Plant Circular RNA Database

Detail information of POPTR_0008s18260_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0008s18260_circ_g.1
					
						ID in PlantcircBase
						pop_circ_002425
					
						Alias
						Chr08:12420862|12422495
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr8: 12227608-12229241  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							POPTR_0008s18260						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						stem cambium
					
						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_0008s18260.1:2

General Information
CircRNA Name	POPTR_0008s18260_circ_g.1
ID in PlantcircBase	pop_circ_002425
Alias	Chr08:12420862\|12422495
Organism	Populus trichocarpa
Position	chr8: 12227608-12229241 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	find_circ
Parent gene	POPTR_0008s18260
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	NA
Support reads	NA
Tissues	stem cambium
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_0008s18260.1:2

			
						 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  
						
							TCACCGATTTCATAATCCTGACTCCTCGAAAGCTCAACCAACAGTTTTGCAATCTGATTGTCCA
CATCCATTTGCTCCAATATCGTAGCACCATCATTTGcttgcatttctgaaccatgacatcaaag
tactgctgctcttgcttgcgcaatgtttgaaacttttcaactgtatcaatgtccaccttatgtt
tagtcttt

									
								

					

						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: 668
Transcript exons: 12227608-12227956,12228923-12229241
CTTGCATTTCTGAACCATGACATCAAAGTACTGCTGCTCTTGCTTGCGCAATGTTTGAAACTTT
TCAACTGTATCAATGTCCACCTTATGTTTAGTCTTTGGCTTAGGTGGTTCAAAGGGGCACGTCA
GGATAGCAATTTTTGCATCTTCAATTTGCTTTGGCATCTGCGGATGACTCATTTCCTTGTCAAC
AAGTATCCCATATATTAGTTCAGTATCTTCCAACTTGCCTCCTACTTTCCCTTCAACTTTTATC
AAATCTAAATTAACATCTTTCCTCTCTAAATCCGCAACAGCAAGAACTGCTTTAACTGAAATCT
CTGCTAAACTGCGCTTGCACCGATTCACAATTTTGGAGGACAAAGTAGTCATGCAAGTTTGAAC
CAAGGGCTCCATATTATTAACTCCAAAATCATACTTCTGAGAGATCTTCTCCAAATGCTCCACA
GCAATTCTAGAAGCAGTCTCATAACCCTCAGCAACACGAATAGGGTGAATCCCGCGCTCCAAAA
GCTTCTGAGACTGCTCTAAAAGAGCACCAGCCAAAACAACAACACCAGTAGTCCCATCACCGAT
TTCATAATCCTGACTCCTCGAAAGCTCAACCAACAGTTTTGCAATCTGATTGTCCACATCCATT
TGCTCCAATATCGTAGCACCATCATTTG"
						
					

						Genomic sequence
						
							CTTGCATTTCTGAACCATGACATCAAAGTACTGCTGCTCTTGCTTGCGCAATGTTTGAAACTTT
TCAACTGTATCAATGTCCACCTTATGTTTAGTCTTTGGCTTAGGTGGTTCAAAGGGGCACGTCA
GGATAGCAATTTTTGCATCTTCAATTTGCTTTGGCATCTGCGGATGACTCATTTCCTTGTCAAC
AAGTATCCCATATATTAGTTCAGTATCTTCCAACTTGCCTCCTACTTTCCCTTCAACTTTTATC
AAATCTAAATTAACATCTTTCCTCTCTAAATCCGCAACAGCAAGAACTGCTTTAACTGAAATCT
CTGCTAAACTGCGCTTGCACCGATTCACACTGCAAAACAAAGAGACATGTAATAATCACAGTGC
ATAGCATGTGTCTAGCAGTAAAGGCATTCAACTAGCACTCATCTTCCTAGCATGCCCAAATTCA
AAGTCAAAACACCTTTAATAGAGAATGGGAGTTCCCAGAATGTAAATGGGTTGATTCAACTACT
CAAAAATCCAGTTAATGCACAGCTGTACACTCATCTTTCCAATCCCTAATTTGATACCAAAACC
ACAGACCTCAGTGGAGATTTAAAGTTGAAAAACCCTAAACTCAGCTATGACAGTGCTCCATACA
TGTGCATGAGGAAAGAAAACCTAAAGACAGCTTAGAATATTTATGGAAAAGGGAAACATAAATA
GGTGTGAAAAACTATGAAGATTTATATATGGCAATTATCATTACTACAAAACTAGGAATATTTA
TGAATCATCTGGACAGTCATCGCACTACATCCGCATACTAAAAACAACTACTCTTTGCTTATGG
TGACACATGCTAAAACATCTCGTCTTGTGACTTTGGTTTGCCATATTTTCAGTTTTCCATGGTC
TCTATGAGATGATTTAGGCATTTAGAGCAGTGCCTATAAAAATAAAAAAATCATCCTTTCTAAG
CATATTTGCAGTTTGAAGTTTGATAGAGTTATTAACAGGCAGCAGAGGAAACACACAAAAAGGT
ATTCTAGATAAGATCCAAGCTACTAGCATAAAATTATAAGACTCTGTATCGTGGTGCAGAGCCA
AAGGTTCATTAAGAAACTTGTGGTTTATAATAGATTACATCACCGGATACACAAATGTACTGAA
TTGCACATACACGCAAGAAATTTAAGAAATACGTATGCACAAAGAGAAACAGTCTAGTGTAGCA
ATAACATAACATAAACAACAATAAAGAAGAAACAATGAACATAACAGCAAATCGTTTGACAAGT
GCAATACCACAAAAACAGAGCAGAACCAAACTTACATTTTGGAGGACAAAGTAGTCATGCAAGT
TTGAACCAAGGGCTCCATATTATTAACTCCAAAATCATACTTCTGAGAGATCTTCTCCAAATGC
TCCACAGCAATTCTAGAAGCAGTCTCATAACCCTCAGCAACACGAATAGGGTGAATCCCGCGCT
CCAAAAGCTTCTGAGACTGCTCTAAAAGAGCACCAGCCAAAACAACAACACCAGTAGTCCCATC
ACCGATTTCATAATCCTGACTCCTCGAAAGCTCAACCAACAGTTTTGCAATCTGATTGTCCACA
TCCATTTGCTCCAATATCGTAGCACCATCATTTG
						
