Plant Circular RNA Database

Detail information of Solyc12g013870.1_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc12g013870.1_circ_g.2
					
						ID in PlantcircBase
						sly_circ_003554
					
						Alias
						12:4658515|4661158, Slcirc181
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr12: 4658515-4661158  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc12g013870.1						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc12g013870.1_circ_g.1 						
					
						Support reads
						53/23
					
						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  
						
							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
						Solyc12g013870.1.1:7

General Information
CircRNA Name	Solyc12g013870.1_circ_g.2
ID in PlantcircBase	sly_circ_003554
Alias	12:4658515\|4661158, Slcirc181
Organism	Solanum lycopersicum
Position	chr12: 4658515-4661158 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc12g013870.1
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc12g013870.1_circ_g.1
Support reads	53/23
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	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	Solyc12g013870.1.1:7

			
						 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  
						
							GGACAAAGTCCTCAAAATCCATTGAGGCATCATTGAGACTTGATGCTGTAGCTAGTGCAGGATT
CAAAGTTTCTCGAACTAAAATGGCCAGTTTGATTAGcttttggaatatgcagcctaccacaggc
tattaagggtgatgctgatattttactgaaaggagtgagagacaagaacaccattgaagatgtg
aaacgtat

									
								

					

						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: 655
Transcript exons: 4658515-4658624,4658779-4658910,4658989-4659062,4659158-
4659263,4660544-4660612,4660898-4660962,4661060-4661158
CTTTTGGAATATGCAGCCTACCACAGGCTATTAAGGGTGATGCTGATATTTTACTGAAAGGAGT
GAGAGACAAGAACACCATTGAAGATGTGAAACGTATTGTTGAACTGGCAAAACGGGCATCATTA
AGACGAGAAGTTTTACATACTGAGTTTCTGACTCCACCTGTATTAAAAGAGTCAATGCTAGTCT
TAGAAAGGTTAGCTGATCTCAGAATAGTTGCACAAGGAGGATACCCAGAGGCTGAACGATGCCG
ACTCTCAGTTGGACACGTGGAGGCATTAACAAGTGATCCAGATAATGTTGCAGCCTTGAGTATT
TCAGGGAACTTTTCATTTCAACCTTGTTCTCATGGTGATTTCCTTGGTGCAATCCTTGGTACAG
GGATTGCAAGGAATAAGCTGGGAGATATACTCTTGCAGGGTGAAAAGGGAGCTCATGTTCTTGT
TGTTCCAGAACTTTCTGACTTCCTTATATCAGCATTGGACAAGGTTGGAAATGTTTCTGTCTCT
TGCAAGAAGATTCCATTGCTTGCCCTTGAATATGAACCACCAAGGACAAAGTCCTCAAAATCCA
TTGAGGCATCATTGAGACTTGATGCTGTAGCTAGTGCAGGATTCAAAGTTTCTCGAACTAAAAT
GGCCAGTTTGATTAG
						
					

