Plant Circular RNA Database

Detail information of POPTR_0002s09410_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0002s09410_circ_g.1
					
						ID in PlantcircBase
						pop_circ_000667
					
						Alias
						Chr02:6693833-6695837
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr2: 6702754-6704758  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0002s09410						
					
						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_0002s09410.1:2

General Information
CircRNA Name	POPTR_0002s09410_circ_g.1
ID in PlantcircBase	pop_circ_000667
Alias	Chr02:6693833-6695837
Organism	Populus trichocarpa
Position	chr2: 6702754-6704758 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0002s09410
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_0002s09410.1:2

			
						 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  
						
							AACATACTCCCGCTGGGTGGTTGCAAGCGAACCAAGGACAGTCAAATACCAGGTGCCTCTGGGT
TGAAATTTCCTCAAAATATGATCCTCGTCAACCTTTccatagagcccttctggcacgggtaaga
gcaacattcattcggcggatatcagcaacaaagccaacaccgtgacttgaggcccgtacacaag
acataata

									
								

					

						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
						
							CCATAGAGCCCTTCTGGCACGGGTAAGAGCAACATTCATTCGGCGGATATCAGCAACAAAGCCA
ACACCGTGACTTGAGGCCCGTACACAAGACATAATAATGACATCACGCTCCTGGCCTTGGAAAG
CATCGACGGTATTAATATAGATATCTTTCCCTTCTTCAGACTTTAAAACAGCTAAAAACTCTTG
CTGGAGGCATTTCAACTGCAACTTATATGGAGTTATTATGCCAACCGAGATTCTTCCCATGCCC
AAGGATTTTAAAGATTTCTGAAGATGCTCATACAACTGAAGACAAAATTGTGCTTCATGAACGT
TCTGATAAGATACTGATCCACCTCTGTGTGACTCCCGCCCATGAGTAACATCATAGAACAGATA
AGGTCTAAGTAAAGGGTCCTTGTAGTATGTTTCATCAGGTAAATTAGCAACACTTTCACTGTCA
GTGAGACGTCCTTGGTAAAAGTACCGTGAAGGGAAATCTCGTATTTGAGGATGCATCCTATATT
GTACAGATAATAACATTGTTGGGCACCCTGCTTGCTGAAACCTTTCGAAAAGACTTCTACTGTA
TAACAAGGTTCCAGCTGCCTTACTGATAACTGTTGCAGGAAGCTGCTGAGGATCGCCAACAAGA
ACGCACCTTGCAGCACCAAGTGCGAGAGGAGGAAGAACAGCTACTTCGCTGGCTTGAGCTGCCT
CGTCAATAACTACCATATCAAAACCATGAGTGAGCCGAGAGAACAACTTGCGACCACTGCTTGA
GACAGTAGTGAAAACAATCTCAGCCTCATTGGCAAAACTTGCCTCGAGACTAGCACGGGCTTCT
TCCAGATTAAAATTGCTACCAGCACGAAATCTGGGTTCTAAAATGAGAAGACGAGAGATCTCAA
CTAGAACTTTATCCCTGCTTTCAACAGCAGCTGCAAGGTTCTGAAGTAATGCATCTCGGTTTTG
GTCCCTAGCCATGAGAATATCAGGATCAACACCAACAGATCCTTGGGAACGACCGTCCACTGCT
GCAACATTAAGCTTATTTTGAAGGTCAGCGATGTGTGCCGAGAAATAAGCTTCCTGAACTCTTA
AATCTTGCATCCATTTTGAAATTTCTTCGCGGCTCTTGATTAGAAGTTGTTCAGTTCTCCGCTC
AACAGAAACTGCCTGAGCAGCACGTGATTGTGAATCAACCCCAACTCTGGCCACATCAGGCCTG
TAAACTTTCATCTCACCATCAATAAATCCACGATCAAGAACACGTGCAAGAAGTTCATCAGTTG
CAGCATTAGAAGGAGCACAGACTAACATTCTGGGCTTTGGACAGAGTTTCGAAAGGGAGCGGAA
GAGATTCTGGTCCATGTTATGAAGAACTTCATCAATTGACCCCATAGCAATATTGTCAGGATTG
CTTTCATTGGCATGCTTATAACTCTGTGGTGCCAGTTTCTTAAGCAAAGAGGTATAGTAATGCT
GATACTGAACCAGATGGATGACATTTAGCATTCCCCAGACTGTATGTGTCTTTCCTGTCCCTGG
AGGCCCTTGTACAAGAGTAAAGGGCCACGGCTCTTGCCTCTTAGTTACCCCACTACTTGTACCA
GCAGCAGTATGCATTGCAGCCCACTGGATTGCAGCCAGCTGGGGTCCATTGAATGTCCTACGCA
AATGGTCAACAAAATTCTGTGTAAAGCATTCAGGCATGGCTGGGGTCTGCTGCTCATATTTTGG
GAAGTGATCTGGACTGGGCTTTAGGATTGCAGTTTGCATCTACCAGGATGGAAATAAAACTTTT
AGTTTCCTGTGTTTATAGGTGTATGTATTGAATATGAAGCAAAGACAAAACTTGGGTATTCATA
AAGAAAAATTTGTTACCTGTAAATTAAGACGGCAAAATGCATGCAAAGCAACATACTCCCGCTG
GGTGGTTGCAAGCGAACCAAGGACAGTCAAATACCAGGTGCCTCTGGGTTGAAATTTCCTCAAA
ATATGATCCTCGTCAACCTTT
						
