Plant Circular RNA Database

Detail information of Solyc11g010560.1_circ_g.4

			
						 General Information
					
						CircRNA Name
						Solyc11g010560.1_circ_g.4
					
						ID in PlantcircBase
						sly_circ_003270
					
						Alias
						11:3616069|3625131
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr11: 3616069-3625131  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc11g010560.1						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc11g010560.1_circ_g.2 Solyc11g010560.1_circ_g.3 Solyc11g010560.1_circ_g.5 Solyc11g010560.1_circ_g.6 Solyc11g010560.1_circ_g.7 						
					
						Support reads
						5
					
						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
						Solyc11g010560.1.1:9

General Information
CircRNA Name	Solyc11g010560.1_circ_g.4
ID in PlantcircBase	sly_circ_003270
Alias	11:3616069\|3625131
Organism	Solanum lycopersicum
Position	chr11: 3616069-3625131 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc11g010560.1
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc11g010560.1_circ_g.2 Solyc11g010560.1_circ_g.3 Solyc11g010560.1_circ_g.5 Solyc11g010560.1_circ_g.6 Solyc11g010560.1_circ_g.7
Support reads	5
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	Solyc11g010560.1.1:9

			
						 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  
						
							GCAGTATTGATACGAACTGTAACATCATCGGGAAATTCGACAATGGATGGACCTTCATCTTCAA
AAAGAGGTCTCACACGACAAAACACCTTTATACTTCctgtaacatctgaatagttgaatcacgc
tgttgtatctgcaatttttgttcttgctccaactgtaaaagttgagctacttggtttctaagtt
gagtattt

						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: 1136
Transcript exons: 3616069-3616215,3619452-3619625,3619868-3620019,3621560-
3621598,3622074-3622165,3623130-3623288,3624053-3624147,
3624768-3624874,3624961-3625131
CTGTAACATCTGAATAGTTGAATCACGCTGTTGTATCTGCAATTTTTGTTCTTGCTCCAACTGT
AAAAGTTGAGCTACTTGGTTTCTAAGTTGAGTATTTTGATCCTTCTCAATCTTAAATTTATCCA
TAATCATGATATTCTCAGCCTTAAGATCTGACTCTAGTGTAGAAGAAACTTTCTGGGCATTCTG
AACTTCATTGAAGAGTAGAACTCCCTGATCGTTGGCCTGTTTCAGTTCCTGTTTTAGCCCAACT
ATTTCTTGTTTCAGATCAGTAATCTCATTCTCCTTGTCATAAAGTTCCTTGCGTGTATCATTGG
CAATATCTCTCCATTTCTTGATTGTATCTCTATTCCCAAGGCTTAGTGTGGCATTTCTAGCTCT
AGCAGAAAAATTGAGGGAAGATAACGTCTCAGACAAATTTGAAGCATTCGGACAGACATTAACA
ATCAGAAGCGTCTTTGCACTTTCACCTCGTCCTCTAGTGTGACAAGCTCTAGTCATGAGCATAT
CTAGTGAGTCTGCAAGTATTTTGGTGAGAACTGAATTTCCATATGGAACAATGTCTTTTTTTGA
TGTCAAGGAATTCAAAACATCTCCCAATGCAGAAAGAGATTTCATGACATGAAGCAACTCTGTT
GCATGCTCCCCACTATCCTCTTCAATACTGCTTTCACTTCCAGCCAAATCAACAAGAGAAAGCT
TGCTGTATGAGGTCTCTCCAGTGATTGAGTTGGTATAATGTATATGTACTGTGACGATCAGATG
AGAAACTCTAAACTTTGACACATCACTTCCTCGATTCTGAAAAGCAAGTTTGAGAACTTGGCCA
AAATCCATTGGATTTTCAACCCTTTCCATTGTGTGGGTCTTTCCTGAGTGTTCTTGCCCATAAG
CAAATATAGCCACATTGTATCCATCAAATGCTGACTGAACAAATGGCTGAACATCACTAAAAAG
TTCAACTTGTCCTACATGAGGTCCATAAACCCTGTCTAACTCAAAATCCTTCTTCGGATTTGCT
ACATTATCATCAGCAGTATTGATACGAACTGTAACATCATCGGGAAATTCGACAATGGATGGAC
CTTCATCTTCAAAAAGAGGTCTCACACGACAAAACACCTTTATACTTC
						
