Plant Circular RNA Database

Detail information of POPTR_0006s11400_circ_g.2

			
						 General Information
					
						CircRNA Name
						POPTR_0006s11400_circ_g.2
					
						ID in PlantcircBase
						pop_circ_001849
					
						Alias
						Chr06:8820659-8822557
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr6: 8628342-8630240  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0006s11400						
					
						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_0006s11400.1:4

General Information
CircRNA Name	POPTR_0006s11400_circ_g.2
ID in PlantcircBase	pop_circ_001849
Alias	Chr06:8820659-8822557
Organism	Populus trichocarpa
Position	chr6: 8628342-8630240 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0006s11400
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_0006s11400.1:4

			
						 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  
						
							GAGCGTTGTGACCAACTTCACTGTTGCCCATGTCATCCTCACTTGGAAGCCCAACAGCAGTACC
ATGAGCCTTAATCAATCTCCATCTTTCAGGGGCAGTctgcaagcaaaggtgcgaacaccattat
gcaccaagtattcaccagatgtcctttctatctcaggaggagtaacgaggtattggcttggaag
cttcaact

									
								

					

						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
						
							CTGCAAGCAAAGGTGCGAACACCATTATGCACCAAGTATTCACCAGATGTCCTTTCTATCTCAG
GAGGAGTAACGAGGTATTGGCTTGGAAGCTTCAACTCACCATCATATTGAAGCATTCCAGCATA
ATGAATTTTAGGGACTCGAACCCGATCAAATTTGTCAAAATCCGCATATTCAAGAGCCTTAGCA
AGCATAGTCATGCGATCTGCTCGGAAGTTGAAAGTGACAACAGCATCACCATCCTTAATTGGTC
CCACGGGATTTCCACTCTCATCAACAATGACAAAAGGAGGTAAGTACTGGTCATTCGCCTTGGG
TTCTGCTCTCAGTTTCTTGACGGCTTCAACAGCACTTCTAAACTTGTATGGGGCTTCACCAAGT
ACTTGGGCATCCCATCCTCGTTTCACCACATTCCAATCATTCTGCAGAAGATTTGCAGAAAGGG
TTCAGGCATGCATAAAGGAATAAAGCTAAATCTATAACTCTAAAGGAGCACAAACTGATATCTA
TAACAACATTCAAGGAAAAGATCACGTTTGTAATTTATGCAAGTTACTTATAATTGACATCACC
AAGAAGGTAATTACTATCCTCTTCCTAACTTATAAAGGAAGGATATCCATTACCTTCATCTTAT
CAACAACAACAACAAAGCCTTATTTTCAAACTATTCAGGGTTGGCTACACTGTTGAACCATTCA
GCATGATCATAAAATAAATCCTCCTCAATAAAAAGATAGTTTAATCCTTTGGTAGTTGATGCCG
CTTCCATCCACATAATTTTTAGTCTCTTTCTACCTCTTTACCTTCATCTTATAAGGAAATCTTA
ATTTGCATCAGATTGGTATGCAGGCACGTCATTAATATACCAGCTATAAGCCACTGGTTGCCAC
CCAAAAAGACCAAAGTGGCTAAGAATGATTCTTCATTCCTCCCCAAAATCTTGTTTGAGTAGGT
CCTAGGTGTCATTTCTCCTCTGTCCAAGCCGCACCTCTTTTGGAGGGGAATAGGGCCCCGATGG
TGTGTAATATATACTTAGTGATGAGTTTCCATAGAAATTAAGTTACAAAAATGAAGCAGGAAAA
AAACAGCAATTCATACGAGAATAGACCATAAATGGGAAGCATCACTGGAATTCTTCCCCTTAAT
TAAGAAAAAAATTTACAGCCATACCTCATAGCGGTCCATTGTGACATACATGCGCCCACCACCA
GATGCAATTTGTGCATCAACAGCTTTCTCACGTAAATTTGACAGGTCTTTCTCAAGAGTCTCCA
CAAAGCCAACACTTGACCCGTCTAAAACATCACGGCCATCAGTAAGAAAGTGAACACGGATTCT
TTTAGCACCGCGTTCAGCAGCACCTTTCAGCAACAACTGCAGAAAGAGAAAGGACAAGGAAAAA
GGTATCAGGGAAAACACTACATGATTTCAGGAGAACAAAGCAAGCACAATGATGAGTAATAAAA
ACCAAATCTTACCTGCAACTGATCAAGCCTTGAGTGAACTCCACCATCGCTCAATAGTCCAATG
AGATGCAACGTGCCATTGTCGAAAGATTGTTTAATGTAATTAAATCCCTCTCCGTCATAGATTT
TTCCAGAGGCAAGAGCAAGATCAACAAGCTTCGCTCTACATTCCCAAGTAAATAAACATAAAAC
ATGTTATATTAGTTATCGTATTTTATTCTTAAACTCTTTAAGAGAATGAACCATCTGCATAAGA
AACTATTGGAATAGAAATAGGAAAAGAGAAGTAAGTTAGTTACCCCTGAGCAAAGATGCGACCA
GCACCAAGAGCGTTGTGACCAACTTCACTGTTGCCCATGTCATCCTCACTTGGAAGCCCAACAG
CAGTACCATGAGCCTTAATCAATCTCCATCTTTCAGGGGCAGT
						