					

			
		

Sequences
Splice junction sequence	AACATACTCCCGCTGGGTGGTTGCAAGCGAACCAAGGACAGTCAAATACCAGGTGCCTCTGGGT TGAAATTTCCTCAAAATATGATCCTCGTCAACCTTTccatagagcccttctggcacgggtaaga gcaacattcattcggcggatatcagcaacaaagccaacaccgtgacttgaggcccgtacacaag acataata
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	CCATAGAGCCCTTCTGGCACGGGTAAGAGCAACATTCATTCGGCGGATATCAGCAACAAAGCCA ACACCGTGACTTGAGGCCCGTACACAAGACATAATAATGACATCACGCTCCTGGCCTTGGAAAG CATCGACGGTATTAATATAGATATCTTTCCCTTCTTCAGACTTTAAAACAGCTAAAAACTCTTG CTGGAGGCATTTCAACTGCAACTTATATGGAGTTATTATGCCAACCGAGATTCTTCCCATGCCC AAGGATTTTAAAGATTTCTGAAGATGCTCATACAACTGAAGACAAAATTGTGCTTCATGAACGT TCTGATAAGATACTGATCCACCTCTGTGTGACTCCCGCCCATGAGTAACATCATAGAACAGATA AGGTCTAAGTAAAGGGTCCTTGTAGTATGTTTCATCAGGTAAATTAGCAACACTTTCACTGTCA GTGAGACGTCCTTGGTAAAAGTACCGTGAAGGGAAATCTCGTATTTGAGGATGCATCCTATATT GTACAGATAATAACATTGTTGGGCACCCTGCTTGCTGAAACCTTTCGAAAAGACTTCTACTGTA TAACAAGGTTCCAGCTGCCTTACTGATAACTGTTGCAGGAAGCTGCTGAGGATCGCCAACAAGA ACGCACCTTGCAGCACCAAGTGCGAGAGGAGGAAGAACAGCTACTTCGCTGGCTTGAGCTGCCT CGTCAATAACTACCATATCAAAACCATGAGTGAGCCGAGAGAACAACTTGCGACCACTGCTTGA GACAGTAGTGAAAACAATCTCAGCCTCATTGGCAAAACTTGCCTCGAGACTAGCACGGGCTTCT TCCAGATTAAAATTGCTACCAGCACGAAATCTGGGTTCTAAAATGAGAAGACGAGAGATCTCAA CTAGAACTTTATCCCTGCTTTCAACAGCAGCTGCAAGGTTCTGAAGTAATGCATCTCGGTTTTG GTCCCTAGCCATGAGAATATCAGGATCAACACCAACAGATCCTTGGGAACGACCGTCCACTGCT GCAACATTAAGCTTATTTTGAAGGTCAGCGATGTGTGCCGAGAAATAAGCTTCCTGAACTCTTA AATCTTGCATCCATTTTGAAATTTCTTCGCGGCTCTTGATTAGAAGTTGTTCAGTTCTCCGCTC AACAGAAACTGCCTGAGCAGCACGTGATTGTGAATCAACCCCAACTCTGGCCACATCAGGCCTG TAAACTTTCATCTCACCATCAATAAATCCACGATCAAGAACACGTGCAAGAAGTTCATCAGTTG CAGCATTAGAAGGAGCACAGACTAACATTCTGGGCTTTGGACAGAGTTTCGAAAGGGAGCGGAA GAGATTCTGGTCCATGTTATGAAGAACTTCATCAATTGACCCCATAGCAATATTGTCAGGATTG CTTTCATTGGCATGCTTATAACTCTGTGGTGCCAGTTTCTTAAGCAAAGAGGTATAGTAATGCT GATACTGAACCAGATGGATGACATTTAGCATTCCCCAGACTGTATGTGTCTTTCCTGTCCCTGG AGGCCCTTGTACAAGAGTAAAGGGCCACGGCTCTTGCCTCTTAGTTACCCCACTACTTGTACCA GCAGCAGTATGCATTGCAGCCCACTGGATTGCAGCCAGCTGGGGTCCATTGAATGTCCTACGCA AATGGTCAACAAAATTCTGTGTAAAGCATTCAGGCATGGCTGGGGTCTGCTGCTCATATTTTGG GAAGTGATCTGGACTGGGCTTTAGGATTGCAGTTTGCATCTACCAGGATGGAAATAAAACTTTT AGTTTCCTGTGTTTATAGGTGTATGTATTGAATATGAAGCAAAGACAAAACTTGGGTATTCATA AAGAAAAATTTGTTACCTGTAAATTAAGACGGCAAAATGCATGCAAAGCAACATACTCCCGCTG GGTGGTTGCAAGCGAACCAAGGACAGTCAAATACCAGGTGCCTCTGGGTTGAAATTTCCTCAAA ATATGATCCTCGTCAACCTTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.469289759

