Plant Circular RNA Database

Detail information of POPTR_0001s38490_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0001s38490_circ_g.1
					
						ID in PlantcircBase
						pop_circ_000431
					
						Alias
						Chr01:39114262-39116047
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr1: 37644836-37646621  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0001s38490						
					
						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  
						
							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_0001s38490.1:3

General Information
CircRNA Name	POPTR_0001s38490_circ_g.1
ID in PlantcircBase	pop_circ_000431
Alias	Chr01:39114262-39116047
Organism	Populus trichocarpa
Position	chr1: 37644836-37646621 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0001s38490
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	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_0001s38490.1:3

			
						 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  
						
							TGCACAGCGTGGGATCCAGCTGGTAGCCACCGCTCATGGAATCACAATAGAGAATTTGATATTG
AATCCTTCTCTGGAGATGCTTGTTGGAGGAATACAGgttggtgactttgctattgacaatcgag
caggcatcagccaaacattgcatcgcattagtgccataagaaatcgagagggccaaatcattgg
tcttactt

									
								

					

						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
						
							GTTGGTGACTTTGCTATTGACAATCGAGCAGGCATCAGCCAAACATTGCATCGCATTAGTGCCA
TAAGAAATCGAGAGGGCCAAATCATTGGTCTTACTTGTCGTGTTGGTCGGGCAATACCAGGCAG
TGCTAGTTTGCTGAGAGATTTAGTTCACGATGGTGCTTCCCTTTTGTTCATTGGTCCTCCAGGG
GTGGGAAAGACTACAATTATCAGGTTAGCTGTTCTTGATTTTATGGACATGATATGATTTCACA
CAAAAGCTTCTATTTTGTTCTAAATTGTTTTCTGCATCGAGTTGTTATGCATTAAAAGAAATGA
GCAATTGCCTATGTTGTAATTAGGTTGAGGAGTGTTTTGAGCACTGTAGTGAGCTACTGACTCT
TGATTATTGAAGGTTTTATTTAGAAGAAGAATAATGATTCTTATTTTATTTCACCTGAATCTAC
TTGCCTGCCTAATTAAAGTGGGCATGCTACTTTTAGATGTGAGACTTCGTTAATGAATTGTGTC
CTAAAAGTAAAAGGCGTTTCATGTTAGTTTGGCTTTAAACTATGTCAGAGTCCCATGTTATAAA
GAACCATGGTGCTCTACTTTAAGAGCAATGTATAATAGTTTTTGTTTTGGAAAATTTAGTATTC
TTCTATAGGTTTTTGCTTTCTTAAAATTCCCCCGGCTAACTTGTTTGTTTTTCTTATGCTTTTC
AATTTCTCAATGCCCCTTATTTCACCACTACTGTTGACTCAGACCATCTTTGCATTTGTTATTC
ATCCTTAAATATTTCTATGCAAATGTTTTGTTCCATTTCTGAAGACATCTAATATCCCGGGCGT
GGGAAAATAGATGAAGTCAAAATATGCTATCTTTCGCTTATATTTTGTAGCAGGAGAGAATTTT
CGTTGCTGAATTTATTATATGCTTAACAATGGTGTAAACCAGTCTTACTCAGGGATTTGAGTAC
CGAGTTTGCATCTGGGCTGTTCTAATAGTAGATTGTTGCTACTCTTGGTGCATCCATCATTCTT
TAGGGTGACCTAAAATCCTAAGTTTTGCAGGGAAATTGCTCGAATGCTTGCAAATGATTACAAG
AAACGAGTGATGATTGTTGATACATCCAATGAGATAGGAGGTGATGGTGATATACCTCATGCTG
GAATAGGCAATGCTCGACGGATGCAAGTTCCTGATTTAGATATGCAACATAAGGTATAGGCTGG
AAGTGTGTGATCTCCTTTATGGGCCTGTCTACAGTGCATCTGTTTTCATGAAACAAAGTTGACT
AGCTGAAGTTTGATAAGAAGTGTTGTTAATGACATTAATAGATATTTCAATTATAAAGTGACAT
GACTAGCATTAATTAAGCATATACGCATGTTATGCCCTTGGGAAATGAAATCTCTGAAGCATAT
AACACTACTGTTTAGTAATTGGCATATGATCATTGTACTACTACAATGAGCAATGCATGCCATT
TTTTTTAGTTTTGTTCACAACATGATTTTATTGTTTTTACTTCCTGATCCGGAGACCTAGATGC
GTTATTTTGTAATTTTATTGTCAGCGGGGGCAAATGCTTACAAGTTTCTAATGTTTAGGTATTA
ATAGAGGCAGTTGAAAATCATATGCCTCAAGTGATTGTGATAGATGAAATTGGGACAAAACTTG
AAGCAATGGCTGCAAGTACAATTGCACAGCGTGGGATCCAGCTGGTAGCCACCGCTCATGGAAT
CACAATAGAGAATTTGATATTGAATCCTTCTCTGGAGATGCTTGTTGGAGGAATACAG
						