						Genomic sequence
						
							CTTTTGGAATATGCAGCCTACCACAGGCTATTAAGGGTGATGCTGATATTTTACTGAAAGGAGT
GAGAGACAAGAACACCATTGAAGATGTGAAACGTATTGTTGAACTGGTACATATACATCTACCT
GACCAATCACTCCTCTCAATTAACAGTTGAGAAGTCTTGTCTAGTTTTTCAACTCTTTGGTCCT
TGTTGTAGAAAAAGCACCAAAACATTGTCCTAAGTCTTAATCTAAACTGATTATCACTTGCGTA
CTTCTCAGGCAAAACGGGCATCATTAAGACGAGAAGTTTTACATACTGAGTTTCTGACTCCACC
TGTATTAAAAGAGTCAATGCTAGTCTTAGAAAGGTTAGCTGATCTCAGAATAGTTGCACAAGGA
GGATACCCAGAGGTTGGACACAGTTTGTTTTACAAAACTAGTTTGAGCAATAAAGCTGCTTGAA
TTTATATTTACTGTCTCCTTAAACAGGCTGAACGATGCCGACTCTCAGTTGGACACGTGGAGGC
ATTAACAAGTGATCCAGATAATGTTGCAGCCTTGAGGTATGTCCTCCTGTAATTGTTCAGTTAT
GCCTGCTGTTTAATTCGACCAATCAAAAAATCCTCTTTATTATTGTGAAAAATGGTCCTCTGTC
CAGTATTTCAGGGAACTTTTCATTTCAACCTTGTTCTCATGGTGATTTCCTTGGTGCAATCCTT
GGTACAGGGATTGCAAGGAATAAGCTGGGAGATATACTCTTGCAGGTATTTTGTTTATTTATTT
TTTGGAGGTTTTCTATCTCTCTTACAAGTTTTGGCAACACCTAGTTGATTTCATCATTTGTTCG
CTTAAAAAAAATATATGTAAAAGAAAGATAGAAGTGACAGAGGGTGATCAATTGTTGATCAAAT
AGAGGGCTCTTGGGCAGAGAGTTGCGGTCATTACACCTAAGAGAGGATCCACCTCTTTGTAGCT
GAGTTATTATGTACTCCCTCTGTTCCATTTTAGTTGGCCCTTATACTAAAAATAGATTTTCTTG
TTTACTTGTCAATTTCAGCAAATCAAGAGAGATTATTATTTTCTTCTCATATTAACCTTATCAT
GGGTAAGTATATGAAGTAATAGTTGTCAAACCTAGATTTTCAAAGGACAATTATAAGGATAATT
TAGTAAACAAACTCCTAATAAATAGTTTCTCAAGAGAAATGTCAAATCAACAAGGGCCAAGTAA
AATGGAACATAAAAGATGAGTCAGAACTAATATGTGGAGGTAGTGTATGCTTAAGAAGTAAACT
TGTTGATCAATACTTTGATATCTAATGACTACTTTGTTTTAGTGTGGAAGTGGTGATTCAAACA
CCCTCAACGAAATGTAGAAGTAGCACAAAGCTTGTTGAATGAAGCAACATCCAAGATAGATTAT
TGAAATGTCCCTTCAACACCGAGAACATACTACTAAATTAGCTTAGGCACATAAAAAACTAGAG
TATGACAATGCATGTAATTGTGTAAGTCTAGTATAAAATAAAGTGGGAGGAAAACCATGAGGTC
TAAGGTTCAAATTCCAGCAGAAGCAAAATACACTAGGTGATCTCTTCCATCTACCTAAACCTTG
GGGGTTAGAGTTAGCCGATACTTGTGTTGGTGGAAGTAACTGGTATCTGATGGAATAGTCAAGG
TGCCCACAAGTTAGCCTGAATGCTGCCGTCGTAAAAAAATACAAAGAACCAGAGCACAACAAAG
AATCCTTGCTTAGCTACTATATAAAAGCAAACTGCCTCCTAAAACAGAAAAATGGTTGAGCTTC
TTTGGAGATTGTTAAATGGCTGTTTTAAACTAACATCAAAGTTACGCTTCAGATATTTAAATGT
TTCTGAATTTCTGTTCTTTTGAAACTATATTAAATTCTTACTTTCTTTCACACGCTCCGACTAA
TTTCATGGTGTTGGTCTTGTGTGCGTATTTGTGCAACTGTTGTAACGTATTCCACTTCCCATTT
CTTCTACGTGTTGGATTATCCTGAACATCGCTTTCTGATGTTTAGGGTGAAAAGGGAGCTCATG
TTCTTGTTGTTCCAGAACTTTCTGACTTCCTTATATCAGCATTGGACAAGGTAACGGTACTTTG
CAGATTACTTCCTCTTACAGTATCTTACCAATTCGCCACTAGCTTCTACTAGCCAATTAGAGTG
AAATTCTAAGTAATTGTGAATATCAAGGAATACTGTGCTCACTGCCATCATCCACTTTATCACA
TGATATTACATTGAATTGGAGAATGACTGAGCATGAATTTTCTTCATAAAAAATAGTTGACAGA
AATCCCAAAGGAGCGAACAGTCGTAATTTTTTTAAAAAAAATTGGAATAATAAGGCTTCCACTT
AATATTTTCTTGTAGGTTGGAAATGTTTCTGTCTCTTGCAAGAAGATTCCATTGCTTGCCCTTG
AATATGAACCACCAAGGTCGAAAGTGTTACACTTATAGTTCCTTTGATTTCTTCCCTTCATACA
CAACACATTTTTATCTAGGATATTTCCACTTTTATTTTACTTTTTCCAGGACAAAGTCCTCAAA
ATCCATTGAGGCATCATTGAGACTTGATGCTGTAGCTAGTGCAGGATTCAAAGTTTCTCGAACT
AAAATGGCCAGTTTGATTAG
						
					

			
		

