserved circRNAs	NA
PMCS	0.344270007

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							94486960-94484387(+)
94485538-94484385(-)
						
						Potential amino acid sequence
						
							MNLLHHLLLLPRRATSILLHSTPAHPLQQPF*(+)
MSSNIILRHRVVKLLRRYLEDVHDFVEIETPILSRSTPEGARDYLVPSRVQPGTFYALPQSPQL
FKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMEMAFTSMEDMLKLNEDLIRKVAAEDV
QVLNAVRLKLPFLVTTADDAKDSSKEEIRLRYRCLDLRRPQMSSNIILRHRVVKLLRRYLEDVH
DFVEIETPILSRSTPEGARDYLVPSRVQPGTFYALPQSPQLFKQMLMVSGFDKYYQIARCFRDE
DLRADRQPEFTQLDMEMAFTSMEDMLKLNEDLIRKVAAEDVQVLNAVRLKLPFLVTTADDAKDS
SKEEIRLRYRCLDLRRPQMSSNIILRHRVVKLLRRYLEDVHDFVEIETPILSRSTPEGARDYLV
PSRVQPGTFYALPQSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMEMAFTSME
DMLKLNEDLIRKVAAEDVQVLNAVRLKLPFLVTTADDAKDSSKEEIRLRYRCLDLRRPQMSSNI
ILRHRVVKLLRRYLEDVHDFVEIETPILSRSTPEGARDYLVPSRVQPGTFYALPQSPQLFKQML
MVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMEMAFTSMEDMLKLNEDLIRK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	94486960-94484387(+) 94485538-94484385(-)
Potential amino acid sequence	MNLLHHLLLLPRRATSILLHSTPAHPLQQPF*(+) MSSNIILRHRVVKLLRRYLEDVHDFVEIETPILSRSTPEGARDYLVPSRVQPGTFYALPQSPQL FKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMEMAFTSMEDMLKLNEDLIRKVAAEDV QVLNAVRLKLPFLVTTADDAKDSSKEEIRLRYRCLDLRRPQMSSNIILRHRVVKLLRRYLEDVH DFVEIETPILSRSTPEGARDYLVPSRVQPGTFYALPQSPQLFKQMLMVSGFDKYYQIARCFRDE DLRADRQPEFTQLDMEMAFTSMEDMLKLNEDLIRKVAAEDVQVLNAVRLKLPFLVTTADDAKDS SKEEIRLRYRCLDLRRPQMSSNIILRHRVVKLLRRYLEDVHDFVEIETPILSRSTPEGARDYLV PSRVQPGTFYALPQSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMEMAFTSME DMLKLNEDLIRKVAAEDVQVLNAVRLKLPFLVTTADDAKDSSKEEIRLRYRCLDLRRPQMSSNI ILRHRVVKLLRRYLEDVHDFVEIETPILSRSTPEGARDYLVPSRVQPGTFYALPQSPQLFKQML MVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMEMAFTSMEDMLKLNEDLIRK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yin et al., 2018; Wang et al., 2018b

circRNA

Detail information of Solyc01g106740.2_circ_g.2

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