					

			
		

Sequences
Splice junction sequence	TCACCGATTTCATAATCCTGACTCCTCGAAAGCTCAACCAACAGTTTTGCAATCTGATTGTCCA CATCCATTTGCTCCAATATCGTAGCACCATCATTTGcttgcatttctgaaccatgacatcaaag tactgctgctcttgcttgcgcaatgtttgaaacttttcaactgtatcaatgtccaccttatgtt tagtcttt
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: 668 Transcript exons: 12227608-12227956,12228923-12229241 CTTGCATTTCTGAACCATGACATCAAAGTACTGCTGCTCTTGCTTGCGCAATGTTTGAAACTTT TCAACTGTATCAATGTCCACCTTATGTTTAGTCTTTGGCTTAGGTGGTTCAAAGGGGCACGTCA GGATAGCAATTTTTGCATCTTCAATTTGCTTTGGCATCTGCGGATGACTCATTTCCTTGTCAAC AAGTATCCCATATATTAGTTCAGTATCTTCCAACTTGCCTCCTACTTTCCCTTCAACTTTTATC AAATCTAAATTAACATCTTTCCTCTCTAAATCCGCAACAGCAAGAACTGCTTTAACTGAAATCT CTGCTAAACTGCGCTTGCACCGATTCACAATTTTGGAGGACAAAGTAGTCATGCAAGTTTGAAC CAAGGGCTCCATATTATTAACTCCAAAATCATACTTCTGAGAGATCTTCTCCAAATGCTCCACA GCAATTCTAGAAGCAGTCTCATAACCCTCAGCAACACGAATAGGGTGAATCCCGCGCTCCAAAA GCTTCTGAGACTGCTCTAAAAGAGCACCAGCCAAAACAACAACACCAGTAGTCCCATCACCGAT TTCATAATCCTGACTCCTCGAAAGCTCAACCAACAGTTTTGCAATCTGATTGTCCACATCCATT TGCTCCAATATCGTAGCACCATCATTTG"
Genomic sequence	CTTGCATTTCTGAACCATGACATCAAAGTACTGCTGCTCTTGCTTGCGCAATGTTTGAAACTTT TCAACTGTATCAATGTCCACCTTATGTTTAGTCTTTGGCTTAGGTGGTTCAAAGGGGCACGTCA GGATAGCAATTTTTGCATCTTCAATTTGCTTTGGCATCTGCGGATGACTCATTTCCTTGTCAAC AAGTATCCCATATATTAGTTCAGTATCTTCCAACTTGCCTCCTACTTTCCCTTCAACTTTTATC AAATCTAAATTAACATCTTTCCTCTCTAAATCCGCAACAGCAAGAACTGCTTTAACTGAAATCT CTGCTAAACTGCGCTTGCACCGATTCACACTGCAAAACAAAGAGACATGTAATAATCACAGTGC ATAGCATGTGTCTAGCAGTAAAGGCATTCAACTAGCACTCATCTTCCTAGCATGCCCAAATTCA AAGTCAAAACACCTTTAATAGAGAATGGGAGTTCCCAGAATGTAAATGGGTTGATTCAACTACT CAAAAATCCAGTTAATGCACAGCTGTACACTCATCTTTCCAATCCCTAATTTGATACCAAAACC ACAGACCTCAGTGGAGATTTAAAGTTGAAAAACCCTAAACTCAGCTATGACAGTGCTCCATACA TGTGCATGAGGAAAGAAAACCTAAAGACAGCTTAGAATATTTATGGAAAAGGGAAACATAAATA GGTGTGAAAAACTATGAAGATTTATATATGGCAATTATCATTACTACAAAACTAGGAATATTTA TGAATCATCTGGACAGTCATCGCACTACATCCGCATACTAAAAACAACTACTCTTTGCTTATGG TGACACATGCTAAAACATCTCGTCTTGTGACTTTGGTTTGCCATATTTTCAGTTTTCCATGGTC TCTATGAGATGATTTAGGCATTTAGAGCAGTGCCTATAAAAATAAAAAAATCATCCTTTCTAAG CATATTTGCAGTTTGAAGTTTGATAGAGTTATTAACAGGCAGCAGAGGAAACACACAAAAAGGT ATTCTAGATAAGATCCAAGCTACTAGCATAAAATTATAAGACTCTGTATCGTGGTGCAGAGCCA AAGGTTCATTAAGAAACTTGTGGTTTATAATAGATTACATCACCGGATACACAAATGTACTGAA TTGCACATACACGCAAGAAATTTAAGAAATACGTATGCACAAAGAGAAACAGTCTAGTGTAGCA ATAACATAACATAAACAACAATAAAGAAGAAACAATGAACATAACAGCAAATCGTTTGACAAGT GCAATACCACAAAAACAGAGCAGAACCAAACTTACATTTTGGAGGACAAAGTAGTCATGCAAGT TTGAACCAAGGGCTCCATATTATTAACTCCAAAATCATACTTCTGAGAGATCTTCTCCAAATGC TCCACAGCAATTCTAGAAGCAGTCTCATAACCCTCAGCAACACGAATAGGGTGAATCCCGCGCT CCAAAAGCTTCTGAGACTGCTCTAAAAGAGCACCAGCCAAAACAACAACACCAGTAGTCCCATC ACCGATTTCATAATCCTGACTCCTCGAAAGCTCAACCAACAGTTTTGCAATCTGATTGTCCACA TCCATTTGCTCCAATATCGTAGCACCATCATTTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_031162* 						
					