Sequences
Splice junction sequence	GGACAAAGTCCTCAAAATCCATTGAGGCATCATTGAGACTTGATGCTGTAGCTAGTGCAGGATT CAAAGTTTCTCGAACTAAAATGGCCAGTTTGATTAGcttttggaatatgcagcctaccacaggc tattaagggtgatgctgatattttactgaaaggagtgagagacaagaacaccattgaagatgtg aaacgtat
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: 655 Transcript exons: 4658515-4658624,4658779-4658910,4658989-4659062,4659158- 4659263,4660544-4660612,4660898-4660962,4661060-4661158 CTTTTGGAATATGCAGCCTACCACAGGCTATTAAGGGTGATGCTGATATTTTACTGAAAGGAGT GAGAGACAAGAACACCATTGAAGATGTGAAACGTATTGTTGAACTGGCAAAACGGGCATCATTA AGACGAGAAGTTTTACATACTGAGTTTCTGACTCCACCTGTATTAAAAGAGTCAATGCTAGTCT TAGAAAGGTTAGCTGATCTCAGAATAGTTGCACAAGGAGGATACCCAGAGGCTGAACGATGCCG ACTCTCAGTTGGACACGTGGAGGCATTAACAAGTGATCCAGATAATGTTGCAGCCTTGAGTATT TCAGGGAACTTTTCATTTCAACCTTGTTCTCATGGTGATTTCCTTGGTGCAATCCTTGGTACAG GGATTGCAAGGAATAAGCTGGGAGATATACTCTTGCAGGGTGAAAAGGGAGCTCATGTTCTTGT TGTTCCAGAACTTTCTGACTTCCTTATATCAGCATTGGACAAGGTTGGAAATGTTTCTGTCTCT TGCAAGAAGATTCCATTGCTTGCCCTTGAATATGAACCACCAAGGACAAAGTCCTCAAAATCCA TTGAGGCATCATTGAGACTTGATGCTGTAGCTAGTGCAGGATTCAAAGTTTCTCGAACTAAAAT GGCCAGTTTGATTAG
Genomic sequence	CTTTTGGAATATGCAGCCTACCACAGGCTATTAAGGGTGATGCTGATATTTTACTGAAAGGAGT GAGAGACAAGAACACCATTGAAGATGTGAAACGTATTGTTGAACTGGTACATATACATCTACCT GACCAATCACTCCTCTCAATTAACAGTTGAGAAGTCTTGTCTAGTTTTTCAACTCTTTGGTCCT TGTTGTAGAAAAAGCACCAAAACATTGTCCTAAGTCTTAATCTAAACTGATTATCACTTGCGTA CTTCTCAGGCAAAACGGGCATCATTAAGACGAGAAGTTTTACATACTGAGTTTCTGACTCCACC TGTATTAAAAGAGTCAATGCTAGTCTTAGAAAGGTTAGCTGATCTCAGAATAGTTGCACAAGGA GGATACCCAGAGGTTGGACACAGTTTGTTTTACAAAACTAGTTTGAGCAATAAAGCTGCTTGAA TTTATATTTACTGTCTCCTTAAACAGGCTGAACGATGCCGACTCTCAGTTGGACACGTGGAGGC ATTAACAAGTGATCCAGATAATGTTGCAGCCTTGAGGTATGTCCTCCTGTAATTGTTCAGTTAT GCCTGCTGTTTAATTCGACCAATCAAAAAATCCTCTTTATTATTGTGAAAAATGGTCCTCTGTC CAGTATTTCAGGGAACTTTTCATTTCAACCTTGTTCTCATGGTGATTTCCTTGGTGCAATCCTT GGTACAGGGATTGCAAGGAATAAGCTGGGAGATATACTCTTGCAGGTATTTTGTTTATTTATTT TTTGGAGGTTTTCTATCTCTCTTACAAGTTTTGGCAACACCTAGTTGATTTCATCATTTGTTCG CTTAAAAAAAATATATGTAAAAGAAAGATAGAAGTGACAGAGGGTGATCAATTGTTGATCAAAT AGAGGGCTCTTGGGCAGAGAGTTGCGGTCATTACACCTAAGAGAGGATCCACCTCTTTGTAGCT GAGTTATTATGTACTCCCTCTGTTCCATTTTAGTTGGCCCTTATACTAAAAATAGATTTTCTTG TTTACTTGTCAATTTCAGCAAATCAAGAGAGATTATTATTTTCTTCTCATATTAACCTTATCAT GGGTAAGTATATGAAGTAATAGTTGTCAAACCTAGATTTTCAAAGGACAATTATAAGGATAATT TAGTAAACAAACTCCTAATAAATAGTTTCTCAAGAGAAATGTCAAATCAACAAGGGCCAAGTAA AATGGAACATAAAAGATGAGTCAGAACTAATATGTGGAGGTAGTGTATGCTTAAGAAGTAAACT TGTTGATCAATACTTTGATATCTAATGACTACTTTGTTTTAGTGTGGAAGTGGTGATTCAAACA CCCTCAACGAAATGTAGAAGTAGCACAAAGCTTGTTGAATGAAGCAACATCCAAGATAGATTAT TGAAATGTCCCTTCAACACCGAGAACATACTACTAAATTAGCTTAGGCACATAAAAAACTAGAG TATGACAATGCATGTAATTGTGTAAGTCTAGTATAAAATAAAGTGGGAGGAAAACCATGAGGTC TAAGGTTCAAATTCCAGCAGAAGCAAAATACACTAGGTGATCTCTTCCATCTACCTAAACCTTG GGGGTTAGAGTTAGCCGATACTTGTGTTGGTGGAAGTAACTGGTATCTGATGGAATAGTCAAGG TGCCCACAAGTTAGCCTGAATGCTGCCGTCGTAAAAAAATACAAAGAACCAGAGCACAACAAAG AATCCTTGCTTAGCTACTATATAAAAGCAAACTGCCTCCTAAAACAGAAAAATGGTTGAGCTTC TTTGGAGATTGTTAAATGGCTGTTTTAAACTAACATCAAAGTTACGCTTCAGATATTTAAATGT TTCTGAATTTCTGTTCTTTTGAAACTATATTAAATTCTTACTTTCTTTCACACGCTCCGACTAA TTTCATGGTGTTGGTCTTGTGTGCGTATTTGTGCAACTGTTGTAACGTATTCCACTTCCCATTT CTTCTACGTGTTGGATTATCCTGAACATCGCTTTCTGATGTTTAGGGTGAAAAGGGAGCTCATG TTCTTGTTGTTCCAGAACTTTCTGACTTCCTTATATCAGCATTGGACAAGGTAACGGTACTTTG CAGATTACTTCCTCTTACAGTATCTTACCAATTCGCCACTAGCTTCTACTAGCCAATTAGAGTG AAATTCTAAGTAATTGTGAATATCAAGGAATACTGTGCTCACTGCCATCATCCACTTTATCACA TGATATTACATTGAATTGGAGAATGACTGAGCATGAATTTTCTTCATAAAAAATAGTTGACAGA AATCCCAAAGGAGCGAACAGTCGTAATTTTTTTAAAAAAAATTGGAATAATAAGGCTTCCACTT AATATTTTCTTGTAGGTTGGAAATGTTTCTGTCTCTTGCAAGAAGATTCCATTGCTTGCCCTTG AATATGAACCACCAAGGTCGAAAGTGTTACACTTATAGTTCCTTTGATTTCTTCCCTTCATACA CAACACATTTTTATCTAGGATATTTCCACTTTTATTTTACTTTTTCCAGGACAAAGTCCTCAAA ATCCATTGAGGCATCATTGAGACTTGATGCTGTAGCTAGTGCAGGATTCAAAGTTTCTCGAACT AAAATGGCCAGTTTGATTAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.530292452

