Plant Circular RNA Database

Detail information of POPTR_0004s18290_circ_ag.1

			
						 General Information
					
						CircRNA Name
						POPTR_0004s18290_circ_ag.1
					
						ID in PlantcircBase
						pop_circ_001361
					
						Alias
						Chr04:19480972-19485265 
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr4: 18234458-18238751  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						CIRI2; circRNA_finder
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							POPTR_0004s18290_circ_ag.2 POPTR_0004s18290_circ_ag.3 POPTR_0004s18290_circ_ag.4 POPTR_0004s18290_circ_ag.5 POPTR_0004s18290_circ_ag.6 						
					
						Support reads
						6
					
						Tissues
						leaf; cambium; xylem
					
						Exon boundary  
						
							NA-NA							"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-CA							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
						NA

General Information
CircRNA Name	POPTR_0004s18290_circ_ag.1
ID in PlantcircBase	pop_circ_001361
Alias	Chr04:19480972-19485265
Organism	Populus trichocarpa
Position	chr4: 18234458-18238751 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	ag-circRNA
Identification method	CIRI2; circRNA_finder
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	POPTR_0004s18290_circ_ag.2 POPTR_0004s18290_circ_ag.3 POPTR_0004s18290_circ_ag.4 POPTR_0004s18290_circ_ag.5 POPTR_0004s18290_circ_ag.6
Support reads	6
Tissues	leaf; cambium; xylem
Exon boundary	NA-NA "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-CA 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	NA

			
						 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  
						
							ATATTTCCCCATAGAACCTCCCATGGATGCCTAAACCTTAAAGGAGATGATGTGATGCTATCTA
GCTCAGTGATTTCCACAGATGTCCTCGCGTGATCAGggtacaattccgagtttgctcagcacaa
attgcttcatctcggtggggttatcctctagctctttgtctacaagaaagatattattatatat
acaattac

									
								

					

