Plant Circular RNA Database

Detail information of Solyc11g013400.1_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc11g013400.1_circ_g.2
					
						ID in PlantcircBase
						sly_circ_003304
					
						Alias
						11:6414685|6415189, Slcirc166
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr11: 6414685-6415189  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI, circseq_cup
					
						Parent gene
						
							Solyc11g013400.1						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc11g013400.1_circ_g.1 Solyc11g013400.1_circ_ag.1 						
					
						Support reads
						48/23
					
						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
						Solyc11g013400.1.1:3

General Information
CircRNA Name	Solyc11g013400.1_circ_g.2
ID in PlantcircBase	sly_circ_003304
Alias	11:6414685\|6415189, Slcirc166
Organism	Solanum lycopersicum
Position	chr11: 6414685-6415189 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI, circseq_cup
Parent gene	Solyc11g013400.1
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc11g013400.1_circ_g.1 Solyc11g013400.1_circ_ag.1
Support reads	48/23
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	Solyc11g013400.1.1:3

			
						 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  
						
							AATAAAATAATTTCAGGACATGAACAATTTTGAGAGTGATCCTGAAGAATTTGCACGAACATTT
TGTGAAGATATGAAAATTGAAGACCCAGAAGTTGGAtcacagttgacagaatttcggtcatatg
aaggacaagatatgcacactggcgagaaagttgttcccatcaaggtgtcgcatttgttttttgt
tgatattg

						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: 204
Transcript exons: 6414685-6414756,6414939-6414986,6415106-6415189
TCACAGTTGACAGAATTTCGGTCATATGAAGGACAAGATATGCACACTGGCGAGAAAGTTGTTC
CCATCAAGCTTGACCTCCGAGTAAATCACACAGTTATCAAGGACCACTTTTTTTGGGACATGAA
CAATTTTGAGAGTGATCCTGAAGAATTTGCACGAACATTTTGTGAAGATATGAAAATTGAAGAC
CCAGAAGTTGGA
						
						Genomic sequence
						
							TCACAGTTGACAGAATTTCGGTCATATGAAGGACAAGATATGCACACTGGCGAGAAAGTTGTTC
CCATCAAGGTGTCGCATTTGTTTTTTGTTGATATTGATGACATTACGTTGAAAGATTATTCATA
CCAAAAGAAAATCAATGTGAAAGAGACCTATCTTACTGATTTTGGTGGTCTCAACTGTCGATGG
TTCATCATTATATTTAGGTACTTATATTTATCTATTTCCCTTTCTTTTCCGGGCTCATCCAGCT
TGACCTCCGAGTAAATCACACAGTTATCAAGGACCACTTTTTTTGGGTAAGTTTTTGGATGTCT
CATTCGTCATCTATCTTGCTTTGGTAAGAGTTGTGATCAAATTAGCAACTACTCTGCCTCATTT
GTTGCTAATTAATCAATGAGGAATAAAATAATTTCAGGACATGAACAATTTTGAGAGTGATCCT
GAAGAATTTGCACGAACATTTTGTGAAGATATGAAAATTGAAGACCCAGAAGTTGGA

Sequences
Splice junction sequence	AATAAAATAATTTCAGGACATGAACAATTTTGAGAGTGATCCTGAAGAATTTGCACGAACATTT TGTGAAGATATGAAAATTGAAGACCCAGAAGTTGGAtcacagttgacagaatttcggtcatatg aaggacaagatatgcacactggcgagaaagttgttcccatcaaggtgtcgcatttgttttttgt tgatattg
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: 204 Transcript exons: 6414685-6414756,6414939-6414986,6415106-6415189 TCACAGTTGACAGAATTTCGGTCATATGAAGGACAAGATATGCACACTGGCGAGAAAGTTGTTC CCATCAAGCTTGACCTCCGAGTAAATCACACAGTTATCAAGGACCACTTTTTTTGGGACATGAA CAATTTTGAGAGTGATCCTGAAGAATTTGCACGAACATTTTGTGAAGATATGAAAATTGAAGAC CCAGAAGTTGGA
Genomic sequence	TCACAGTTGACAGAATTTCGGTCATATGAAGGACAAGATATGCACACTGGCGAGAAAGTTGTTC CCATCAAGGTGTCGCATTTGTTTTTTGTTGATATTGATGACATTACGTTGAAAGATTATTCATA CCAAAAGAAAATCAATGTGAAAGAGACCTATCTTACTGATTTTGGTGGTCTCAACTGTCGATGG TTCATCATTATATTTAGGTACTTATATTTATCTATTTCCCTTTCTTTTCCGGGCTCATCCAGCT TGACCTCCGAGTAAATCACACAGTTATCAAGGACCACTTTTTTTGGGTAAGTTTTTGGATGTCT CATTCGTCATCTATCTTGCTTTGGTAAGAGTTGTGATCAAATTAGCAACTACTCTGCCTCATTT GTTGCTAATTAATCAATGAGGAATAAAATAATTTCAGGACATGAACAATTTTGAGAGTGATCCT GAAGAATTTGCACGAACATTTTGTGAAGATATGAAAATTGAAGACCCAGAAGTTGGA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.387798573

Conservation Information
Conserved circRNAs	NA
PMCS	0.387798573

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6414725-6415186(+)
6414754-6414958(-)
6414711-6414969(-)
						
						Potential amino acid sequence
						
							MHTGEKVVPIKLDLRVNHTVIKDHFFWDMNNFESDPEEFARTFCEDMKIEDPEVGSQLTEFRSY
EGQDMHTGEKVVPIKLDLRVNHTVIKDHFFWDMNNFESDPEEFARTFCEDMKIEDPEVGSQLTE
FRSYEGQDMHTGEKVVPIKLDLRVNHTVIKDHFFWDMNNFESDPEEFARTFCEDMKIEDPEVGS
QLTEFRSYEGQDMHTGEKVVPIKLDLRVNHTVIKDHFFWDMNNFESDPEEFARTFCEDMKIEDP
EVG(+)
MGTTFSPVCISCPSYDRNSVNCDPTSGSSIFISSQNVRANSSGSLSKLFMSQKKWSLITV*(-)
MTEILSTVIQLLGLQFSYLHKMFVQILQDHSQNCSCPKKSGP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6414725-6415186(+) 6414754-6414958(-) 6414711-6414969(-)
Potential amino acid sequence	MHTGEKVVPIKLDLRVNHTVIKDHFFWDMNNFESDPEEFARTFCEDMKIEDPEVGSQLTEFRSY EGQDMHTGEKVVPIKLDLRVNHTVIKDHFFWDMNNFESDPEEFARTFCEDMKIEDPEVGSQLTE FRSYEGQDMHTGEKVVPIKLDLRVNHTVIKDHFFWDMNNFESDPEEFARTFCEDMKIEDPEVGS QLTEFRSYEGQDMHTGEKVVPIKLDLRVNHTVIKDHFFWDMNNFESDPEEFARTFCEDMKIEDP EVG(+) MGTTFSPVCISCPSYDRNSVNCDPTSGSSIFISSQNVRANSSGSLSKLFMSQKKWSLITV(-) MTEILSTVIQLLGLQFSYLHKMFVQILQDHSQNCSCPKKSGP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016; Tan et al., 2017; Yin et al., 2018; Wang et al., 2018b

circRNA

Detail information of Solyc11g013400.1_circ_g.2

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