						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	GCAGTATTGATACGAACTGTAACATCATCGGGAAATTCGACAATGGATGGACCTTCATCTTCAA AAAGAGGTCTCACACGACAAAACACCTTTATACTTCctgtaacatctgaatagttgaatcacgc tgttgtatctgcaatttttgttcttgctccaactgtaaaagttgagctacttggtttctaagtt gagtattt
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: 1136 Transcript exons: 3616069-3616215,3619452-3619625,3619868-3620019,3621560- 3621598,3622074-3622165,3623130-3623288,3624053-3624147, 3624768-3624874,3624961-3625131 CTGTAACATCTGAATAGTTGAATCACGCTGTTGTATCTGCAATTTTTGTTCTTGCTCCAACTGT AAAAGTTGAGCTACTTGGTTTCTAAGTTGAGTATTTTGATCCTTCTCAATCTTAAATTTATCCA TAATCATGATATTCTCAGCCTTAAGATCTGACTCTAGTGTAGAAGAAACTTTCTGGGCATTCTG AACTTCATTGAAGAGTAGAACTCCCTGATCGTTGGCCTGTTTCAGTTCCTGTTTTAGCCCAACT ATTTCTTGTTTCAGATCAGTAATCTCATTCTCCTTGTCATAAAGTTCCTTGCGTGTATCATTGG CAATATCTCTCCATTTCTTGATTGTATCTCTATTCCCAAGGCTTAGTGTGGCATTTCTAGCTCT AGCAGAAAAATTGAGGGAAGATAACGTCTCAGACAAATTTGAAGCATTCGGACAGACATTAACA ATCAGAAGCGTCTTTGCACTTTCACCTCGTCCTCTAGTGTGACAAGCTCTAGTCATGAGCATAT CTAGTGAGTCTGCAAGTATTTTGGTGAGAACTGAATTTCCATATGGAACAATGTCTTTTTTTGA TGTCAAGGAATTCAAAACATCTCCCAATGCAGAAAGAGATTTCATGACATGAAGCAACTCTGTT GCATGCTCCCCACTATCCTCTTCAATACTGCTTTCACTTCCAGCCAAATCAACAAGAGAAAGCT TGCTGTATGAGGTCTCTCCAGTGATTGAGTTGGTATAATGTATATGTACTGTGACGATCAGATG AGAAACTCTAAACTTTGACACATCACTTCCTCGATTCTGAAAAGCAAGTTTGAGAACTTGGCCA AAATCCATTGGATTTTCAACCCTTTCCATTGTGTGGGTCTTTCCTGAGTGTTCTTGCCCATAAG CAAATATAGCCACATTGTATCCATCAAATGCTGACTGAACAAATGGCTGAACATCACTAAAAAG TTCAACTTGTCCTACATGAGGTCCATAAACCCTGTCTAACTCAAAATCCTTCTTCGGATTTGCT ACATTATCATCAGCAGTATTGATACGAACTGTAACATCATCGGGAAATTCGACAATGGATGGAC CTTCATCTTCAAAAAGAGGTCTCACACGACAAAACACCTTTATACTTC
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
						0.473501518

Conservation Information
Conserved circRNAs	NA
PMCS	0.473501518

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3625075-3616082(+)
3624772-3625125(-)
						
						Potential amino acid sequence
						
							MDGPSSSKRGLTRQNTFILPVTSE*(+)
MERVENPMDFGQVLKLAFQNRGSDVSKFRVSHLIVTVHIHYTNSITGETSYSKLSLVDLAGSES
SIEEDSGEHATELLHVMKSLSALGDVLNSLTSKKDIVPYGNSVLTKILADSLDMLMTRACHTRG
RGESAKTLLIVNVCPNASNLSETLSSLNFSARARNATLSLGNRDTIKKWRDIANDTRKELYDKE
NEITDLKQEIVGLKQELKQANDQGVLLFNEVQNAQKVSSTLESDLKAENIMIMDKFKIEKDQNT
QLRNQVAQLLQLEQEQKLQIQQRDSTIQMLQEV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	3625075-3616082(+) 3624772-3625125(-)
Potential amino acid sequence	MDGPSSSKRGLTRQNTFILPVTSE(+) MERVENPMDFGQVLKLAFQNRGSDVSKFRVSHLIVTVHIHYTNSITGETSYSKLSLVDLAGSES SIEEDSGEHATELLHVMKSLSALGDVLNSLTSKKDIVPYGNSVLTKILADSLDMLMTRACHTRG RGESAKTLLIVNVCPNASNLSETLSSLNFSARARNATLSLGNRDTIKKWRDIANDTRKELYDKE NEITDLKQEIVGLKQELKQANDQGVLLFNEVQNAQKVSSTLESDLKAENIMIMDKFKIEKDQNT QLRNQVAQLLQLEQEQKLQIQQRDSTIQMLQEV(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc11g010560.1_circ_g.4

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