Plant Circular RNA Database

Detail information of POPTR_0001s44440_circ_g.3

			
						 General Information
					
						CircRNA Name
						POPTR_0001s44440_circ_g.3
					
						ID in PlantcircBase
						pop_circ_000488
					
						Alias
						Chr01:44337211|44337438
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr1: 44859989-44860216  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							POPTR_0001s44440						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							POPTR_0001s44440_circ_g.1 POPTR_0001s44440_circ_g.2 POPTR_0001s44440_circ_g.4 POPTR_0001s44440_circ_g.5 POPTR_0001s44440_circ_g.6 POPTR_0001s44440_circ_g.7 POPTR_0001s44440_circ_g.8 						
					
						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  
						
							AA-CC							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_0001s44440.2:1
POPTR_0001s44440.5:1
POPTR_0001s44440.1:1
POPTR_0001s44440.3:1

General Information
CircRNA Name	POPTR_0001s44440_circ_g.3
ID in PlantcircBase	pop_circ_000488
Alias	Chr01:44337211\|44337438
Organism	Populus trichocarpa
Position	chr1: 44859989-44860216 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	find_circ
Parent gene	POPTR_0001s44440
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	POPTR_0001s44440_circ_g.1 POPTR_0001s44440_circ_g.2 POPTR_0001s44440_circ_g.4 POPTR_0001s44440_circ_g.5 POPTR_0001s44440_circ_g.6 POPTR_0001s44440_circ_g.7 POPTR_0001s44440_circ_g.8
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	AA-CC 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_0001s44440.2:1 POPTR_0001s44440.5:1 POPTR_0001s44440.1:1 POPTR_0001s44440.3:1

			
						 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  
						
							CCGATTGAGAGGTGGCATGCAGATCTTTGTTAAGACCCTTACTGGCAAGACAATCACCTTGGAG
GTGGAGAGTTCTGACACCATCGACAATGTGAAGGCCaagatccaggacaaggaggggatcccac
cagaccagcagaggcttatttttgctggcaagcagcttgaggatggccgtacccttgccgacta
caacattc

						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
						
							AAGATCCAGGACAAGGAGGGGATCCCACCAGACCAGCAGAGGCTTATTTTTGCTGGCAAGCAGC
TTGAGGATGGCCGTACCCTTGCCGACTACAACATTCAGAAGGAGTCTACCCTTCATTTGGTGCT
CCGATTGAGAGGTGGCATGCAGATCTTTGTTAAGACCCTTACTGGCAAGACAATCACCTTGGAG
GTGGAGAGTTCTGACACCATCGACAATGTGAAGGCC

Sequences
Splice junction sequence	CCGATTGAGAGGTGGCATGCAGATCTTTGTTAAGACCCTTACTGGCAAGACAATCACCTTGGAG GTGGAGAGTTCTGACACCATCGACAATGTGAAGGCCaagatccaggacaaggaggggatcccac cagaccagcagaggcttatttttgctggcaagcagcttgaggatggccgtacccttgccgacta caacattc
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	AAGATCCAGGACAAGGAGGGGATCCCACCAGACCAGCAGAGGCTTATTTTTGCTGGCAAGCAGC TTGAGGATGGCCGTACCCTTGCCGACTACAACATTCAGAAGGAGTCTACCCTTCATTTGGTGCT CCGATTGAGAGGTGGCATGCAGATCTTTGTTAAGACCCTTACTGGCAAGACAATCACCTTGGAG GTGGAGAGTTCTGACACCATCGACAATGTGAAGGCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							pbe_circ_000001 zma_circ_008598 osa_circ_025432 zma_circ_004713 
zma_circ_004918 osa_circ_025434 osi_circ_005767 zma_circ_004712 
osa_circ_025430 osa_circ_032040 zma_circ_004711 zma_circ_004710 
ath_circ_029472 osa_circ_032039 zma_circ_004706 zma_circ_004705 
zma_circ_004708 zma_circ_004707 zma_circ_004709 zma_circ_004704 
ath_circ_029799 ath_circ_029798 zma_circ_008308 osa_circ_032070 
osa_circ_032038 						
					
						PMCS
						1.86268867

Conservation Information
Conserved circRNAs	pbe_circ_000001 zma_circ_008598 osa_circ_025432 zma_circ_004713 zma_circ_004918 osa_circ_025434 osi_circ_005767 zma_circ_004712 osa_circ_025430 osa_circ_032040 zma_circ_004711 zma_circ_004710 ath_circ_029472 osa_circ_032039 zma_circ_004706 zma_circ_004705 zma_circ_004708 zma_circ_004707 zma_circ_004709 zma_circ_004704 ath_circ_029799 ath_circ_029798 zma_circ_008308 osa_circ_032070 osa_circ_032038
PMCS	1.86268867

			
						 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
						NA

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	NA

			
						 Other Information
					
						References
						Zheng et al., 2020

circRNA

Detail information of POPTR_0001s44440_circ_g.3

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