Plant Circular RNA Database

Detail information of POPTR_0006s07740_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0006s07740_circ_g.1
					
						ID in PlantcircBase
						pop_circ_001808
					
						Alias
						Chr06:5884286-5887172
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr6: 5657138-5660024  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0006s07740						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							POPTR_0006s07740_circ_g.2 						
					
						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  
						
							GT-AG							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_0006s07740.1:9

General Information
CircRNA Name	POPTR_0006s07740_circ_g.1
ID in PlantcircBase	pop_circ_001808
Alias	Chr06:5884286-5887172
Organism	Populus trichocarpa
Position	chr6: 5657138-5660024 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0006s07740
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	POPTR_0006s07740_circ_g.2
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	GT-AG 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_0006s07740.1:9

			
						 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  
						
							AAAGAAATTGAATCTCTACTGCAGGTATATGGGCACCATTACAGGTATCAGTGATCTTGATCCT
GTAAGATGGAAAAATTCACAATGGCGTAATTTGCAGgggcagagaagaagagcataaaccctga
gttatggcaagcatgtgcaggaccactagtgaacttgccggcggccggaactcatgtggtctac
ttccccca

									
								

					

						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
						
							GGGCAGAGAAGAAGAGCATAAACCCTGAGTTATGGCAAGCATGTGCAGGACCACTAGTGAACTT
GCCGGCGGCCGGAACTCATGTGGTCTACTTCCCCCAAGGGCATAGTGAACAGGTTCGTGTCTGT
TGCTATTTTGTGCCAAAAATGTGTCCCACCAGCCCGCACCCTTCTTTTATTGGGATTTATCGGC
TAATTATTTGTGGTAAATGGTGTGTTAGGATTTTGATCTGGTGTGTGCTAAGTCTTATAATTTT
ACCTAAACTGGTTGGTTGGGTGTAATAAATAGGTAGATTATAAGGAAAGGAAAAGTAGATCAAG
ATTTGGGATTTACTTTTGAGGGTACTATTTTAGGTGGCAAGTTGAAGCTACCCTTTTTGCCTTG
ATTCAGATTGTGTTAAACTTGATTTAATGCGGCTTTGAGTAATAATAGAAATATTCTCTGGGTA
TGTATGATCTTGCTGTCATGTGCTGCTTTTGAGTACTAAAAACCATCAATGCATCGTGTTATCT
GGCTTGTGTTTATAAAGTCAACTCATGGTCCACGTGAGTTTTCTTTTAATAGAAAACTGTGATG
TTAGTTGATCAAAAATAACAAAAAAATAGGATCTTGAGGTTTTGACTTCTTTGACTCTGTAATT
TATGTTAACTGAAATTTCTCTTAATGTTACAGTTAATCATCAAGAGTCTCACAGGTCATTGTGT