					

			
		

Sequences
Splice junction sequence	TGCACAGCGTGGGATCCAGCTGGTAGCCACCGCTCATGGAATCACAATAGAGAATTTGATATTG AATCCTTCTCTGGAGATGCTTGTTGGAGGAATACAGgttggtgactttgctattgacaatcgag caggcatcagccaaacattgcatcgcattagtgccataagaaatcgagagggccaaatcattgg tcttactt
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	GTTGGTGACTTTGCTATTGACAATCGAGCAGGCATCAGCCAAACATTGCATCGCATTAGTGCCA TAAGAAATCGAGAGGGCCAAATCATTGGTCTTACTTGTCGTGTTGGTCGGGCAATACCAGGCAG TGCTAGTTTGCTGAGAGATTTAGTTCACGATGGTGCTTCCCTTTTGTTCATTGGTCCTCCAGGG GTGGGAAAGACTACAATTATCAGGTTAGCTGTTCTTGATTTTATGGACATGATATGATTTCACA CAAAAGCTTCTATTTTGTTCTAAATTGTTTTCTGCATCGAGTTGTTATGCATTAAAAGAAATGA GCAATTGCCTATGTTGTAATTAGGTTGAGGAGTGTTTTGAGCACTGTAGTGAGCTACTGACTCT TGATTATTGAAGGTTTTATTTAGAAGAAGAATAATGATTCTTATTTTATTTCACCTGAATCTAC TTGCCTGCCTAATTAAAGTGGGCATGCTACTTTTAGATGTGAGACTTCGTTAATGAATTGTGTC CTAAAAGTAAAAGGCGTTTCATGTTAGTTTGGCTTTAAACTATGTCAGAGTCCCATGTTATAAA GAACCATGGTGCTCTACTTTAAGAGCAATGTATAATAGTTTTTGTTTTGGAAAATTTAGTATTC TTCTATAGGTTTTTGCTTTCTTAAAATTCCCCCGGCTAACTTGTTTGTTTTTCTTATGCTTTTC AATTTCTCAATGCCCCTTATTTCACCACTACTGTTGACTCAGACCATCTTTGCATTTGTTATTC ATCCTTAAATATTTCTATGCAAATGTTTTGTTCCATTTCTGAAGACATCTAATATCCCGGGCGT GGGAAAATAGATGAAGTCAAAATATGCTATCTTTCGCTTATATTTTGTAGCAGGAGAGAATTTT CGTTGCTGAATTTATTATATGCTTAACAATGGTGTAAACCAGTCTTACTCAGGGATTTGAGTAC CGAGTTTGCATCTGGGCTGTTCTAATAGTAGATTGTTGCTACTCTTGGTGCATCCATCATTCTT TAGGGTGACCTAAAATCCTAAGTTTTGCAGGGAAATTGCTCGAATGCTTGCAAATGATTACAAG AAACGAGTGATGATTGTTGATACATCCAATGAGATAGGAGGTGATGGTGATATACCTCATGCTG GAATAGGCAATGCTCGACGGATGCAAGTTCCTGATTTAGATATGCAACATAAGGTATAGGCTGG AAGTGTGTGATCTCCTTTATGGGCCTGTCTACAGTGCATCTGTTTTCATGAAACAAAGTTGACT AGCTGAAGTTTGATAAGAAGTGTTGTTAATGACATTAATAGATATTTCAATTATAAAGTGACAT GACTAGCATTAATTAAGCATATACGCATGTTATGCCCTTGGGAAATGAAATCTCTGAAGCATAT AACACTACTGTTTAGTAATTGGCATATGATCATTGTACTACTACAATGAGCAATGCATGCCATT TTTTTTAGTTTTGTTCACAACATGATTTTATTGTTTTTACTTCCTGATCCGGAGACCTAGATGC GTTATTTTGTAATTTTATTGTCAGCGGGGGCAAATGCTTACAAGTTTCTAATGTTTAGGTATTA ATAGAGGCAGTTGAAAATCATATGCCTCAAGTGATTGTGATAGATGAAATTGGGACAAAACTTG AAGCAATGGCTGCAAGTACAATTGCACAGCGTGGGATCCAGCTGGTAGCCACCGCTCATGGAAT CACAATAGAGAATTTGATATTGAATCCTTCTCTGGAGATGCTTGTTGGAGGAATACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.144981915