						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
						
							GGTACAATTCCGAGTTTGCTCAGCACAAATTGCTTCATCTCGGTGGGGTTATCCTCTAGCTCTT
TGTCTACAAGAAAGATATTATTATATATACAATTACATGGTCATCAACAAATATTCTTGAATCT
TGACCATTACATCTGATCAGAAAATCCAATTGTAAGTTGAGAGAGGTTCATTACCCTGGCCAGT
GGGAATGTAAGTGAAAAACCAGTATATAGTTGTATCATCACAAGGGAGGAAACCTGATCGAACC
CCTTTGCCAAATAACAGCAGGAACTTGGAGCCAAAGCCATGATTAACCTTAAAATCCGCATAAC
CCCGAATAGCTGATCGGCCGGCAAAAGCTGGCTTCTTGAAGCCTATAAATCTTGCCACCACTGA
GTTCACCCCATCACAACCAATCAATACCTTCCATAGACATTGAAATTCGCTGGCTTAGAAATAT
TTCCCCCACACACACACGCATATATAAATATATAAACATAGAAACACTGGACTCAGTAGAATTC
TTTCATACTCCACGGTATTAGTACTGAAATAATAGCCACCAAAAAAGTGCAGTGATTTCTATAC
CTTGGTTTTGATGATGGTATCATCAGCAAGATGAACCAGCTTTAAGTAGCCTGATTCCTCAATA
GAAACCACCTTGGAGGAGTACCTTATGGTACCATCTGGGAGTTCTTTTTCAAGGGCTTCCAGCA
ACAATTTTCTTCTCACACAACGAACCTCATGGTCTCCACTGTACACCAAATTAAAGGGCCGATT
ACTAAAATTCACCATCAAATACATGGCATACAAAATTAATGAATATATATGTTTACACTGAATC
CTCATGGCTAGTGTCCGATTACTTACATAGTCCCTTTGACCTTAAAAGATGTCTGTCTGCCAGG
TTTGCTCACAACAGTAGAGCTAGCAACTAATCTGCAGTCAAATGATCCCTTCATATTAGCTTCA
TAGAACCAAAGTCAGGGTCAAATTAACAAGTTTCTACATGTAAATGCTATATTAAGGGCCTTTC
TATCTCAGATTTGACATGCTCCAGTAGTAGAAAGACAATTTTGGGAGTTGAAGCCAACAAAGTA
ACTAGTGAAATGGGATGATGACAAGAAGTTAAACGGCTAGTTATATACCCTTCGAGGAATCCAT
GTTGTTGTCGGAGAGAGTGACCTATACCAACAGCATCTAATGCCCTCCAAGCATTAGTCCATGT
TGTGAAAGCAAATCCTGTGACCCTCAAACCGGCTGATGATTCCAACACTAGGCTTCGAATTCCA
AGCCTACAATTGAATACTCGCAGGTCAAGTTTAACATGGTAATATTTGTTACACGCGTATAATT
AATCTAGTACGTACCTGTGAAGCCCTAAAGATGTTGTAAGTCCAGCTATTCCAGCTCCTACAAT
CACCACTTCTTCAACTAATTCCATAATATTGGAATTAATTCCTCTAGTTAGTACTAAAGAACTT
GGTTTTGTTATGAGAATGGATATGAAGTTTGTTCAAGCTAGAAAGATTGGCTAGAAGAGTAGAA
ATGTAAGGCTATAAATGATGAGATGGGTAATATAAAAAGCAACTATCATCCAAGATGACTATGG
CTTTGACGACGACGATCATTATTATGACATCTATGGTTTGGTCCGAGAAGGAGGCAGGTCGGAT
TTAATTTAATTTATTTAAAAAAAATAAATTGAATTCCACCTTTTTTATATGAGGTCTTTTTTTT
TTTTTTCAATAAGATCATCAAGAATATCTTCAAATTAGTTTATATTTCGTTATATTTTTCAAAT
TTAAAAGGTTAATAAAAATTTTATTTTTAACTACCAAAAATGTTTTTGATGTTATAAAGAAGAA
ACAAATCATAACTAGAGTAGGTGTAACTTTATAATTGCTTTAATAATTGACGAAACTCTTCATT
AACTATGGGTTTAAAAAGGGATACAAAACCAGTAATAATGAAATTGCTTGTTTGTTTTTGTATT
TTAAAAATATTTTAAAAAAAATTAAAATTTTTTTTATTTTAAATTAATATTTTCTATGTTTTCA
AATCATTTTAATTCATTAATATCAAAAATAATTTTTTAAAAATAAAAAAATAATTTTTTAATAT