ATTTGCATGTCAATTTACTTGTAATGCAAATTTTTAACCATGATCATGTCCTTTAAAGCCTGAC
AAATATTGACAATTTTTTGAGGCTTGTGCAAGTTTTCTGTTTCAACTGAACAAGGTGACAGAAC
CAGTAGGTGTAACATGAAAAATATTTTCAGTTATAAATTAGTTTCATGATTATTGTGGATGGAA
TTTTATACTGTCTTTTTTTTTTCCCTCCTTCAGAAGTCAGTTCATGTTCTTACTTGAGAGTAAA
ATTACTGTTTTCAGGTTGCAGCGTCCATGAAAAAGGATGTAGATGCCCAAATCCCAAACTACCC
AAATCTTCCGTCGAAGCTACTTTGTCTCCTTCACAATGTCACCTTACATGTAAAATAGCTAACC
TTTCTGGCCTTCATGTCTAACATCACAAAATTTCTTTATTTGGTCACTCAATTATTTTAGTTCT
TTTGTTTGATTTTGTAGGCGGACCCAGAAACAGATGAAGTTTATGCTCAGATGACCCTTCAACC
TGTTTCTTCCGTAAGAACTTGATTCATAGTAACTAAAAAAAGTATACTTGCTTTCGGTGTTTGG
ACTAAGAAAAGCAACTAGAAATCAACTGGCAATAACCGATCCCTATGCAATTGCCAGAAAATTA
ATAGAATGACTTTAGCATGTTTTTAGTTGCTAACTCCTACTGAATCTATCAGCAACCTTGTCAA
TCCTTTTGCAGTTTGACAAGGATGCATTATTGAGGTCAGATCTTGCACTGAAGTCAAATAAACC
ACAGACAGAGTTTTTCTGTAAAACATTAACAGCAAGTGATACGAGCACTCATGGAGGTTTCTCT
GTTCCTCGTCGCGCAGCTGAGAAAATCTTCCCACCACTTGTAAGCTGTTCTCTGTTAGTCCTAA
AACAGTAGTGTCCATGTTAATCCTAATAGCATTATTTAATCTTTTCCCTTTCCCTTGTATAGAA
TTTCTCCTTGCAACCACCTGCTCAAGAACTTGTAGCCAGGGATTTGCATGATAATGTTTGGACT
TTCCGGCATATCTATCGTGGTATGTTAATTTTGCAGCACCCATGAAAACTAATTAGTTGATACC
CAATGGTTCTTATACTTACAATCAGTAATTGCTTGTTACCAAATTTGTTGTTATCTTATGTAAG
TTCCTGTTTTCTCTAAATCCAGGACAACCAAAGCGTCATTTGCTTACAACTGGATGGAGCCTAT
TTGTCAGTGGAAAGAGGCTTTTTGCCGGTGACTCAGTTTTATTTATTAGGTAAGAATTAGTGAA
TTCTGATTCCATGAATTTATGTGTCAAAAGGACTTATTTTACTGAAATTCGATTCTCATATTCT
TAGGTATCTTAAATCTTGTATACATGCATTTCAAGTTCAGGTCATTTTCTTACTATAAACATGC
CCTTTTAATCAACCTAATGATGCTTATTATATGTGATTAGAGATGAAAAGCAGCAGCTTCTATT
GGGCATCAGAAGGGCTAACAGGCAACCTACCAACTTATCATCATCAGTATTGTCAAGTGATAGC
ATGCATATTGGGATCCTAGCTGCTGCAGCCCATGCAGCAGCAAACAATAGCCCCTTTACTGTGT
TCTACAATCCCAGGTTAATTACTTATATTTTTCTCTGTAGGGTGCTTTTTTAAAAAAAATTCCT
TACTCATAGTAATTAGGTTGTGTGTGTTGGATTAATTGACACCAGATGCAAATTTTGTGCAGGG
CAAGTCCATCAGAATTTGTTATCCCTTTAGCCAAGTATTACAAGGCAGTGTACAGCAACCAAAT
ATCCCTTGGAATGCGCTTTCGCATGATGTTTGAAACTGAAGAGTCAGGAACAAGAAGGTACATT
TGGTCTTTTGGCACTTCTTGAATGTCATTTGAATACTATTGATTTCAAGAATTGTGAACTTGAA
ATGGAATTCTATTGAGACCTGAGGACATGTTGTTGGGAAGGAGTGTGTCATCGGATTAATTTGA
CTCTGAAAAGAGTTTTAGTCGAGCTGATTAGTACCTAGATTCTTTGCCTGGTGTTCTTATAACA
CGATAAACTCAATTTTCTTCACCAATTAGAAAGTTAAAGAAATTGAATCTCTACTGCAGGTATA
TGGGCACCATTACAGGTATCAGTGATCTTGATCCTGTAAGATGGAAAAATTCACAATGGCGTAA
TTTGCAG
						
					

			
		

