Plant Circular RNA Database

Detail information of Solyc01g006360.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc01g006360.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_000018
					
						Alias
						1:958670|964383, Slcirc034
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr1: 958670-964383  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc01g006360.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc01g006360.2_circ_g.1 						
					
						Support reads
						5/36
					
						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  
						
							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
						Solyc01g006360.2.1:7

General Information
CircRNA Name	Solyc01g006360.2_circ_g.2
ID in PlantcircBase	sly_circ_000018
Alias	1:958670\|964383, Slcirc034
Organism	Solanum lycopersicum
Position	chr1: 958670-964383 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc01g006360.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc01g006360.2_circ_g.1
Support reads	5/36
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	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	Solyc01g006360.2.1:7

			
						 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  
						
							CAAGAAACTTCATCACAACATACGTAGGTCCAAGACTCAAAACTTCCCTCAGTGTTTTTGAATC
GAGTCGCTCATTATTGAAAGCAAGGATGGTCAATCCaataaaaactggtgcccataagctcgca
actgtcagtgcattatggttatctgccaaaagagtaacttgcatttaatggaaactgagatcca
gatataat

						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: 663
Transcript exons: 958670-958719,958889-958970,959051-959111,963586-963638,
963741-963930,964067-964190,964281-964383
AATAAAAACTGGTGCCCATAAGCTCGCAACTGTCAGTGCATTATGGTTATTTTTAGAAACAAAA
TCGTGCCAAGAGTACTGCCGAATATCCATTGCCACTATCTGTCTTGTTGGCTTCACCAACGGCT
TAATCAGTAGAAAATAGGCAAAAGCAAATTTAGCTCCCAGGACAACAAGCCAAAAAACCATATA
CTTGATGAAGTCAATAGTTTTCTCATACATGCCCCGACCAACGTAATAGTGTTCCTGGTGCATC
CACTTGATGAAACGGACCACAGACCAATTGTCACATCGACTTGTCAAACTATGACAAGCTGGAA
TCCGCAGCAGAAAGCTGACAAAAAACTTAACTCCAGCATAGATTGCAAGAACAACAATATAAAT
TCTGAAGACAGTAGAGTTGGAATTTTGGCTGCTATTATCTTCAAGCGCTTTCACATAAAGGAAA
CATATGAAGACAGAAGCTATGCTGAACCAAACAAAACGAAGGAAAATCCGACTGACAGCTAAAC
GCCTTGATGTAGAGTATGCACCATACATCATGATAACATCCAGAACACTCTCAAGAAACTTCAT
CACAACATACGTAGGTCCAAGACTCAAAACTTCCCTCAGTGTTTTTGAATCGAGTCGCTCATTA
TTGAAAGCAAGGATGGTCAATCC
						
						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	CAAGAAACTTCATCACAACATACGTAGGTCCAAGACTCAAAACTTCCCTCAGTGTTTTTGAATC GAGTCGCTCATTATTGAAAGCAAGGATGGTCAATCCaataaaaactggtgcccataagctcgca actgtcagtgcattatggttatctgccaaaagagtaacttgcatttaatggaaactgagatcca gatataat
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: 663 Transcript exons: 958670-958719,958889-958970,959051-959111,963586-963638, 963741-963930,964067-964190,964281-964383 AATAAAAACTGGTGCCCATAAGCTCGCAACTGTCAGTGCATTATGGTTATTTTTAGAAACAAAA TCGTGCCAAGAGTACTGCCGAATATCCATTGCCACTATCTGTCTTGTTGGCTTCACCAACGGCT TAATCAGTAGAAAATAGGCAAAAGCAAATTTAGCTCCCAGGACAACAAGCCAAAAAACCATATA CTTGATGAAGTCAATAGTTTTCTCATACATGCCCCGACCAACGTAATAGTGTTCCTGGTGCATC CACTTGATGAAACGGACCACAGACCAATTGTCACATCGACTTGTCAAACTATGACAAGCTGGAA TCCGCAGCAGAAAGCTGACAAAAAACTTAACTCCAGCATAGATTGCAAGAACAACAATATAAAT TCTGAAGACAGTAGAGTTGGAATTTTGGCTGCTATTATCTTCAAGCGCTTTCACATAAAGGAAA CATATGAAGACAGAAGCTATGCTGAACCAAACAAAACGAAGGAAAATCCGACTGACAGCTAAAC GCCTTGATGTAGAGTATGCACCATACATCATGATAACATCCAGAACACTCTCAAGAAACTTCAT CACAACATACGTAGGTCCAAGACTCAAAACTTCCCTCAGTGTTTTTGAATCGAGTCGCTCATTA TTGAAAGCAAGGATGGTCAATCC
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
						0.335552116

Conservation Information
Conserved circRNAs	NA
PMCS	0.335552116

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							964083-959060(+)
964298-958672(-)
						