TTTTTAAAATAAAAAACATTTTAAAAACAATAACAATTAAATTCTCAAACACCCACAATAATTG
CATCCATCTCTCAAGAAGTTTATTATTTGCCCCTGACTTTGTTGAATAGCACCAACCACGTAAG
CAGTCCTTATTAGCTCAAAACTCCTCTCTTTTGCACATTTTTTTCAATCCTCTTATACTCTTCC
TTATCTTTGTCCTTCGTTTCCGCACTCACTTTTTTGTTCAAGGCCTCGGCCAGGCACCTTGCTA
AGACAACTCCATCTTCTAAAGCAGAGCACCCACCTTGACCAATATCTGGAGTCATGGGATGTAG
AGCATCACCAGCAACACAAGCATTGCCTCTGCTTATATTTCCCCATAGCACCTCCCATGGATGC
CTATACCTTAAAGGAGTCAGTGATCTCGACGAAAGATCTTACCTGGTCAGGCACAATATTTACA
AGGTTGCTCAGTGCAAGTTGTTTCATCTTGGCTGGATTATCCTTTAACTCTTTATTATCTGCAA
GAAAAAATGAATTTGTGCAAATAGCGAAAGTGAGAAGACAGATGTTGTGTGTTATAGCCTAAAT
CCTCGACTGAAACCACCTTGGAGGAGTACCTTATGGTACCAATTGGGAGTTCTTTTTCAAGGGC
TTCCAACAACAATTTCTAACACTAGACTTCGAATTCCAAGCCTACAATTAGTCAGAGCAGTCGT
ATACAATTAATCTGCCTAGTTAATTACATTTATGAAGATATTATTCTTGAGTTTATTTATGTAA
TTAGTTCAAGTTTTACAGAATTTAGAGCTACTGAAAACTTACATGATCGTTCATTTTAGGATCC
ATAAAATTAATCGAAGTACACATAAACTGGTTCAAACACTCGTATTAATCTAAAAAAAAAAATT
CTTACTCTTAGTAATGATGTGATTACCTGTGAAGGCCTAATGATGTTGCAAGTCCAGCAATTCC
AGCTTCAACTATCATAACATTTTCAATCACCTCATGATATTTTTGGCCTTCCAAATACCACTAC
TCCAGCACTAGTAGAATTGGTTGTGCTAAGAGGAAAAAAAAAAAGTGGACGGATTCAAGTGATG
AAGACGATCGAAAAGAGTAGTTGATGCCCATAAAGATATGATACGACAACCATGATGAAAGGTG
GCTGCTTGTCTAAATCTGATGATCATCACATGAGTATTATGACGGCAGCAAATACGTATTGTCT
TGAACTAGGCTTAAAGTCGGATCATAAGTTTCGTGTAAAGCTTGAAGCCTACTGACTTTTTAAG
AGTTTGATAGCGGTGTAAATTTTTTTAAAATTTTTATTTTATTTTTTTATATTGTTTTAATTTA
TTAACATTAAAAATACTGTTCATACCAACTTGATCTTGATGTGATATATTAACATGCTACAATA
CAAAGAAAAAGGACTAGCTCCTCTTATATTATTTGTCTCTTGGAAGAGAAATATGTCATGATAG
TAAAAAGGACTAGCTCCTCTTATAGCTTGTATATTGAACTATACGGATTGCATTAACAAACGTA
ATGGATGAAGAACATAATACAATTATTGAATCCAACATAAATAAAAAGGCTTATCTTTATTTCG
AAGCTTACCGATTGCATCAAGAAAAATTACAAAAAGAAAAACACGGCAGGATCTTAATTCATAA
TAAGAGATTTTACGGATTACAAGGACAAGAGCAGGATCAAGAAATATTGAGCTTTCCACAATCA
AAATCAGCTTTCTTTAGTAGCAATCCAGCAAGAAATTTAGCCAAAAATGCATCTCTCAAGATGT
TCATTATTTTTCCATCACCTTGTTGTATAGCACCAACAATATAAGCAGTGCTTATGAGCTCAAA
ACTTCTCCATCTCCTCTCCGCTGCGTATTTTTTCAACCCCATTTCAACCCTCTTGTATTCTTCT
CTCTCTTTCTCTTTACCTTCCACATTTAACTCCTTCTTCAAGGCCTCGGCGAGGCACCTAGCTA
GAACAACACCATCTTCTAAAGCAGCACACCCACCCTGGCCAATATCTGGTGTCATGGGATGGAG
AGCATCACCCGCTACACTAACATTGCCTTTACTTATATTTCCCCATAGAACCTCCCATGGATGC
CTAAACCTTAAAGGAGATGATGTGATGCTATCTAGCTCAGTGATTTCCACAGATGTCCTCGCGT
GATCAG
						
