Plant Circular RNA Database

Detail information of Solyc05g018620.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc05g018620.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_001731
					
						Alias
						5:22621180|22630239
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr5: 22621180-22630239  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc05g018620.2						
					
						Parent gene annotation
						
							Ultraviolet-B receptor UVR8
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc05g018620.2_circ_g.1 Solyc05g018620.2_circ_g.2 Solyc05g018620.2_circ_ag.1 						
					
						Support reads
						8
					
						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
						Solyc05g018620.2.1:6

General Information
CircRNA Name	Solyc05g018620.2_circ_g.3
ID in PlantcircBase	sly_circ_001731
Alias	5:22621180\|22630239
Organism	Solanum lycopersicum
Position	chr5: 22621180-22630239 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc05g018620.2
Parent gene annotation	Ultraviolet-B receptor UVR8
Parent gene strand	-
Alternative splicing	Solyc05g018620.2_circ_g.1 Solyc05g018620.2_circ_g.2 Solyc05g018620.2_circ_ag.1
Support reads	8
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	Solyc05g018620.2.1:6

			
						 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  
						
							GTTGACCATATTTGCTCCAACCATACGTATATAAAGCACCAGAAGAGGATACACAGATAGTATG
ACGCCAACCACATGCAACAATGAACATCTTTTCTCCgttttcatctggaacaacagcatatctc
tccgtaggtgaaacccaagatttttcagctgaaaaagagttaaaagaaaataccaatacatggc
ataattaa

						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: 579
Transcript exons: 22621180-22621235,22621331-22621416,22624006-22624124,22
624251-22624322,22625430-22625501,22630066-22630239
GTTTTCATCTGGAACAACAGCATATCTCTCCGTAGGTGAAACCCAAGATTTTTCAGCTGCTGAT
GGGTCAACCGTCGAAGATCTGATTTGTTGTCCACTTGATCCATCAACACTTAACACTTCTATAA
TCCTTGGGACAGACCTATCAACGGACTCCCCATGACCTAGCTGACCATTTGTACCTCTTCCCCA
GGAAAAGACATTCTGCCTTTCTGTAGCAGCAAGTGTGTGCCTCCAACCGCATGAAATCAGAATT
ACTTTCTGATCATGTGGAAATTTTACTTGAACAGGTGAACAATGATCACAATTGTCATCAACAC
CAACTTGTCCGAACTTGTTCCAACCCCAACCATAGAGTTTTCCATCTGAAGTAAGTGCCATGGT
ATGTCTCCAACCACCTGATATCTGAGAAGTAAAACTTCCATGCAAAGCTTGAACCTTATGAGGA
GAGAGGTGATCCTCAAAATCACCATGTCCTAGTTGACCATATTTGCTCCAACCATACGTATATA
AAGCACCAGAAGAGGATACACAGATAGTATGACGCCAACCACATGCAACAATGAACATCTTTTC
TCC
						
						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	GTTGACCATATTTGCTCCAACCATACGTATATAAAGCACCAGAAGAGGATACACAGATAGTATG ACGCCAACCACATGCAACAATGAACATCTTTTCTCCgttttcatctggaacaacagcatatctc tccgtaggtgaaacccaagatttttcagctgaaaaagagttaaaagaaaataccaatacatggc ataattaa
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: 579 Transcript exons: 22621180-22621235,22621331-22621416,22624006-22624124,22 624251-22624322,22625430-22625501,22630066-22630239 GTTTTCATCTGGAACAACAGCATATCTCTCCGTAGGTGAAACCCAAGATTTTTCAGCTGCTGAT GGGTCAACCGTCGAAGATCTGATTTGTTGTCCACTTGATCCATCAACACTTAACACTTCTATAA TCCTTGGGACAGACCTATCAACGGACTCCCCATGACCTAGCTGACCATTTGTACCTCTTCCCCA GGAAAAGACATTCTGCCTTTCTGTAGCAGCAAGTGTGTGCCTCCAACCGCATGAAATCAGAATT ACTTTCTGATCATGTGGAAATTTTACTTGAACAGGTGAACAATGATCACAATTGTCATCAACAC CAACTTGTCCGAACTTGTTCCAACCCCAACCATAGAGTTTTCCATCTGAAGTAAGTGCCATGGT ATGTCTCCAACCACCTGATATCTGAGAAGTAAAACTTCCATGCAAAGCTTGAACCTTATGAGGA GAGAGGTGATCCTCAAAATCACCATGTCCTAGTTGACCATATTTGCTCCAACCATACGTATATA AAGCACCAGAAGAGGATACACAGATAGTATGACGCCAACCACATGCAACAATGAACATCTTTTC TCC
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
						0.492786994

