Plant Circular RNA Database

Detail information of POPTR_0016s03290_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0016s03290_circ_g.1
					
						ID in PlantcircBase
						pop_circ_003827
					
						Alias
						Chr16:1886899-1888221
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr16: 1687236-1688558  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0016s03290						
					
						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_0016s03290.1:4

General Information
CircRNA Name	POPTR_0016s03290_circ_g.1
ID in PlantcircBase	pop_circ_003827
Alias	Chr16:1886899-1888221
Organism	Populus trichocarpa
Position	chr16: 1687236-1688558 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0016s03290
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_0016s03290.1:4

			
						 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  
						
							GGGCCTCTCCAATCCTTTGCACAACTGCTCTGGCACTTTCAATTTCAGCACAAGCAAAAGATTT
CTCTTGGTTCACTAACTTTTTAGCATCTTCAGAAGCctgaaataacttcattttggctgtcttc
agatgatacacggtaccactgaactgaacacttggaaaggggtggagaactatctgaacgaggc
ttgagttg

									
								

					

						Assembled circRNA sequence  
						
							Yes
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
						
							Transcript length: 481
Transcript exons: 1687236-1687416,1687647-1687730,1687948-1688016,1688412-
1688558
CTGAAATAACTTCATTTTGGCTGTCTTCAGATGATACACGGTACCACTGAACTGAACACTTGGA
AAGGGGTGGAGAACTATCTGAACGAGGCTTGAGTTGTAGAGATGAACCTAGAGTTTCAGAACCA
TCTAGGACATATGGAGCAGATTTATTTTGCTCAGCTCTCTTGCTCTTTGCCAGCTCTTTCTGAA
GTTTAACTGAAACTAGAGATTTCTCCCGAATTTGATTTCGTAGAGCACGAAGCTCATGCTCCAT
GTCTATAACCTTGCTTGGCTGATGCAATAATTTAATTCGTCTAGCCTCCTGAACCTCCTCGACT
AGTTCCTCCACATCAGCAGCCTGGTTTTTTGAATTTTGAGCGTCCCTTTCTTCTTCATCCAGGG
CCTCTCCAATCCTTTGCACAACTGCTCTGGCACTTTCAATTTCAGCACAAGCAAAAGATTTCTC
TTGGTTCACTAACTTTTTAGCATCTTCAGAAGC"
						
					

						Genomic sequence
						
							CTGAAATAACTTCATTTTGGCTGTCTTCAGATGATACACGGTACCACTGAACTGAACACTTGGA
AAGGGGTGGAGAACTATCTGAACGAGGCTTGAGTTGTAGAGATGAACCTAGAGTTTCAGAACCA
TCTAGGACATATGGAGCAGATTTATTTTGCTCAGCTCTCTTGCTCTTTGCCAGCTATAAAGGAA
AAGGAAACCATGCACACAATACACAAACTCAGTTTTCGATGATTTCAGTATCATGTTAGTATGG
AACAGGTGCTAATATTACACAACAAGTATGACATGAACTGAACATTTCAGCATTAAAAAATGTA
TAAGAAGAAAATTATATCATATCAGCCAAAGCAAATGGTGTGAAAGAAATTGTTTTCATGAGAA
ATAAGTTTATGACAACATTAAACAAACCTCTTTCTGAAGTTTAACTGAAACTAGAGATTTCTCC
CGAATTTGATTTCGTAGAGCACGAAGCTCATGCTCCATGTCTATAACCTGCAAAAGCGTTATAT
GCTTTATAGTCAATAAAATATTGTTAAATAAATCCATTACACTGTCACAACTGAATAATCTGAG
CCATGTGCATAAAATGTGGCTAGAGGAAAGAACACGAGGCTAATATTAAATTACCATCAATAGA
TCCCTGTAATAATAAAACAGATCCATCAATATCCTATCTGCTATCACGGGTGAATAGAGAAAAA
TAATGTACCTTGCTTGGCTGATGCAATAATTTAATTCGTCTAGCCTCCTGAACCTCCTCGACTA
GTTCCTCCACATCCTGCAGTAGAAAGCATGTAAATGGATATTTTCATGGCATAATCAATAGTCA
TCTCATGTTCCTATTGATATTGCAGACCTTGTACTTGTATGGTTATAAACAATCGATAGTCATC
TCATGTTCCAATTGATATTGCAGACCTTGTACTTGTATGGTTATATGCAAAATGTTATAGTTGT
AGCTGTATTATAAAGATGATATAGCTAAGCTTCCAGAGGAAAGGTATATTAAATTATCAGATAT
GCATGATAAATTCCAGCATTGTAGTGAACAAAATTATGCAAAATCATGTTTACGTGAAGAATAC
TCAATTTTCACAACAAGGCAGTACAGTTTAGTGTGTTGGGGTGCAACATATAGTTTAATAGAAG
ACATTTAATGATGAAAGAACTCACAGCAGCCTGGTTTTTTGAATTTTGAGCGTCCCTTTCTTCT
TCATCCAGGGCCTCTCCAATCCTTTGCACAACTGCTCTGGCACTTTCAATTTCAGCACAAGCAA
AAGATTTCTCTTGGTTCACTAACTTTTTAGCATCTTCAGAAGC
						
					

			
		