					

			
		

Sequences
Splice junction sequence	ATATTTCCCCATAGAACCTCCCATGGATGCCTAAACCTTAAAGGAGATGATGTGATGCTATCTA GCTCAGTGATTTCCACAGATGTCCTCGCGTGATCAGggtacaattccgagtttgctcagcacaa attgcttcatctcggtggggttatcctctagctctttgtctacaagaaagatattattatatat acaattac
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	GGTACAATTCCGAGTTTGCTCAGCACAAATTGCTTCATCTCGGTGGGGTTATCCTCTAGCTCTT TGTCTACAAGAAAGATATTATTATATATACAATTACATGGTCATCAACAAATATTCTTGAATCT TGACCATTACATCTGATCAGAAAATCCAATTGTAAGTTGAGAGAGGTTCATTACCCTGGCCAGT GGGAATGTAAGTGAAAAACCAGTATATAGTTGTATCATCACAAGGGAGGAAACCTGATCGAACC CCTTTGCCAAATAACAGCAGGAACTTGGAGCCAAAGCCATGATTAACCTTAAAATCCGCATAAC CCCGAATAGCTGATCGGCCGGCAAAAGCTGGCTTCTTGAAGCCTATAAATCTTGCCACCACTGA GTTCACCCCATCACAACCAATCAATACCTTCCATAGACATTGAAATTCGCTGGCTTAGAAATAT TTCCCCCACACACACACGCATATATAAATATATAAACATAGAAACACTGGACTCAGTAGAATTC TTTCATACTCCACGGTATTAGTACTGAAATAATAGCCACCAAAAAAGTGCAGTGATTTCTATAC CTTGGTTTTGATGATGGTATCATCAGCAAGATGAACCAGCTTTAAGTAGCCTGATTCCTCAATA GAAACCACCTTGGAGGAGTACCTTATGGTACCATCTGGGAGTTCTTTTTCAAGGGCTTCCAGCA ACAATTTTCTTCTCACACAACGAACCTCATGGTCTCCACTGTACACCAAATTAAAGGGCCGATT ACTAAAATTCACCATCAAATACATGGCATACAAAATTAATGAATATATATGTTTACACTGAATC CTCATGGCTAGTGTCCGATTACTTACATAGTCCCTTTGACCTTAAAAGATGTCTGTCTGCCAGG TTTGCTCACAACAGTAGAGCTAGCAACTAATCTGCAGTCAAATGATCCCTTCATATTAGCTTCA TAGAACCAAAGTCAGGGTCAAATTAACAAGTTTCTACATGTAAATGCTATATTAAGGGCCTTTC TATCTCAGATTTGACATGCTCCAGTAGTAGAAAGACAATTTTGGGAGTTGAAGCCAACAAAGTA ACTAGTGAAATGGGATGATGACAAGAAGTTAAACGGCTAGTTATATACCCTTCGAGGAATCCAT GTTGTTGTCGGAGAGAGTGACCTATACCAACAGCATCTAATGCCCTCCAAGCATTAGTCCATGT TGTGAAAGCAAATCCTGTGACCCTCAAACCGGCTGATGATTCCAACACTAGGCTTCGAATTCCA AGCCTACAATTGAATACTCGCAGGTCAAGTTTAACATGGTAATATTTGTTACACGCGTATAATT AATCTAGTACGTACCTGTGAAGCCCTAAAGATGTTGTAAGTCCAGCTATTCCAGCTCCTACAAT CACCACTTCTTCAACTAATTCCATAATATTGGAATTAATTCCTCTAGTTAGTACTAAAGAACTT GGTTTTGTTATGAGAATGGATATGAAGTTTGTTCAAGCTAGAAAGATTGGCTAGAAGAGTAGAA ATGTAAGGCTATAAATGATGAGATGGGTAATATAAAAAGCAACTATCATCCAAGATGACTATGG CTTTGACGACGACGATCATTATTATGACATCTATGGTTTGGTCCGAGAAGGAGGCAGGTCGGAT TTAATTTAATTTATTTAAAAAAAATAAATTGAATTCCACCTTTTTTATATGAGGTCTTTTTTTT TTTTTTCAATAAGATCATCAAGAATATCTTCAAATTAGTTTATATTTCGTTATATTTTTCAAAT TTAAAAGGTTAATAAAAATTTTATTTTTAACTACCAAAAATGTTTTTGATGTTATAAAGAAGAA ACAAATCATAACTAGAGTAGGTGTAACTTTATAATTGCTTTAATAATTGACGAAACTCTTCATT AACTATGGGTTTAAAAAGGGATACAAAACCAGTAATAATGAAATTGCTTGTTTGTTTTTGTATT TTAAAAATATTTTAAAAAAAATTAAAATTTTTTTTATTTTAAATTAATATTTTCTATGTTTTCA AATCATTTTAATTCATTAATATCAAAAATAATTTTTTAAAAATAAAAAAATAATTTTTTAATAT