Conservation Information
Conserved circRNAs	NA
PMCS	0.530292452

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4658852-4658545(+)
4658598-4661090(-)
						
						Potential amino acid sequence
						
							MLVLERLADLRIVAQGGYPEAERCRLSVGHVEALTSDPDNVAALSISGNFSFQPCSHGDFLGAI
LGTGIARNKLGDILLQGEKGAHVLVVPELSDFLISALDKVGNVSVSCKKIPLLALEYEPPRTKS
SKSIEASLRLDAVASAGFKVSRTKMASLISFWNMQPTTGY*(+)
MVFLSLTPFSKISASPLIACGRLHIPKANQTGHFSSRNFESCTSYSIKSQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4658852-4658545(+) 4658598-4661090(-)
Potential amino acid sequence	MLVLERLADLRIVAQGGYPEAERCRLSVGHVEALTSDPDNVAALSISGNFSFQPCSHGDFLGAI LGTGIARNKLGDILLQGEKGAHVLVVPELSDFLISALDKVGNVSVSCKKIPLLALEYEPPRTKS SKSIEASLRLDAVASAGFKVSRTKMASLISFWNMQPTTGY(+) MVFLSLTPFSKISASPLIACGRLHIPKANQTGHFSSRNFESCTSYSIKSQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Tan et al., 2017; Yin et al., 2018; Wang et al., 2018b

circRNA

Detail information of Solyc12g013870.1_circ_g.2

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