Conservation Information
Conserved circRNAs	NA
PMCS	0.469289759

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							6704651-6702776(+)
6704647-6702823(+)
6704522-6704752(-)
6702790-6704752(-)
						
					

						Potential amino acid sequence
						
							MQSNILPLGGCKRTKDSQIPGASGLKFPQNMILVNLSIEPFWHG*(+)
MHAKQHTPAGWLQANQGQSNTRCLWVEISSKYDPRQPFHRALLARVRATFIRRISATKPTP*(+
)
MQTAILKPSPDHFPKYEQQTPAMPECFTQNFVDHLRRTFNGPQLAAIQWAAMHTAAGTSSGVTK
RQEPWPFTLVQGPPGTGKTHTVWGMLNVIHLVQYQHYYTSLLKKLAPQSYKHANESNPDNIAMG
SIDEVLHNMDQNLFRSLSKLCPKPRMLVCAPSNAATDELLARVLDRGFIDGEMKVYRPDVARVG
VDSQSRAAQAVSVERRTEQLLIKSREEISKWMQDLRVQEAYFSAHIADLQNKLNVAAVDGRSQG
SVGVDPDILMARDQNRDALLQNLAAAVESRDKVLVEISRLLILEPRFRAGSNFNLEEARASLEA
SFANEAEIVFTTVSSSGRKLFSRLTHGFDMVVIDEAAQASEVAVLPPLALGAARCVLVGDPQQL
PATVISKAAGTLLYSRSLFERFQQAGCPTMLLSVQYRMHPQIRDFPSRYFYQGRLTDSESVANL
PDETYYKDPLLRPYLFYDVTHGRESHRGGSVSYQNVHEAQFCLQLYEHLQKSLKSLGMGRISVG
IITPYKLQLKCLQQEFLAVLKSEEGKDIYINTVDAFQGQERDVIIMSCVRASSHGVGFVADIRR
MNVALTRARRALWKG*(-)
MLLLPVPEGLYGKVDEDHILRKFQPRGTWYLTVLGSLATTQREYVALHAFCRLNLQMQTAILKP
SPDHFPKYEQQTPAMPECFTQNFVDHLRRTFNGPQLAAIQWAAMHTAAGTSSGVTKRQEPWPFT
LVQGPPGTGKTHTVWGMLNVIHLVQYQHYYTSLLKKLAPQSYKHANESNPDNIAMGSIDEVLHN
MDQNLFRSLSKLCPKPRMLVCAPSNAATDELLARVLDRGFIDGEMKVYRPDVARVGVDSQSRAA
QAVSVERRTEQLLIKSREEISKWMQDLRVQEAYFSAHIADLQNKLNVAAVDGRSQGSVGVDPDI
LMARDQNRDALLQNLAAAVESRDKVLVEISRLLILEPRFRAGSNFNLEEARASLEASFANEAEI
VFTTVSSSGRKLFSRLTHGFDMVVIDEAAQASEVAVLPPLALGAARCVLVGDPQQLPATVISKA
AGTLLYSRSLFERFQQAGCPTMLLSVQYRMHPQIRDFPSRYFYQGRLTDSESVANLPDETYYKD
PLLRPYLFYDVTHGRESHRGGSVSYQNVHEAQFCLQLYEHLQKSLKSLGMGRISVGIITPYKLQ
LKCLQQEFLAVLKSEEGKDIYINTVDAFQGQERDVIIMSCVRASSHGVGFVADIRRMNVALTRA