Sequences
Splice junction sequence	GGGCCTCTCCAATCCTTTGCACAACTGCTCTGGCACTTTCAATTTCAGCACAAGCAAAAGATTT CTCTTGGTTCACTAACTTTTTAGCATCTTCAGAAGCctgaaataacttcattttggctgtcttc agatgatacacggtaccactgaactgaacacttggaaaggggtggagaactatctgaacgaggc ttgagttg
Assembled circRNA sequence	Yes 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	Transcript length: 481 Transcript exons: 1687236-1687416,1687647-1687730,1687948-1688016,1688412- 1688558 CTGAAATAACTTCATTTTGGCTGTCTTCAGATGATACACGGTACCACTGAACTGAACACTTGGA AAGGGGTGGAGAACTATCTGAACGAGGCTTGAGTTGTAGAGATGAACCTAGAGTTTCAGAACCA TCTAGGACATATGGAGCAGATTTATTTTGCTCAGCTCTCTTGCTCTTTGCCAGCTCTTTCTGAA GTTTAACTGAAACTAGAGATTTCTCCCGAATTTGATTTCGTAGAGCACGAAGCTCATGCTCCAT GTCTATAACCTTGCTTGGCTGATGCAATAATTTAATTCGTCTAGCCTCCTGAACCTCCTCGACT AGTTCCTCCACATCAGCAGCCTGGTTTTTTGAATTTTGAGCGTCCCTTTCTTCTTCATCCAGGG CCTCTCCAATCCTTTGCACAACTGCTCTGGCACTTTCAATTTCAGCACAAGCAAAAGATTTCTC TTGGTTCACTAACTTTTTAGCATCTTCAGAAGC"
Genomic sequence	CTGAAATAACTTCATTTTGGCTGTCTTCAGATGATACACGGTACCACTGAACTGAACACTTGGA AAGGGGTGGAGAACTATCTGAACGAGGCTTGAGTTGTAGAGATGAACCTAGAGTTTCAGAACCA TCTAGGACATATGGAGCAGATTTATTTTGCTCAGCTCTCTTGCTCTTTGCCAGCTATAAAGGAA AAGGAAACCATGCACACAATACACAAACTCAGTTTTCGATGATTTCAGTATCATGTTAGTATGG AACAGGTGCTAATATTACACAACAAGTATGACATGAACTGAACATTTCAGCATTAAAAAATGTA TAAGAAGAAAATTATATCATATCAGCCAAAGCAAATGGTGTGAAAGAAATTGTTTTCATGAGAA ATAAGTTTATGACAACATTAAACAAACCTCTTTCTGAAGTTTAACTGAAACTAGAGATTTCTCC CGAATTTGATTTCGTAGAGCACGAAGCTCATGCTCCATGTCTATAACCTGCAAAAGCGTTATAT GCTTTATAGTCAATAAAATATTGTTAAATAAATCCATTACACTGTCACAACTGAATAATCTGAG CCATGTGCATAAAATGTGGCTAGAGGAAAGAACACGAGGCTAATATTAAATTACCATCAATAGA TCCCTGTAATAATAAAACAGATCCATCAATATCCTATCTGCTATCACGGGTGAATAGAGAAAAA TAATGTACCTTGCTTGGCTGATGCAATAATTTAATTCGTCTAGCCTCCTGAACCTCCTCGACTA GTTCCTCCACATCCTGCAGTAGAAAGCATGTAAATGGATATTTTCATGGCATAATCAATAGTCA TCTCATGTTCCTATTGATATTGCAGACCTTGTACTTGTATGGTTATAAACAATCGATAGTCATC TCATGTTCCAATTGATATTGCAGACCTTGTACTTGTATGGTTATATGCAAAATGTTATAGTTGT AGCTGTATTATAAAGATGATATAGCTAAGCTTCCAGAGGAAAGGTATATTAAATTATCAGATAT GCATGATAAATTCCAGCATTGTAGTGAACAAAATTATGCAAAATCATGTTTACGTGAAGAATAC TCAATTTTCACAACAAGGCAGTACAGTTTAGTGTGTTGGGGTGCAACATATAGTTTAATAGAAG ACATTTAATGATGAAAGAACTCACAGCAGCCTGGTTTTTTGAATTTTGAGCGTCCCTTTCTTCT TCATCCAGGGCCTCTCCAATCCTTTGCACAACTGCTCTGGCACTTTCAATTTCAGCACAAGCAA AAGATTTCTCTTGGTTCACTAACTTTTTAGCATCTTCAGAAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.415970093

Conservation Information
Conserved circRNAs	NA
PMCS	0.415970093

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1687723-1688553(-)
1687252-1688553(-)
						
						Potential amino acid sequence
						
							MEHELRALRNQIREKSLVSVKLQKELAKSKRAEQNKSAPYVLDGSETLGSSLQLKPRSDSSPPL
SKCSVQWYRVSSEDSQNEVISGF*(-)
MKLFQASEDAKKLVNQEKSFACAEIESARAVVQRIGEALDEEERDAQNSKNQAADVEELVEEVQ
EARRIKLLHQPSKVIDMEHELRALRNQIREKSLVSVKLQKELAKSKRAEQNKSAPYVLDGSETL
GSSLQLKPRSDSSPPLSKCSVQWYRVSSEDSQNEVISGF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1687723-1688553(-) 1687252-1688553(-)
Potential amino acid sequence	MEHELRALRNQIREKSLVSVKLQKELAKSKRAEQNKSAPYVLDGSETLGSSLQLKPRSDSSPPL SKCSVQWYRVSSEDSQNEVISGF(-) MKLFQASEDAKKLVNQEKSFACAEIESARAVVQRIGEALDEEERDAQNSKNQAADVEELVEEVQ EARRIKLLHQPSKVIDMEHELRALRNQIREKSLVSVKLQKELAKSKRAEQNKSAPYVLDGSETL GSSLQLKPRSDSSPPLSKCSVQWYRVSSEDSQNEVISGF(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0016s03290_circ_g.1

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