Conservation Information
Conserved circRNAs	NA
PMCS	0.144981915

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							37645904-37646618(+)
37644888-37646435(-)
37644926-37646557(-)
						
						Potential amino acid sequence
						
							MLANDYKKRVMIVDTSNEIGGDGDIPHAGIGNARRMQVPDLDMQHKVLIEAVENHMPQVIVIDE
IGTKLEAMAASTIAQRGIQLVATAHGITIENLILNPSLEMLVGGIQVGDFAIDNRAGISQTLHR
ISAIRNREGQIIGLTCRVGRAIPGSASLLRDLVHDGASLLFIGPPGVGKTTIIREIARMLANDY
KKRVMIVDTSNEIGGDGDIPHAGIGNARRMQVPDLDMQHKVLIEAVENHMPQVIVIDEIGTKLE
AMAASTIAQRGIQLVATAHGITIENLILNPSLEMLVGGIQVGDFAIDNRAGISQTLHRISAIRN
REGQIIGLTCRVGRAIPGSASLLRDLVHDGASLLFIGPPGVGKTTIIREIARMLANDYKKRVMI
VDTSNEIGGDGDIPHAGIGNARRMQVPDLDMQHKVLIEAVENHMPQVIVIDEIGTKLEAMAAST
IAQRGIQLVATAHGITIENLILNPSLEMLVGGIQVGDFAIDNRAGISQTLHRISAIRNREGQII
GLTCRVGRAIPGSASLLRDLVHDGASLLFIGPPGVGKTTIIREIARMLANDYKKRVMIVDTSNE
IGGDGDIPHAGIGNARRMQVPDLDMQHKVLIEAVENHMPQVIVIDEIGTKLEAMAASTIAQRGI
QLVATAHGITIENLILNPSLEMLVGGIQ(+)
MQCLADACSIVNSKVTNLYSSNKHLQRRIQYQILYCDSMSGGYQLDPTLCNCTCSHCFKFCPNF
IYHNHLRHMIFNCLY*(-)
MIWPSRFLMALMRCNVWLMPARLSIAKSPTCIPPTSISREGFNIKFSIVIP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	37645904-37646618(+) 37644888-37646435(-) 37644926-37646557(-)
Potential amino acid sequence	MLANDYKKRVMIVDTSNEIGGDGDIPHAGIGNARRMQVPDLDMQHKVLIEAVENHMPQVIVIDE IGTKLEAMAASTIAQRGIQLVATAHGITIENLILNPSLEMLVGGIQVGDFAIDNRAGISQTLHR ISAIRNREGQIIGLTCRVGRAIPGSASLLRDLVHDGASLLFIGPPGVGKTTIIREIARMLANDY KKRVMIVDTSNEIGGDGDIPHAGIGNARRMQVPDLDMQHKVLIEAVENHMPQVIVIDEIGTKLE AMAASTIAQRGIQLVATAHGITIENLILNPSLEMLVGGIQVGDFAIDNRAGISQTLHRISAIRN REGQIIGLTCRVGRAIPGSASLLRDLVHDGASLLFIGPPGVGKTTIIREIARMLANDYKKRVMI VDTSNEIGGDGDIPHAGIGNARRMQVPDLDMQHKVLIEAVENHMPQVIVIDEIGTKLEAMAAST IAQRGIQLVATAHGITIENLILNPSLEMLVGGIQVGDFAIDNRAGISQTLHRISAIRNREGQII GLTCRVGRAIPGSASLLRDLVHDGASLLFIGPPGVGKTTIIREIARMLANDYKKRVMIVDTSNE IGGDGDIPHAGIGNARRMQVPDLDMQHKVLIEAVENHMPQVIVIDEIGTKLEAMAASTIAQRGI QLVATAHGITIENLILNPSLEMLVGGIQ(+) MQCLADACSIVNSKVTNLYSSNKHLQRRIQYQILYCDSMSGGYQLDPTLCNCTCSHCFKFCPNF IYHNHLRHMIFNCLY(-) MIWPSRFLMALMRCNVWLMPARLSIAKSPTCIPPTSISREGFNIKFSIVIP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0001s38490_circ_g.1

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