					

			
		

Sequences
Splice junction sequence	GAGCGTTGTGACCAACTTCACTGTTGCCCATGTCATCCTCACTTGGAAGCCCAACAGCAGTACC ATGAGCCTTAATCAATCTCCATCTTTCAGGGGCAGTctgcaagcaaaggtgcgaacaccattat gcaccaagtattcaccagatgtcctttctatctcaggaggagtaacgaggtattggcttggaag cttcaact
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	CTGCAAGCAAAGGTGCGAACACCATTATGCACCAAGTATTCACCAGATGTCCTTTCTATCTCAG GAGGAGTAACGAGGTATTGGCTTGGAAGCTTCAACTCACCATCATATTGAAGCATTCCAGCATA ATGAATTTTAGGGACTCGAACCCGATCAAATTTGTCAAAATCCGCATATTCAAGAGCCTTAGCA AGCATAGTCATGCGATCTGCTCGGAAGTTGAAAGTGACAACAGCATCACCATCCTTAATTGGTC CCACGGGATTTCCACTCTCATCAACAATGACAAAAGGAGGTAAGTACTGGTCATTCGCCTTGGG TTCTGCTCTCAGTTTCTTGACGGCTTCAACAGCACTTCTAAACTTGTATGGGGCTTCACCAAGT ACTTGGGCATCCCATCCTCGTTTCACCACATTCCAATCATTCTGCAGAAGATTTGCAGAAAGGG TTCAGGCATGCATAAAGGAATAAAGCTAAATCTATAACTCTAAAGGAGCACAAACTGATATCTA TAACAACATTCAAGGAAAAGATCACGTTTGTAATTTATGCAAGTTACTTATAATTGACATCACC AAGAAGGTAATTACTATCCTCTTCCTAACTTATAAAGGAAGGATATCCATTACCTTCATCTTAT CAACAACAACAACAAAGCCTTATTTTCAAACTATTCAGGGTTGGCTACACTGTTGAACCATTCA GCATGATCATAAAATAAATCCTCCTCAATAAAAAGATAGTTTAATCCTTTGGTAGTTGATGCCG CTTCCATCCACATAATTTTTAGTCTCTTTCTACCTCTTTACCTTCATCTTATAAGGAAATCTTA ATTTGCATCAGATTGGTATGCAGGCACGTCATTAATATACCAGCTATAAGCCACTGGTTGCCAC CCAAAAAGACCAAAGTGGCTAAGAATGATTCTTCATTCCTCCCCAAAATCTTGTTTGAGTAGGT CCTAGGTGTCATTTCTCCTCTGTCCAAGCCGCACCTCTTTTGGAGGGGAATAGGGCCCCGATGG TGTGTAATATATACTTAGTGATGAGTTTCCATAGAAATTAAGTTACAAAAATGAAGCAGGAAAA AAACAGCAATTCATACGAGAATAGACCATAAATGGGAAGCATCACTGGAATTCTTCCCCTTAAT TAAGAAAAAAATTTACAGCCATACCTCATAGCGGTCCATTGTGACATACATGCGCCCACCACCA GATGCAATTTGTGCATCAACAGCTTTCTCACGTAAATTTGACAGGTCTTTCTCAAGAGTCTCCA CAAAGCCAACACTTGACCCGTCTAAAACATCACGGCCATCAGTAAGAAAGTGAACACGGATTCT TTTAGCACCGCGTTCAGCAGCACCTTTCAGCAACAACTGCAGAAAGAGAAAGGACAAGGAAAAA GGTATCAGGGAAAACACTACATGATTTCAGGAGAACAAAGCAAGCACAATGATGAGTAATAAAA ACCAAATCTTACCTGCAACTGATCAAGCCTTGAGTGAACTCCACCATCGCTCAATAGTCCAATG AGATGCAACGTGCCATTGTCGAAAGATTGTTTAATGTAATTAAATCCCTCTCCGTCATAGATTT TTCCAGAGGCAAGAGCAAGATCAACAAGCTTCGCTCTACATTCCCAAGTAAATAAACATAAAAC ATGTTATATTAGTTATCGTATTTTATTCTTAAACTCTTTAAGAGAATGAACCATCTGCATAAGA AACTATTGGAATAGAAATAGGAAAAGAGAAGTAAGTTAGTTACCCCTGAGCAAAGATGCGACCA GCACCAAGAGCGTTGTGACCAACTTCACTGTTGCCCATGTCATCCTCACTTGGAAGCCCAACAG CAGTACCATGAGCCTTAATCAATCTCCATCTTTCAGGGGCAGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.199958017

