Plant Circular RNA Database

Detail information of POPTR_0001s46420_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0001s46420_circ_g.1
					
						ID in PlantcircBase
						pop_circ_000516
					
						Alias
						Chr01:49383148|49388995
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr1: 46809211-46815058  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							POPTR_0001s46420						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							POPTR_0001s46420_circ_g.2 POPTR_0001s46420_circ_g.3 POPTR_0001s46420_circ_g.4 POPTR_0001s46420_circ_g.5 POPTR_0001s46420_circ_g.6 						
					
						Support reads
						NA
					
						Tissues
						stem cambium
					
						Exon boundary  
						
							No-No							"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  
						
							TT-AT							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
						POPTR_0001s46420.1:9

General Information
CircRNA Name	POPTR_0001s46420_circ_g.1
ID in PlantcircBase	pop_circ_000516
Alias	Chr01:49383148\|49388995
Organism	Populus trichocarpa
Position	chr1: 46809211-46815058 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	find_circ
Parent gene	POPTR_0001s46420
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	POPTR_0001s46420_circ_g.2 POPTR_0001s46420_circ_g.3 POPTR_0001s46420_circ_g.4 POPTR_0001s46420_circ_g.5 POPTR_0001s46420_circ_g.6
Support reads	NA
Tissues	stem cambium
Exon boundary	No-No "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	TT-AT 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	POPTR_0001s46420.1:9

			
						 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  
						
							CCAAGTCTGAATTCATGCTACTGGTTCTATTCCTCAACCATCGCTCATCACTTGTAGCTCCTCC
CATTTTCTTTCTTGCATTAGCATGAACGTGACTTTCtttgcaatacagggtttggcgagttgct
ttgagcagcaagcacacgcacctcatgcattagccgcatgagggtgtcctttctaaaccgctga
gcgttttc

						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	CCAAGTCTGAATTCATGCTACTGGTTCTATTCCTCAACCATCGCTCATCACTTGTAGCTCCTCC CATTTTCTTTCTTGCATTAGCATGAACGTGACTTTCtttgcaatacagggtttggcgagttgct ttgagcagcaagcacacgcacctcatgcattagccgcatgagggtgtcctttctaaaccgctga gcgttttc
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
						0.096382855

Conservation Information
Conserved circRNAs	NA
PMCS	0.096382855

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ptc-miR530b 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	ptc-miR530b
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zheng et al., 2020

circRNA

Detail information of POPTR_0001s46420_circ_g.1

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