Sequences
Splice junction sequence	AAAGAAATTGAATCTCTACTGCAGGTATATGGGCACCATTACAGGTATCAGTGATCTTGATCCT GTAAGATGGAAAAATTCACAATGGCGTAATTTGCAGgggcagagaagaagagcataaaccctga gttatggcaagcatgtgcaggaccactagtgaacttgccggcggccggaactcatgtggtctac ttccccca
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	GGGCAGAGAAGAAGAGCATAAACCCTGAGTTATGGCAAGCATGTGCAGGACCACTAGTGAACTT GCCGGCGGCCGGAACTCATGTGGTCTACTTCCCCCAAGGGCATAGTGAACAGGTTCGTGTCTGT TGCTATTTTGTGCCAAAAATGTGTCCCACCAGCCCGCACCCTTCTTTTATTGGGATTTATCGGC TAATTATTTGTGGTAAATGGTGTGTTAGGATTTTGATCTGGTGTGTGCTAAGTCTTATAATTTT ACCTAAACTGGTTGGTTGGGTGTAATAAATAGGTAGATTATAAGGAAAGGAAAAGTAGATCAAG ATTTGGGATTTACTTTTGAGGGTACTATTTTAGGTGGCAAGTTGAAGCTACCCTTTTTGCCTTG ATTCAGATTGTGTTAAACTTGATTTAATGCGGCTTTGAGTAATAATAGAAATATTCTCTGGGTA TGTATGATCTTGCTGTCATGTGCTGCTTTTGAGTACTAAAAACCATCAATGCATCGTGTTATCT GGCTTGTGTTTATAAAGTCAACTCATGGTCCACGTGAGTTTTCTTTTAATAGAAAACTGTGATG TTAGTTGATCAAAAATAACAAAAAAATAGGATCTTGAGGTTTTGACTTCTTTGACTCTGTAATT TATGTTAACTGAAATTTCTCTTAATGTTACAGTTAATCATCAAGAGTCTCACAGGTCATTGTGT ATTTGCATGTCAATTTACTTGTAATGCAAATTTTTAACCATGATCATGTCCTTTAAAGCCTGAC AAATATTGACAATTTTTTGAGGCTTGTGCAAGTTTTCTGTTTCAACTGAACAAGGTGACAGAAC CAGTAGGTGTAACATGAAAAATATTTTCAGTTATAAATTAGTTTCATGATTATTGTGGATGGAA TTTTATACTGTCTTTTTTTTTTCCCTCCTTCAGAAGTCAGTTCATGTTCTTACTTGAGAGTAAA ATTACTGTTTTCAGGTTGCAGCGTCCATGAAAAAGGATGTAGATGCCCAAATCCCAAACTACCC AAATCTTCCGTCGAAGCTACTTTGTCTCCTTCACAATGTCACCTTACATGTAAAATAGCTAACC TTTCTGGCCTTCATGTCTAACATCACAAAATTTCTTTATTTGGTCACTCAATTATTTTAGTTCT TTTGTTTGATTTTGTAGGCGGACCCAGAAACAGATGAAGTTTATGCTCAGATGACCCTTCAACC TGTTTCTTCCGTAAGAACTTGATTCATAGTAACTAAAAAAAGTATACTTGCTTTCGGTGTTTGG ACTAAGAAAAGCAACTAGAAATCAACTGGCAATAACCGATCCCTATGCAATTGCCAGAAAATTA ATAGAATGACTTTAGCATGTTTTTAGTTGCTAACTCCTACTGAATCTATCAGCAACCTTGTCAA TCCTTTTGCAGTTTGACAAGGATGCATTATTGAGGTCAGATCTTGCACTGAAGTCAAATAAACC ACAGACAGAGTTTTTCTGTAAAACATTAACAGCAAGTGATACGAGCACTCATGGAGGTTTCTCT GTTCCTCGTCGCGCAGCTGAGAAAATCTTCCCACCACTTGTAAGCTGTTCTCTGTTAGTCCTAA AACAGTAGTGTCCATGTTAATCCTAATAGCATTATTTAATCTTTTCCCTTTCCCTTGTATAGAA TTTCTCCTTGCAACCACCTGCTCAAGAACTTGTAGCCAGGGATTTGCATGATAATGTTTGGACT TTCCGGCATATCTATCGTGGTATGTTAATTTTGCAGCACCCATGAAAACTAATTAGTTGATACC CAATGGTTCTTATACTTACAATCAGTAATTGCTTGTTACCAAATTTGTTGTTATCTTATGTAAG TTCCTGTTTTCTCTAAATCCAGGACAACCAAAGCGTCATTTGCTTACAACTGGATGGAGCCTAT TTGTCAGTGGAAAGAGGCTTTTTGCCGGTGACTCAGTTTTATTTATTAGGTAAGAATTAGTGAA TTCTGATTCCATGAATTTATGTGTCAAAAGGACTTATTTTACTGAAATTCGATTCTCATATTCT TAGGTATCTTAAATCTTGTATACATGCATTTCAAGTTCAGGTCATTTTCTTACTATAAACATGC CCTTTTAATCAACCTAATGATGCTTATTATATGTGATTAGAGATGAAAAGCAGCAGCTTCTATT GGGCATCAGAAGGGCTAACAGGCAACCTACCAACTTATCATCATCAGTATTGTCAAGTGATAGC ATGCATATTGGGATCCTAGCTGCTGCAGCCCATGCAGCAGCAAACAATAGCCCCTTTACTGTGT TCTACAATCCCAGGTTAATTACTTATATTTTTCTCTGTAGGGTGCTTTTTTAAAAAAAATTCCT TACTCATAGTAATTAGGTTGTGTGTGTTGGATTAATTGACACCAGATGCAAATTTTGTGCAGGG CAAGTCCATCAGAATTTGTTATCCCTTTAGCCAAGTATTACAAGGCAGTGTACAGCAACCAAAT ATCCCTTGGAATGCGCTTTCGCATGATGTTTGAAACTGAAGAGTCAGGAACAAGAAGGTACATT TGGTCTTTTGGCACTTCTTGAATGTCATTTGAATACTATTGATTTCAAGAATTGTGAACTTGAA ATGGAATTCTATTGAGACCTGAGGACATGTTGTTGGGAAGGAGTGTGTCATCGGATTAATTTGA CTCTGAAAAGAGTTTTAGTCGAGCTGATTAGTACCTAGATTCTTTGCCTGGTGTTCTTATAACA CGATAAACTCAATTTTCTTCACCAATTAGAAAGTTAAAGAAATTGAATCTCTACTGCAGGTATA TGGGCACCATTACAGGTATCAGTGATCTTGATCCTGTAAGATGGAAAAATTCACAATGGCGTAA TTTGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.135406726