Conservation Information
Conserved circRNAs	NA
PMCS	0.199958017

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8629881-8628452(+)
8630173-8630218(-)
						
						Potential amino acid sequence
						
							MQRAIVERLFNVIKSLSVIDFSRGKSKINKLRSLSKDATSTKSVVTNFTVAHVILTWKPNSSTM
SLNQSPSFRGSLQAKVRTPLCTKYSPDVLSISGGVTRYWLGSFNSPSY*(+)
MGNSEVGHNALGAGRIFAQGAKLVDLALASGKIYDGEGFNYIKQSFDNGTLHLIGLLSDGGVHS
RLDQLQLLLKGAAERGAKRIRVHFLTDGRDVLDGSSVGFVETLEKDLSNLREKAVDAQIASGGG
RMYVTMDRYENDWNVVKRGWDAQVLGEAPYKFRSAVEAVKKLRAEPKANDQYLPPFVIVDESGN
PVGPIKDGDAVVTFNFRADRMTMLAKALEYADFDKFDRVRVPKIHYAGMLQYDGELKLPSQYLV
TPPEIERTSGEYLVHNGVRTFACRLPLKDGD*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	8629881-8628452(+) 8630173-8630218(-)
Potential amino acid sequence	MQRAIVERLFNVIKSLSVIDFSRGKSKINKLRSLSKDATSTKSVVTNFTVAHVILTWKPNSSTM SLNQSPSFRGSLQAKVRTPLCTKYSPDVLSISGGVTRYWLGSFNSPSY(+) MGNSEVGHNALGAGRIFAQGAKLVDLALASGKIYDGEGFNYIKQSFDNGTLHLIGLLSDGGVHS RLDQLQLLLKGAAERGAKRIRVHFLTDGRDVLDGSSVGFVETLEKDLSNLREKAVDAQIASGGG RMYVTMDRYENDWNVVKRGWDAQVLGEAPYKFRSAVEAVKKLRAEPKANDQYLPPFVIVDESGN PVGPIKDGDAVVTFNFRADRMTMLAKALEYADFDKFDRVRVPKIHYAGMLQYDGELKLPSQYLV TPPEIERTSGEYLVHNGVRTFACRLPLKDGD(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0006s11400_circ_g.2

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