Plant Circular RNA Database

Detail information of POPTR_0004s02080_circ_g.2

			
						 General Information
					
						CircRNA Name
						POPTR_0004s02080_circ_g.2
					
						ID in PlantcircBase
						pop_circ_001187
					
						Alias
						Chr04:1430114-1430342 
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr4: 1306834-1307062  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2; circRNA_finder
					
						Parent gene
						
							POPTR_0004s02080						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							POPTR_0004s02080_circ_g.1 POPTR_0004s02080_circ_g.3 POPTR_0004s02080_circ_g.4 POPTR_0004s02080_circ_g.5 						
					
						Support reads
						2
					
						Tissues
						leaf; cambium; xylem
					
						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  
						
							GT-AA							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_0004s02080.2:1
POPTR_0004s02080.1:1

General Information
CircRNA Name	POPTR_0004s02080_circ_g.2
ID in PlantcircBase	pop_circ_001187
Alias	Chr04:1430114-1430342
Organism	Populus trichocarpa
Position	chr4: 1306834-1307062 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRI2; circRNA_finder
Parent gene	POPTR_0004s02080
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	POPTR_0004s02080_circ_g.1 POPTR_0004s02080_circ_g.3 POPTR_0004s02080_circ_g.4 POPTR_0004s02080_circ_g.5
Support reads	2
Tissues	leaf; cambium; xylem
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	GT-AA 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_0004s02080.2:1 POPTR_0004s02080.1:1

			
						 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  
						
							TTGATCAGGTGGGATGCCCTCCTTGTCTTGAATCTTGGCCTTGACGTTGTCGATGGTGTCGCTG
CTCTCTACCTCTAGAGTAATGGTCTTCCCTGTCAAGggtcttcacaaaaatctgcataccccct
cggagacggaggacaaggtgaagggtagactctttttggatattgtagtcagccagagtccggc
catcttcg

						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
						
							GGTCTTCACAAAAATCTGCATACCCCCTCGGAGACGGAGGACAAGGTGAAGGGTAGACTCTTTT
TGGATATTGTAGTCAGCCAGAGTCCGGCCATCTTCGAGCTGCTTTCCGGCAAAGATCAAGCGTT
GTTGATCAGGTGGGATGCCCTCCTTGTCTTGAATCTTGGCCTTGACGTTGTCGATGGTGTCGCT
GCTCTCTACCTCTAGAGTAATGGTCTTCCCTGTCAAG

Sequences
Splice junction sequence	TTGATCAGGTGGGATGCCCTCCTTGTCTTGAATCTTGGCCTTGACGTTGTCGATGGTGTCGCTG CTCTCTACCTCTAGAGTAATGGTCTTCCCTGTCAAGggtcttcacaaaaatctgcataccccct cggagacggaggacaaggtgaagggtagactctttttggatattgtagtcagccagagtccggc catcttcg
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	GGTCTTCACAAAAATCTGCATACCCCCTCGGAGACGGAGGACAAGGTGAAGGGTAGACTCTTTT TGGATATTGTAGTCAGCCAGAGTCCGGCCATCTTCGAGCTGCTTTCCGGCAAAGATCAAGCGTT GTTGATCAGGTGGGATGCCCTCCTTGTCTTGAATCTTGGCCTTGACGTTGTCGATGGTGTCGCT GCTCTCTACCTCTAGAGTAATGGTCTTCCCTGTCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_013229 osa_circ_013227 zma_circ_004737 zma_circ_004926 
osa_circ_013251 osa_circ_013247 osi_circ_003676 ath_circ_029798 
ath_circ_029470 osa_circ_013248 gma_circ_008848 zma_circ_004921 
ath_circ_029472 osi_circ_012543 zma_circ_008602 zma_circ_004950 
zma_circ_004938* zma_circ_008604 zma_circ_004945 zma_circ_004935 
ath_circ_029799 zma_circ_004736 zma_circ_008311 osa_circ_013245 
						
						PMCS
						0.816868013

Conservation Information
Conserved circRNAs	osa_circ_013229 osa_circ_013227 zma_circ_004737 zma_circ_004926 osa_circ_013251 osa_circ_013247 osi_circ_003676 ath_circ_029798 ath_circ_029470 osa_circ_013248 gma_circ_008848 zma_circ_004921 ath_circ_029472 osi_circ_012543 zma_circ_008602 zma_circ_004950 zma_circ_004938* zma_circ_008604 zma_circ_004945 zma_circ_004935 ath_circ_029799 zma_circ_004736 zma_circ_008311 osa_circ_013245
PMCS	0.816868013

			
						 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
						Song et al., 2020

circRNA

Detail information of POPTR_0004s02080_circ_g.2

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