TTTTTAAAATAAAAAACATTTTAAAAACAATAACAATTAAATTCTCAAACACCCACAATAATTG CATCCATCTCTCAAGAAGTTTATTATTTGCCCCTGACTTTGTTGAATAGCACCAACCACGTAAG CAGTCCTTATTAGCTCAAAACTCCTCTCTTTTGCACATTTTTTTCAATCCTCTTATACTCTTCC TTATCTTTGTCCTTCGTTTCCGCACTCACTTTTTTGTTCAAGGCCTCGGCCAGGCACCTTGCTA AGACAACTCCATCTTCTAAAGCAGAGCACCCACCTTGACCAATATCTGGAGTCATGGGATGTAG AGCATCACCAGCAACACAAGCATTGCCTCTGCTTATATTTCCCCATAGCACCTCCCATGGATGC CTATACCTTAAAGGAGTCAGTGATCTCGACGAAAGATCTTACCTGGTCAGGCACAATATTTACA AGGTTGCTCAGTGCAAGTTGTTTCATCTTGGCTGGATTATCCTTTAACTCTTTATTATCTGCAA GAAAAAATGAATTTGTGCAAATAGCGAAAGTGAGAAGACAGATGTTGTGTGTTATAGCCTAAAT CCTCGACTGAAACCACCTTGGAGGAGTACCTTATGGTACCAATTGGGAGTTCTTTTTCAAGGGC TTCCAACAACAATTTCTAACACTAGACTTCGAATTCCAAGCCTACAATTAGTCAGAGCAGTCGT ATACAATTAATCTGCCTAGTTAATTACATTTATGAAGATATTATTCTTGAGTTTATTTATGTAA TTAGTTCAAGTTTTACAGAATTTAGAGCTACTGAAAACTTACATGATCGTTCATTTTAGGATCC ATAAAATTAATCGAAGTACACATAAACTGGTTCAAACACTCGTATTAATCTAAAAAAAAAAATT CTTACTCTTAGTAATGATGTGATTACCTGTGAAGGCCTAATGATGTTGCAAGTCCAGCAATTCC AGCTTCAACTATCATAACATTTTCAATCACCTCATGATATTTTTGGCCTTCCAAATACCACTAC TCCAGCACTAGTAGAATTGGTTGTGCTAAGAGGAAAAAAAAAAAGTGGACGGATTCAAGTGATG AAGACGATCGAAAAGAGTAGTTGATGCCCATAAAGATATGATACGACAACCATGATGAAAGGTG GCTGCTTGTCTAAATCTGATGATCATCACATGAGTATTATGACGGCAGCAAATACGTATTGTCT TGAACTAGGCTTAAAGTCGGATCATAAGTTTCGTGTAAAGCTTGAAGCCTACTGACTTTTTAAG AGTTTGATAGCGGTGTAAATTTTTTTAAAATTTTTATTTTATTTTTTTATATTGTTTTAATTTA TTAACATTAAAAATACTGTTCATACCAACTTGATCTTGATGTGATATATTAACATGCTACAATA CAAAGAAAAAGGACTAGCTCCTCTTATATTATTTGTCTCTTGGAAGAGAAATATGTCATGATAG TAAAAAGGACTAGCTCCTCTTATAGCTTGTATATTGAACTATACGGATTGCATTAACAAACGTA ATGGATGAAGAACATAATACAATTATTGAATCCAACATAAATAAAAAGGCTTATCTTTATTTCG AAGCTTACCGATTGCATCAAGAAAAATTACAAAAAGAAAAACACGGCAGGATCTTAATTCATAA TAAGAGATTTTACGGATTACAAGGACAAGAGCAGGATCAAGAAATATTGAGCTTTCCACAATCA AAATCAGCTTTCTTTAGTAGCAATCCAGCAAGAAATTTAGCCAAAAATGCATCTCTCAAGATGT TCATTATTTTTCCATCACCTTGTTGTATAGCACCAACAATATAAGCAGTGCTTATGAGCTCAAA ACTTCTCCATCTCCTCTCCGCTGCGTATTTTTTCAACCCCATTTCAACCCTCTTGTATTCTTCT CTCTCTTTCTCTTTACCTTCCACATTTAACTCCTTCTTCAAGGCCTCGGCGAGGCACCTAGCTA GAACAACACCATCTTCTAAAGCAGCACACCCACCCTGGCCAATATCTGGTGTCATGGGATGGAG AGCATCACCCGCTACACTAACATTGCCTTTACTTATATTTCCCCATAGAACCTCCCATGGATGC CTAAACCTTAAAGGAGATGATGTGATGCTATCTAGCTCAGTGATTTCCACAGATGTCCTCGCGT GATCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.093175559

Conservation Information
Conserved circRNAs	NA
PMCS	0.093175559

			
						 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_0004s18290_circ_ag.1

Address

Any questions?

Supported by