Plant Circular RNA Database

Detail information of POPTR_0001s26430_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0001s26430_circ_g.1
					
						ID in PlantcircBase
						pop_circ_000272
					
						Alias
						Chr01:26669331-26670054
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr1: 25467003-25467726  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0001s26430						
					
						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  
						
							CT-AC							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_0001s26430.1:3

General Information
CircRNA Name	POPTR_0001s26430_circ_g.1
ID in PlantcircBase	pop_circ_000272
Alias	Chr01:26669331-26670054
Organism	Populus trichocarpa
Position	chr1: 25467003-25467726 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0001s26430
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	CT-AC 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_0001s26430.1:3

			
						 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  
						
							ATCACAAGACCCTTCGCGTTATCAGAAACTCTAGGCCAAGGGTCCCTCTTGAAATCAATGACGG
AGCGAATAATTGCCTGCGCTACCCCTTGCTCAGTTTagcttccataaggatctgaagatctgca
tcagcaatatgttggccgagcttttgcaacccaaccctaagctcctcaaggttaatgctgcctt
tttttcca

						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
						
							AGCTTCCATAAGGATCTGAAGATCTGCATCAGCAATATGTTGGCCGAGCTTTTGCAACCCAACC
CTAAGCTCCTCAAGGTTAATGCTGCCTTTTTTTCCAGTGTCCATCGAATCAAAGGCATCCTTTA
TGCCAGCTACTTCCTCCACTGACAAGTGTTCAGCTATCACCTACAGATGGACAACTCAAAAAAT
CACTCTTTTTTATTTCACAGAGAGTGTGCAGGATTGTTAGGGAGGGAGGGAGGGTATAGATGAG
CACCACATGGCCAAAATAATTTAGTGAATGATATGAGTTTCCATGGAAAAAAGGTTCCATAATA
ATCAAAGCTATAAATAGTTGTTGAGTGAACAAATTAAGAATCATTACCCTCAGAGCTCTTTTCT
TGAGCTTATTCATCACAGAAAACTGTTTGAGCCTTGCTTTCACAGTCTCACCGAGTGGGACATT
TGGAGCCTTCTTTGCATTTTGTATCCAAGGATGCTCTGAAACAAAGAGTCGGGATAATTTTGCA
TGTTAACAAATAAGCATGCACTCTATAGCAGACATTGGACTAATAGAAGAATAAACTACCAAGC
ACTTGCTGAGCTGTAAGCCTTAGCTTAGGATCAGGATTAAGCATTTTCATCACAAGACCCTTCG
CGTTATCAGAAACTCTAGGCCAAGGGTCCCTCTTGAAATCAATGACGGAGCGAATAATTGCCTG
CGCTACCCCTTGCTCAGTTT

Sequences
Splice junction sequence	ATCACAAGACCCTTCGCGTTATCAGAAACTCTAGGCCAAGGGTCCCTCTTGAAATCAATGACGG AGCGAATAATTGCCTGCGCTACCCCTTGCTCAGTTTagcttccataaggatctgaagatctgca tcagcaatatgttggccgagcttttgcaacccaaccctaagctcctcaaggttaatgctgcctt tttttcca
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	AGCTTCCATAAGGATCTGAAGATCTGCATCAGCAATATGTTGGCCGAGCTTTTGCAACCCAACC CTAAGCTCCTCAAGGTTAATGCTGCCTTTTTTTCCAGTGTCCATCGAATCAAAGGCATCCTTTA TGCCAGCTACTTCCTCCACTGACAAGTGTTCAGCTATCACCTACAGATGGACAACTCAAAAAAT CACTCTTTTTTATTTCACAGAGAGTGTGCAGGATTGTTAGGGAGGGAGGGAGGGTATAGATGAG CACCACATGGCCAAAATAATTTAGTGAATGATATGAGTTTCCATGGAAAAAAGGTTCCATAATA ATCAAAGCTATAAATAGTTGTTGAGTGAACAAATTAAGAATCATTACCCTCAGAGCTCTTTTCT TGAGCTTATTCATCACAGAAAACTGTTTGAGCCTTGCTTTCACAGTCTCACCGAGTGGGACATT TGGAGCCTTCTTTGCATTTTGTATCCAAGGATGCTCTGAAACAAAGAGTCGGGATAATTTTGCA TGTTAACAAATAAGCATGCACTCTATAGCAGACATTGGACTAATAGAAGAATAAACTACCAAGC ACTTGCTGAGCTGTAAGCCTTAGCTTAGGATCAGGATTAAGCATTTTCATCACAAGACCCTTCG CGTTATCAGAAACTCTAGGCCAAGGGTCCCTCTTGAAATCAATGACGGAGCGAATAATTGCCTG CGCTACCCCTTGCTCAGTTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							csa_circ_000595 						
					
						PMCS
						0.216151899

Conservation Information
Conserved circRNAs	csa_circ_000595
PMCS	0.216151899

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25467126-25467722(-)
25467630-25467711(-)
						
						Potential amino acid sequence
						
							MPLIRWTLEKKAALTLRSLGLGCKSSANILLMQIFRSLWKLN*(-)
MKMLNPDPKLRLTAQQVLEHPWIQNAKKAPNVPLGETVKARLKQFSVMNKLKKRALRVIAEHLS
VEEVAGIKDAFDSMDTGKKGSINLEELRVGLQKLGQHIADADLQILMEAKLSKG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	25467126-25467722(-) 25467630-25467711(-)
Potential amino acid sequence	MPLIRWTLEKKAALTLRSLGLGCKSSANILLMQIFRSLWKLN(-) MKMLNPDPKLRLTAQQVLEHPWIQNAKKAPNVPLGETVKARLKQFSVMNKLKKRALRVIAEHLS VEEVAGIKDAFDSMDTGKKGSINLEELRVGLQKLGQHIADADLQILMEAKLSKG(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0001s26430_circ_g.1

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