Conservation Information
Conserved circRNAs	NA
PMCS	0.135406726

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5658125-5657155(+)
5657158-5659974(-)
5657181-5660006(-)
						
						Potential amino acid sequence
						
							MKKDVDAQIPNYPNLPSKLLCLLHNVTLHADPETDEVYAQMTLQPVSSFDKDALLRSDLALKSN
KPQTEFFCKTLTASDTSTHGGFSVPRRAAEKIFPPLNFSLQPPAQELVARDLHDNVWTFRHIYR
GQPKRHLLTTGWSLFVSGKRLFAGDSVLFIRDEKQQLLLGIRRANRQPTNLSSSVLSSDSMHIG
ILAAAAHAAANNSPFTVFYNPRASPSEFVIPLAKYYKAVYSNQISLGMRFRMMFETEESGTRRY
MGTITGISDLDPVRWKNSQWRNLQGQRRRA*(+)
MLFFSAPANYAIVNFSILQDQDH*(-)
MLAITQGLCSSSLPLQITPL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5658125-5657155(+) 5657158-5659974(-) 5657181-5660006(-)
Potential amino acid sequence	MKKDVDAQIPNYPNLPSKLLCLLHNVTLHADPETDEVYAQMTLQPVSSFDKDALLRSDLALKSN KPQTEFFCKTLTASDTSTHGGFSVPRRAAEKIFPPLNFSLQPPAQELVARDLHDNVWTFRHIYR GQPKRHLLTTGWSLFVSGKRLFAGDSVLFIRDEKQQLLLGIRRANRQPTNLSSSVLSSDSMHIG ILAAAAHAAANNSPFTVFYNPRASPSEFVIPLAKYYKAVYSNQISLGMRFRMMFETEESGTRRY MGTITGISDLDPVRWKNSQWRNLQGQRRRA(+) MLFFSAPANYAIVNFSILQDQDH(-) MLAITQGLCSSSLPLQITPL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0006s07740_circ_g.1

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