Conservation Information
Conserved circRNAs	NA
PMCS	0.492786994

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							22630202-22621215(+)
22630224-22624023(+)
22630232-22621182(-)
22621383-22630139(-)
						
						Potential amino acid sequence
						
							MTPTTCNNEHLFSVFIWNNSISLRR*(+)
MNIFSPFSSGTTAYLSVGETQDFSAADGSTVEDLICCPLDPSTLNTSIILGTDLSTDSP*(+)
MFIVACGWRHTICVSSSGALYTYGWSKYGQLGHGDFEDHLSPHKVQALHGSFTSQISGGWRHTM
ALTSDGKLYGWGWNKFGQVGVDDNCDHCSPVQVKFPHDQKVILISCGWRHTLAATERQNVFSWG
RGTNGQLGHGESVDRSVPRIIEVLSVDGSSGQQIRSSTVDPSAAEKSWVSPTERYAVVPDENGE
KMFIVACGWRHTICVSSSGALYTYGWSKYGQLGHGDFEDHLSPHKVQALHGSFTSQISGGWRHT
MALTSDGKLYGWGWNKFGQVGVDDNCDHCSPVQVKFPHDQKVILISCGWRHTLAATERQNVFSW
GRGTNGQLGHGESVDRSVPRIIEVLSVDGSSGQQIRSSTVDPSAAEKSWVSPTERYAVVPDENG
EKMFIVACGWRHTICVSSSGALYTYGWSKYGQLGHGDFEDHLSPHKVQALHGSFTSQISGGWRH
TMALTSDGKLYGWGWNKFGQVGVDDNCDHCSPVQVKFPHDQKVILISCGWRHTLAATERQNVFS
WGRGTNGQLGHGESVDRSVPRIIEVLSVDGSSGQQIRSSTVDPSAAEKSWVSPTERYAVVPDEN
GEKMFIVACGWRHTICVSSSGALYTYGWSKYGQLGHGDFEDHLSPHKVQALHGSFTSQISGGWR
HTMALTSDGKLYGWGWNKFGQVGVDDNCDHCSPVQVKFPHDQKVILISCGWRHTLAATERQNVF
SWGRGTNGQLGHGESVDRSVPRIIEVLSVDGSSGQQIRSSTVDPSAAEKSWVSPTERYAVVPDE
N(-)
MDQVDNKSDLRRLTHQQLKNLGFHLRRDMLLFQMKTEKRCSLLHVVGVILSVYPLLVLYIRMVG
ANMVN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	22630202-22621215(+) 22630224-22624023(+) 22630232-22621182(-) 22621383-22630139(-)
Potential amino acid sequence	MTPTTCNNEHLFSVFIWNNSISLRR(+) MNIFSPFSSGTTAYLSVGETQDFSAADGSTVEDLICCPLDPSTLNTSIILGTDLSTDSP(+) MFIVACGWRHTICVSSSGALYTYGWSKYGQLGHGDFEDHLSPHKVQALHGSFTSQISGGWRHTM ALTSDGKLYGWGWNKFGQVGVDDNCDHCSPVQVKFPHDQKVILISCGWRHTLAATERQNVFSWG RGTNGQLGHGESVDRSVPRIIEVLSVDGSSGQQIRSSTVDPSAAEKSWVSPTERYAVVPDENGE KMFIVACGWRHTICVSSSGALYTYGWSKYGQLGHGDFEDHLSPHKVQALHGSFTSQISGGWRHT MALTSDGKLYGWGWNKFGQVGVDDNCDHCSPVQVKFPHDQKVILISCGWRHTLAATERQNVFSW GRGTNGQLGHGESVDRSVPRIIEVLSVDGSSGQQIRSSTVDPSAAEKSWVSPTERYAVVPDENG EKMFIVACGWRHTICVSSSGALYTYGWSKYGQLGHGDFEDHLSPHKVQALHGSFTSQISGGWRH TMALTSDGKLYGWGWNKFGQVGVDDNCDHCSPVQVKFPHDQKVILISCGWRHTLAATERQNVFS WGRGTNGQLGHGESVDRSVPRIIEVLSVDGSSGQQIRSSTVDPSAAEKSWVSPTERYAVVPDEN GEKMFIVACGWRHTICVSSSGALYTYGWSKYGQLGHGDFEDHLSPHKVQALHGSFTSQISGGWR HTMALTSDGKLYGWGWNKFGQVGVDDNCDHCSPVQVKFPHDQKVILISCGWRHTLAATERQNVF SWGRGTNGQLGHGESVDRSVPRIIEVLSVDGSSGQQIRSSTVDPSAAEKSWVSPTERYAVVPDE N(-) MDQVDNKSDLRRLTHQQLKNLGFHLRRDMLLFQMKTEKRCSLLHVVGVILSVYPLLVLYIRMVG ANMVN*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc05g018620.2_circ_g.3

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