Plant Circular RNA Database

Detail information of Solyc07g017990.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc07g017990.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_002238
					
						Alias
						7:8759478|8765570, Slcirc118
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr7: 8759478-8765570  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc07g017990.2						
					
						Parent gene annotation
						
							DNA ligase
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						88/17
					
						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  
						
							GC-AG							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
						Solyc07g017990.2.1:5

General Information
CircRNA Name	Solyc07g017990.2_circ_g.1
ID in PlantcircBase	sly_circ_002238
Alias	7:8759478\|8765570, Slcirc118
Organism	Solanum lycopersicum
Position	chr7: 8759478-8765570 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc07g017990.2
Parent gene annotation	DNA ligase
Parent gene strand	+
Alternative splicing	NA
Support reads	88/17
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	GC-AG 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	Solyc07g017990.2.1:5

			
						 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  
						
							AGCATACTTTTTGCAGGTTCATTTCTTTTTGCAGAGTAGGCACTGGAGTTTCTGATGAGGAACG
CAATACCATAGTAACTCGATTAAAACCTTATTTCAGgggagccctgttggtcgatcattgctca
tagtgttgacgatgtcgataaattctttaaaggaactgttgagaataggtttgtttcgtcttca
tctgttct

						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: 379
Transcript exons: 8759478-8759553,8763062-8763186,8763264-8763298,8763684-
8763742,8765487-8765570
GGGAGCCCTGTTGGTCGATCATTGCTCATAGTGTTGACGATGTCGATAAATTCTTTAAAGGAAC
TGTTGAGAATAGAGACGAAGGAATAGTTTTGAAAGATTTAACTTCAAAATGGGAACCAAGTGAT
CGGAGTGGAAAATGGCTAAAGTTGAAGCCTGATTATGTTCGACCTGGCTCTGATTTGGATGTTC
TTATTATCGGAGGCTACTATGGTTCTGGGCGACATGGAGGAGAGGTAGCTCAATTTCTGGTGGG
TCTTGCTGAGCCTCCGGCTCCAAATACATATCCCAGAAGGTTCATTTCTTTTTGCAGAGTAGGC
ACTGGAGTTTCTGATGAGGAACGCAATACCATAGTAACTCGATTAAAACCTTATTTCAG
						
						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	AGCATACTTTTTGCAGGTTCATTTCTTTTTGCAGAGTAGGCACTGGAGTTTCTGATGAGGAACG CAATACCATAGTAACTCGATTAAAACCTTATTTCAGgggagccctgttggtcgatcattgctca tagtgttgacgatgtcgataaattctttaaaggaactgttgagaataggtttgtttcgtcttca tctgttct
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: 379 Transcript exons: 8759478-8759553,8763062-8763186,8763264-8763298,8763684- 8763742,8765487-8765570 GGGAGCCCTGTTGGTCGATCATTGCTCATAGTGTTGACGATGTCGATAAATTCTTTAAAGGAAC TGTTGAGAATAGAGACGAAGGAATAGTTTTGAAAGATTTAACTTCAAAATGGGAACCAAGTGAT CGGAGTGGAAAATGGCTAAAGTTGAAGCCTGATTATGTTCGACCTGGCTCTGATTTGGATGTTC TTATTATCGGAGGCTACTATGGTTCTGGGCGACATGGAGGAGAGGTAGCTCAATTTCTGGTGGG TCTTGCTGAGCCTCCGGCTCCAAATACATATCCCAGAAGGTTCATTTCTTTTTGCAGAGTAGGC ACTGGAGTTTCTGATGAGGAACGCAATACCATAGTAACTCGATTAAAACCTTATTTCAG
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
						0.511309819

Conservation Information
Conserved circRNAs	NA
PMCS	0.511309819

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to chilling stress

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to chilling stress

			
						 Other Information
					
						References
						Zuo et al., 2016; Yin et al., 2018; Wang et al., 2018b

circRNA

Detail information of Solyc07g017990.2_circ_g.1

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