Plant Circular RNA Database

Detail information of Solyc03g124030.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc03g124030.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_001239
					
						Alias
						3:64786533|64792347
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr3: 70733483-70739297  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc03g124030.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc03g124030.2_circ_g.1 Solyc03g124030.2_circ_g.3 Solyc03g124030.2_circ_g.4 Solyc03g124030.2_circ_g.5 						
					
						Support reads
						17
					
						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
						Solyc03g124030.2.1:6

General Information
CircRNA Name	Solyc03g124030.2_circ_g.2
ID in PlantcircBase	sly_circ_001239
Alias	3:64786533\|64792347
Organism	Solanum lycopersicum
Position	chr3: 70733483-70739297 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc03g124030.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc03g124030.2_circ_g.1 Solyc03g124030.2_circ_g.3 Solyc03g124030.2_circ_g.4 Solyc03g124030.2_circ_g.5
Support reads	17
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	Solyc03g124030.2.1:6

			
						 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  
						
							AGCAAAAAATAAGTCAGCTGAAGAAAACCTTAATCAATTCTTCAAGAAGGGAAGAGGCTCGATT
GTACTCCCCCAGTTCTGATAAGGTCACAGCAGCTCCttgtataaacatccgctcagcatcacca
acatttccgttctctttcaaaatgataccctgcacaaatcgagatgaagaaatctataaaccta
caatagaa

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	AGCAAAAAATAAGTCAGCTGAAGAAAACCTTAATCAATTCTTCAAGAAGGGAAGAGGCTCGATT GTACTCCCCCAGTTCTGATAAGGTCACAGCAGCTCCttgtataaacatccgctcagcatcacca acatttccgttctctttcaaaatgataccctgcacaaatcgagatgaagaaatctataaaccta caatagaa
Assembled circRNA sequence	NA 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	NA
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.165134679

Conservation Information
Conserved circRNAs	NA
PMCS	0.165134679

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							70739082-70733485(-)
						
						Potential amino acid sequence
						
							MDYEGSAAAFRMSAMVSGTIDFEVQRGLTNALIAARKPDEAVQMLLASRKSLKEEKTSGSSDGT
KNSAAKSKSEVDPIQVDLLLGKAYSEWGHISDAVSVYNQLISTYPDDFRGYLAKGIILKENGNV
GDAERMFIQGAAVTLSELGEYNRASSLLEELIKKKPSDPDVYRLLGEVKYGLMDYEGSAAAFRM
SAMVSGTIDFEVQRGLTNALIAARKPDEAVQMLLASRKSLKEEKTSGSSDGTKNSAAKSKSEVD
PIQVDLLLGKAYSEWGHISDAVSVYNQLISTYPDDFRGYLAKGIILKENGNVGDAERMFIQGAA
VTLSELGEYNRASSLLEELIKKKPSDPDVYRLLGEVKYGLMDYEGSAAAFRMSAMVSGTIDFEV
QRGLTNALIAARKPDEAVQMLLASRKSLKEEKTSGSSDGTKNSAAKSKSEVDPIQVDLLLGKAY
SEWGHISDAVSVYNQLISTYPDDFRGYLAKGIILKENGNVGDAERMFIQGAAVTLSELGEYNRA
SSLLEELIKKKPSDPDVYRLLGEVKYGLMDYEGSAAAFRMSAMVSGTIDFEVQRGLTNALIAAR
KPDEAVQMLLASRKSLKEEKTSGSSDGTKNSAAKSKSEVDPIQVDLLLGKAYSEWGHISDAVSV
YNQLISTYPDDFRGYLAKGIILKENGNVGDAERMFIQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	70739082-70733485(-)
Potential amino acid sequence	MDYEGSAAAFRMSAMVSGTIDFEVQRGLTNALIAARKPDEAVQMLLASRKSLKEEKTSGSSDGT KNSAAKSKSEVDPIQVDLLLGKAYSEWGHISDAVSVYNQLISTYPDDFRGYLAKGIILKENGNV GDAERMFIQGAAVTLSELGEYNRASSLLEELIKKKPSDPDVYRLLGEVKYGLMDYEGSAAAFRM SAMVSGTIDFEVQRGLTNALIAARKPDEAVQMLLASRKSLKEEKTSGSSDGTKNSAAKSKSEVD PIQVDLLLGKAYSEWGHISDAVSVYNQLISTYPDDFRGYLAKGIILKENGNVGDAERMFIQGAA VTLSELGEYNRASSLLEELIKKKPSDPDVYRLLGEVKYGLMDYEGSAAAFRMSAMVSGTIDFEV QRGLTNALIAARKPDEAVQMLLASRKSLKEEKTSGSSDGTKNSAAKSKSEVDPIQVDLLLGKAY SEWGHISDAVSVYNQLISTYPDDFRGYLAKGIILKENGNVGDAERMFIQGAAVTLSELGEYNRA SSLLEELIKKKPSDPDVYRLLGEVKYGLMDYEGSAAAFRMSAMVSGTIDFEVQRGLTNALIAAR KPDEAVQMLLASRKSLKEEKTSGSSDGTKNSAAKSKSEVDPIQVDLLLGKAYSEWGHISDAVSV YNQLISTYPDDFRGYLAKGIILKENGNVGDAERMFIQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc03g124030.2_circ_g.2

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