Plant Circular RNA Database

Detail information of Solyc04g015450.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc04g015450.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_001314
					
						Alias
						SL3.0ch04:5644196|5649599
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 5643944-5649347  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI; find_circ
					
						Parent gene
						
							Solyc04g015450.2						
					
						Parent gene annotation
						
							Translation factor GUF1 homolog, chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc04g015450.2_circ_g.2 Solyc04g015450.2_circ_g.3 						
					
						Support reads
						NA
					
						Tissues
						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
						Solyc04g015450.2.1:7

General Information
CircRNA Name	Solyc04g015450.2_circ_g.1
ID in PlantcircBase	sly_circ_001314
Alias	SL3.0ch04:5644196\|5649599
Organism	Solanum lycopersicum
Position	chr4: 5643944-5649347 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI; find_circ
Parent gene	Solyc04g015450.2
Parent gene annotation	Translation factor GUF1 homolog, chloroplastic
Parent gene strand	-
Alternative splicing	Solyc04g015450.2_circ_g.2 Solyc04g015450.2_circ_g.3
Support reads	NA
Tissues	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	Solyc04g015450.2.1:7

			
						 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  
						
							TAGAGGAGTCGGGAATTCAGAGAGTAACCTTAACAAATGGCTCTTCAATTGACCGTCTTTTTCC
AGGTTCAGGAAGCAAAGATGGATTTGAACACTCAACctgtttcttgagcagtttcttttttctc
gagatgtcaccacctacatgaacgaagatggaatgtaaaaaaaaactaagagatcatacacatg
tcaatgtg

						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	TAGAGGAGTCGGGAATTCAGAGAGTAACCTTAACAAATGGCTCTTCAATTGACCGTCTTTTTCC AGGTTCAGGAAGCAAAGATGGATTTGAACACTCAACctgtttcttgagcagtttcttttttctc gagatgtcaccacctacatgaacgaagatggaatgtaaaaaaaaactaagagatcatacacatg tcaatgtg
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
						0.142598498

Conservation Information
Conserved circRNAs	NA
PMCS	0.142598498

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5649285-5643951(+)
5649142-5643946(-)
5644166-5649151(-)
						
						Potential amino acid sequence
						
							MALQLTVFFQVQEAKMDLNTQPVS*(+)
MELAQDRRGIFKEMKYITENRASIIYELPLAEMVGDFFDQLKSRSKGYASMEYNFIGYTESDLI
KLDILINGDRVEPLATIVHKDKAYSVGRALTQKLKELIPRQMFKVPIQATIGSKVIASEAISAI
RKDVLAKCYGGDISRKKKLLKKQVECSNPSLLPEPGKRRSIEEPFVKIELLTPKEYIGALMELA
QDRRGIFKEMKYITENRASIIYELPLAEMVGDFFDQLKSRSKGYASMEYNFIGYTESDLIKLDI
LINGDRVEPLATIVHKDKAYSVGRALTQKLKELIPRQMFKVPIQATIGSKVIASEAISAIRKDV
LAKCYGGDISRKKKLLKKQVECSNPSLLPEPGKRRSIEEPFVKIELLTPKEYIGALMELAQDRR
GIFKEMKYITENRASIIYELPLAEMVGDFFDQLKSRSKGYASMEYNFIGYTESDLIKLDILING
DRVEPLATIVHKDKAYSVGRALTQKLKELIPRQMFKVPIQATIGSKVIASEAISAIRKDVLAKC
YGGDISRKKKLLKKQVECSNPSLLPEPGKRRSIEEPFVKIELLTPKEYIGALMELAQDRRGIFK
EMKYITENRASIIYELPLAEMVGDFFDQLKSRSKGYASMEYNFIGYTESDLIKLDILINGDRVE
PLATIVHKDKAYSVGRALTQKLKELIPRQMFKVPIQATIGSKVIASEAISAIRKDVLAKCYGGD
ISRKKKLLKKQ(-)
MFSPSAMVVTSREKRNCSRNRLSVQIHLCFLNLEKDGQLKSHLLRLSCSHQKNI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to low-temperature stress (acting as miRNA sponges)

Functional Information
Coding potential	Y
Potential coding position	5649285-5643951(+) 5649142-5643946(-) 5644166-5649151(-)
Potential amino acid sequence	MALQLTVFFQVQEAKMDLNTQPVS(+) MELAQDRRGIFKEMKYITENRASIIYELPLAEMVGDFFDQLKSRSKGYASMEYNFIGYTESDLI KLDILINGDRVEPLATIVHKDKAYSVGRALTQKLKELIPRQMFKVPIQATIGSKVIASEAISAI RKDVLAKCYGGDISRKKKLLKKQVECSNPSLLPEPGKRRSIEEPFVKIELLTPKEYIGALMELA QDRRGIFKEMKYITENRASIIYELPLAEMVGDFFDQLKSRSKGYASMEYNFIGYTESDLIKLDI LINGDRVEPLATIVHKDKAYSVGRALTQKLKELIPRQMFKVPIQATIGSKVIASEAISAIRKDV LAKCYGGDISRKKKLLKKQVECSNPSLLPEPGKRRSIEEPFVKIELLTPKEYIGALMELAQDRR GIFKEMKYITENRASIIYELPLAEMVGDFFDQLKSRSKGYASMEYNFIGYTESDLIKLDILING DRVEPLATIVHKDKAYSVGRALTQKLKELIPRQMFKVPIQATIGSKVIASEAISAIRKDVLAKC YGGDISRKKKLLKKQVECSNPSLLPEPGKRRSIEEPFVKIELLTPKEYIGALMELAQDRRGIFK EMKYITENRASIIYELPLAEMVGDFFDQLKSRSKGYASMEYNFIGYTESDLIKLDILINGDRVE PLATIVHKDKAYSVGRALTQKLKELIPRQMFKVPIQATIGSKVIASEAISAIRKDVLAKCYGGD ISRKKKLLKKQ(-) MFSPSAMVVTSREKRNCSRNRLSVQIHLCFLNLEKDGQLKSHLLRLSCSHQKNI(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to low-temperature stress (acting as miRNA sponges)

			
						 Other Information
					
						References
						Yang et al., 2020

circRNA

Detail information of Solyc04g015450.2_circ_g.1

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