Plant Circular RNA Database

Detail information of POPTR_0005s18300_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0005s18300_circ_g.1
					
						ID in PlantcircBase
						pop_circ_001602
					
						Alias
						Chr05:11667855-11673449
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr5: 16437231-16442825  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0005s18300						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						stem xylem
					
						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  
						
							GT-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
						POPTR_0005s18300.1:7

General Information
CircRNA Name	POPTR_0005s18300_circ_g.1
ID in PlantcircBase	pop_circ_001602
Alias	Chr05:11667855-11673449
Organism	Populus trichocarpa
Position	chr5: 16437231-16442825 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0005s18300
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	NA
Support reads	NA
Tissues	stem xylem
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	GT-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	POPTR_0005s18300.1:7

			
						 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  
						
							CGGATACTATGTCGCCATCCTTTTAATGAATCCAAGAGAGCGTATGTGGTTCCACAGCAGGTTG
AGGAGCTTCTAAAGTGTTATTGGCCTGGGAGCTCAGagccctgatgagatcatagacaagtcgc
ttcgaagtgctgatggatcaagtagttgtgaggacctcgtcagtttagctcagacatggttaag
taaaattc

						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	CGGATACTATGTCGCCATCCTTTTAATGAATCCAAGAGAGCGTATGTGGTTCCACAGCAGGTTG AGGAGCTTCTAAAGTGTTATTGGCCTGGGAGCTCAGagccctgatgagatcatagacaagtcgc ttcgaagtgctgatggatcaagtagttgtgaggacctcgtcagtttagctcagacatggttaag taaaattc
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
						0.105430164

Conservation Information
Conserved circRNAs	NA
PMCS	0.105430164

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							16439614-16437235(+)
						
						Potential amino acid sequence
						
							MRSGIPNFCAVALALNDLGYKAVGIRLDSGDLAYLSCEARKFFRAIEKEFGVPGFGKMSITASN
DLNEETLDALNKQGHEVDAYGIGTYLVTCYAQAALGCVFKLVEINNQPRIKLSEDVSKVSIPCK
KRSYRLYGREGYPLVDIMTGENEPSPKVGERILCRHPFNESKRAYVVPQQVEELLKCYWPGSSE
P*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	16439614-16437235(+)
Potential amino acid sequence	MRSGIPNFCAVALALNDLGYKAVGIRLDSGDLAYLSCEARKFFRAIEKEFGVPGFGKMSITASN DLNEETLDALNKQGHEVDAYGIGTYLVTCYAQAALGCVFKLVEINNQPRIKLSEDVSKVSIPCK KRSYRLYGREGYPLVDIMTGENEPSPKVGERILCRHPFNESKRAYVVPQQVEELLKCYWPGSSE P*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0005s18300_circ_g.1

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