						PMCS
						0.547500765

Conservation Information
Conserved circRNAs	osa_circ_031162*
PMCS	0.547500765

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							12227616-12229103(-)
12229214-12229103(-)
						
						Potential amino acid sequence
						
							MQANDGATILEQMDVDNQIAKLLVELSRSQDYEIGDGTTGVVVLAGALLEQSQKLLERGIHPIR
VAEGYETASRIAVEHLEKISQKYDFGVNNMEPLVQTCMTTLSSKIVNRCKRSLAEISVKAVLAV
ADLERKDVNLDLIKVEGKVGGKLEDTELIYGILVDKEMSHPQMPKQIEDAKIAILTCPFEPPKP
KTKHKVDIDTVEKFQTLRKQEQQYFDVMVQKCKQMMVLRYWSKWMWTIRLQNCWLSFRGVRIMK
SVMGLLVLLFWLVLF*(-)
MDVDNQIAKLLVELSRSQDYEIGDGTTGVVVLAGALLEQSQKLLERGIHPIRVAEGYETASRIA
VEHLEKISQKYDFGVNNMEPLVQTCMTTLSSKIVNRCKRSLAEISVKAVLAVADLERKDVNLDL
IKVEGKVGGKLEDTELIYGILVDKEMSHPQMPKQIEDAKIAILTCPFEPPKPKTKHKVDIDTVE
KFQTLRKQEQQYFDVMVQKCKQMMVLRYWSKWMWTIRLQNCWLSFRGVRIMKSVMGLLVLLFWL
VLF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	12227616-12229103(-) 12229214-12229103(-)
Potential amino acid sequence	MQANDGATILEQMDVDNQIAKLLVELSRSQDYEIGDGTTGVVVLAGALLEQSQKLLERGIHPIR VAEGYETASRIAVEHLEKISQKYDFGVNNMEPLVQTCMTTLSSKIVNRCKRSLAEISVKAVLAV ADLERKDVNLDLIKVEGKVGGKLEDTELIYGILVDKEMSHPQMPKQIEDAKIAILTCPFEPPKP KTKHKVDIDTVEKFQTLRKQEQQYFDVMVQKCKQMMVLRYWSKWMWTIRLQNCWLSFRGVRIMK SVMGLLVLLFWLVLF(-) MDVDNQIAKLLVELSRSQDYEIGDGTTGVVVLAGALLEQSQKLLERGIHPIRVAEGYETASRIA VEHLEKISQKYDFGVNNMEPLVQTCMTTLSSKIVNRCKRSLAEISVKAVLAVADLERKDVNLDL IKVEGKVGGKLEDTELIYGILVDKEMSHPQMPKQIEDAKIAILTCPFEPPKPKTKHKVDIDTVE KFQTLRKQEQQYFDVMVQKCKQMMVLRYWSKWMWTIRLQNCWLSFRGVRIMKSVMGLLVLLFWL VLF(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zheng et al., 2020

circRNA

Detail information of POPTR_0008s18260_circ_g.1

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