RRALWKG*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	6704651-6702776(+) 6704647-6702823(+) 6704522-6704752(-) 6702790-6704752(-)
Potential amino acid sequence	MQSNILPLGGCKRTKDSQIPGASGLKFPQNMILVNLSIEPFWHG(+) MHAKQHTPAGWLQANQGQSNTRCLWVEISSKYDPRQPFHRALLARVRATFIRRISATKPTP(+ ) MQTAILKPSPDHFPKYEQQTPAMPECFTQNFVDHLRRTFNGPQLAAIQWAAMHTAAGTSSGVTK RQEPWPFTLVQGPPGTGKTHTVWGMLNVIHLVQYQHYYTSLLKKLAPQSYKHANESNPDNIAMG SIDEVLHNMDQNLFRSLSKLCPKPRMLVCAPSNAATDELLARVLDRGFIDGEMKVYRPDVARVG VDSQSRAAQAVSVERRTEQLLIKSREEISKWMQDLRVQEAYFSAHIADLQNKLNVAAVDGRSQG SVGVDPDILMARDQNRDALLQNLAAAVESRDKVLVEISRLLILEPRFRAGSNFNLEEARASLEA SFANEAEIVFTTVSSSGRKLFSRLTHGFDMVVIDEAAQASEVAVLPPLALGAARCVLVGDPQQL PATVISKAAGTLLYSRSLFERFQQAGCPTMLLSVQYRMHPQIRDFPSRYFYQGRLTDSESVANL PDETYYKDPLLRPYLFYDVTHGRESHRGGSVSYQNVHEAQFCLQLYEHLQKSLKSLGMGRISVG IITPYKLQLKCLQQEFLAVLKSEEGKDIYINTVDAFQGQERDVIIMSCVRASSHGVGFVADIRR MNVALTRARRALWKG(-) MLLLPVPEGLYGKVDEDHILRKFQPRGTWYLTVLGSLATTQREYVALHAFCRLNLQMQTAILKP SPDHFPKYEQQTPAMPECFTQNFVDHLRRTFNGPQLAAIQWAAMHTAAGTSSGVTKRQEPWPFT LVQGPPGTGKTHTVWGMLNVIHLVQYQHYYTSLLKKLAPQSYKHANESNPDNIAMGSIDEVLHN MDQNLFRSLSKLCPKPRMLVCAPSNAATDELLARVLDRGFIDGEMKVYRPDVARVGVDSQSRAA QAVSVERRTEQLLIKSREEISKWMQDLRVQEAYFSAHIADLQNKLNVAAVDGRSQGSVGVDPDI LMARDQNRDALLQNLAAAVESRDKVLVEISRLLILEPRFRAGSNFNLEEARASLEASFANEAEI VFTTVSSSGRKLFSRLTHGFDMVVIDEAAQASEVAVLPPLALGAARCVLVGDPQQLPATVISKA AGTLLYSRSLFERFQQAGCPTMLLSVQYRMHPQIRDFPSRYFYQGRLTDSESVANLPDETYYKD PLLRPYLFYDVTHGRESHRGGSVSYQNVHEAQFCLQLYEHLQKSLKSLGMGRISVGIITPYKLQ LKCLQQEFLAVLKSEEGKDIYINTVDAFQGQERDVIIMSCVRASSHGVGFVADIRRMNVALTRA RRALWKG(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0002s09410_circ_g.1

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