						Potential amino acid sequence
						
							MKTEAMLNQTKRRKIRLTAKRLDVEYAPYIMITSRTLSRNFITTYVGPRLKTSLSVFESSRSLL
KARMVNPIKTGAHKLATVSALWLFLETKSCQEYCRISIATICLVGFTNGLISRK*(+)
MKFLESVLDVIMMYGAYSTSRRLAVSRIFLRFVWFSIASVFICFLYVKALEDNSSQNSNSTVFR
IYIVVLAIYAGVKFFVSFLLRIPACHSLTSRCDNWSVVRFIKWMHQEHYYVGRGMYEKTIDFIK
YMVFWLVVLGAKFAFAYFLLIKPLVKPTRQIVAMDIRQYSWHDFVSKNNHNALTVASLWAPVFI
GLTILAFNNERLDSKTLREVLSLGPTYVVMKFLESVLDVIMMYGAYSTSRRLAVSRIFLRFVWF
SIASVFICFLYVKALEDNSSQNSNSTVFRIYIVVLAIYAGVKFFVSFLLRIPACHSLTSRCDNW
SVVRFIKWMHQEHYYVGRGMYEKTIDFIKYMVFWLVVLGAKFAFAYFLLIKPLVKPTRQIVAMD
IRQYSWHDFVSKNNHNALTVASLWAPVFIGLTILAFNNERLDSKTLREVLSLGPTYVVMKFLES
VLDVIMMYGAYSTSRRLAVSRIFLRFVWFSIASVFICFLYVKALEDNSSQNSNSTVFRIYIVVL
AIYAGVKFFVSFLLRIPACHSLTSRCDNWSVVRFIKWMHQEHYYVGRGMYEKTIDFIKYMVFWL
VVLGAKFAFAYFLLIKPLVKPTRQIVAMDIRQYSWHDFVSKNNHNALTVASLWAPVFIGLTILA
FNNERLDSKTLREVLSLGPTYVVMKFLESVLDVIMMYGAYSTSRRLAVSRIFLRFVWFSIASVF
ICFLYVKALEDNSSQNSNSTVFRIYIVVLAIYAGVKFFVSFLLRIPACHSLTSRCDNWSVVRFI
KWMHQEHYYVGRGMYEKTIDFIKYMVFWLVVLGAKFAFAYFLLIKPLVKPTRQIVAMDIRQYSW
HDFVSKNNHNALTVASLWAPVFI(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	964083-959060(+) 964298-958672(-)
Potential amino acid sequence	MKTEAMLNQTKRRKIRLTAKRLDVEYAPYIMITSRTLSRNFITTYVGPRLKTSLSVFESSRSLL KARMVNPIKTGAHKLATVSALWLFLETKSCQEYCRISIATICLVGFTNGLISRK*(+) MKFLESVLDVIMMYGAYSTSRRLAVSRIFLRFVWFSIASVFICFLYVKALEDNSSQNSNSTVFR IYIVVLAIYAGVKFFVSFLLRIPACHSLTSRCDNWSVVRFIKWMHQEHYYVGRGMYEKTIDFIK YMVFWLVVLGAKFAFAYFLLIKPLVKPTRQIVAMDIRQYSWHDFVSKNNHNALTVASLWAPVFI GLTILAFNNERLDSKTLREVLSLGPTYVVMKFLESVLDVIMMYGAYSTSRRLAVSRIFLRFVWF SIASVFICFLYVKALEDNSSQNSNSTVFRIYIVVLAIYAGVKFFVSFLLRIPACHSLTSRCDNW SVVRFIKWMHQEHYYVGRGMYEKTIDFIKYMVFWLVVLGAKFAFAYFLLIKPLVKPTRQIVAMD IRQYSWHDFVSKNNHNALTVASLWAPVFIGLTILAFNNERLDSKTLREVLSLGPTYVVMKFLES VLDVIMMYGAYSTSRRLAVSRIFLRFVWFSIASVFICFLYVKALEDNSSQNSNSTVFRIYIVVL AIYAGVKFFVSFLLRIPACHSLTSRCDNWSVVRFIKWMHQEHYYVGRGMYEKTIDFIKYMVFWL VVLGAKFAFAYFLLIKPLVKPTRQIVAMDIRQYSWHDFVSKNNHNALTVASLWAPVFIGLTILA FNNERLDSKTLREVLSLGPTYVVMKFLESVLDVIMMYGAYSTSRRLAVSRIFLRFVWFSIASVF ICFLYVKALEDNSSQNSNSTVFRIYIVVLAIYAGVKFFVSFLLRIPACHSLTSRCDNWSVVRFI KWMHQEHYYVGRGMYEKTIDFIKYMVFWLVVLGAKFAFAYFLLIKPLVKPTRQIVAMDIRQYSW HDFVSKNNHNALTVASLWAPVFI(-)
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 Solyc01g006360.2_circ_g.2

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