Plant Circular RNA Database

Detail information of POPTR_0004s23690_circ_g.2

			
						 General Information
					
						CircRNA Name
						POPTR_0004s23690_circ_g.2
					
						ID in PlantcircBase
						pop_circ_001432
					
						Alias
						Chr04:23325007-23330230
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr4: 22322677-22327900  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0004s23690						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							POPTR_0004s23690_circ_g.1 POPTR_0004s23690_circ_g.3 						
					
						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_0004s23690.2:11
POPTR_0004s23690.1:11

General Information
CircRNA Name	POPTR_0004s23690_circ_g.2
ID in PlantcircBase	pop_circ_001432
Alias	Chr04:23325007-23330230
Organism	Populus trichocarpa
Position	chr4: 22322677-22327900 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0004s23690
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	POPTR_0004s23690_circ_g.1 POPTR_0004s23690_circ_g.3
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_0004s23690.2:11 POPTR_0004s23690.1:11

			
						 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  
						
							TTTCTTTTCCGGCAGGGCTTATATTATTTAACTTTTGTTGCAGCTTGGTTACACCAAAAAGCAA
GAAGAAAGACACTTCCGTGGGGTTATTACTTTGGAGatcagtgattatgttcagcacaatgatg
ctattctgctagttgtaatacctgctactcaggcaccagaaatttcttcttctagagccctcag
aatcgcaa

						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
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	TTTCTTTTCCGGCAGGGCTTATATTATTTAACTTTTGTTGCAGCTTGGTTACACCAAAAAGCAA GAAGAAAGACACTTCCGTGGGGTTATTACTTTGGAGatcagtgattatgttcagcacaatgatg ctattctgctagttgtaatacctgctactcaggcaccagaaatttcttcttctagagccctcag aatcgcaa
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	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.1198125

Conservation Information
Conserved circRNAs	NA
PMCS	0.1198125

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							22323213-22327897(+)
22327347-22322713(+)
						
					

						Potential amino acid sequence
						
							MKLRLPNLLSGLQGKSQIVQDELVGLGEQMVSSSEGTRALALELCREFEDKFLLHLMGGEGNGW
KVVASFEGNFPNRIKQLPLDRHFDINNVKRIVLEADGYQPYLISPEKGLRSLIKGVLELAKEPS
KLCVDEVHRVLVDIVSSAANATPGLGRYPPFKREVVAIASSALDGFKNEAKKMVVALVDMERAF
VPPQHFIRLVQRRMDRQRREDELKNKSSKKAVDAEQSILNRASVQQSGGSLKSMKDKSNQQDKD
AQEGSALKTAGPGGEITAGFLLKKSGKTNGWSKRWFVLNEKSGKLGYTKKQEERHFRGVITLEI
SDYVQHNDAILLVVIPATQAPEISSSRALRIAKEYDAESTRTVGVISKIDQAATESKALAAVQA
LLLNQGPPKTSDIPWVALIGQSVSIASAQSASAPENSLETAWRAESESLKSILTGAPPSKLGRV
ALVDALAGQIRSRMKLRLPNLLSGLQGKSQIVQDELVGLGEQMVSSSEGTRALALELCREFEDK
FLLHLMGGEGNGWKVVASFEGNFPNRIKQLPLDRHFDINNVKRIVLEADGYQPYLISPEKGLRS
LIKGVLELAKEPSKLCVDEVHRVLVDIVSSAANATPGLGRYPPFKREVVAIASSALDGFKNEAK
KMVVALVDMERAFVPPQHFIRLVQRRMDRQRREDELKNKSSKKAVDAEQSILNRASVQQSGGSL
KSMKDKSNQQDKDAQEGSALKTAGPGGEITAGFLLKKSGKTNGWSKRWFVLNEKSGKLGYTKKQ
EERHFRGVITLEISDYVQHNDAILLVVIPATQAPEISSSRALRIAKEYDAESTRTVGVISKIDQ
AATESKALAAVQALLLNQGPPKTSDIPWVALIGQSVSIASAQSASAPENSLETAWRAESESLKS
ILTGAPPSKLGRVALVDALAGQIRSRMKLRLPNLLSGLQGKSQIVQDELVGLGEQMVSSSEGTR
ALALELCREFEDKFLLHLMGGEGNGWKVVASFEGNFPNRIKQLPLDRHFDINNVKRIVLEADGY
QPYLISPEKGLRSLIKGVLELAKEPSKLCVDEVHRVLVDIVSSAANATPGLGRYPPFKREVVAI
ASSALDGFKNEAKKMVVALVDMERAFVPPQHFIRLVQRRMDRQRREDELKNKSSKKAVDAEQSI
LNRASVQQSGGSLKSMKDKSNQQDKDAQEGSALKTAGPGGEITAGFLLKKSGKTNGWSKRWFVL
NEKSGKLGYTKKQEERHFRGVITLEISDYVQHNDAILLVVIPATQAPEISSSRALRIAKEYDAE
STRTVGVISKIDQAATESKALAAVQALLLNQGPPKTSDIPWVALIGQSVSIASAQSASAPENSL
ETAWRAESESLKSILTGAPPSKLGRVALVDALAGQIRSRMKLRLPNLLSGLQGKSQIVQDELVG
LGEQMVSSSEGTRALALELCREFEDKFLLHLMGGEGNGWKVVASFEGNFPNRIKQLPLDRHFDI
NNVKRIVLEADGYQPYLISPEKGLRSLIKGVLELAKEPSKLCVDEVHRVLVDIVSSAANATPGL
GRYPPFKREVVAIASSALDGFKNEAKKMVVALVDMERAFVPPQHFIRLVQRRMDRQRREDELKN
KSSKKAVDAEQSILNRASVQQSGGSLKSMKDKSNQQDKDAQEGSALKTAGPGGEITAGFLLKKS
GKTNGWSKRWFVLNEKSGKLGYTKKQEERHFRGVITLE(+)
MKKVASLVTPKSKKKDTSVGLLLWRSVIMFSTMMLFC*(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	22323213-22327897(+) 22327347-22322713(+)
Potential amino acid sequence	MKLRLPNLLSGLQGKSQIVQDELVGLGEQMVSSSEGTRALALELCREFEDKFLLHLMGGEGNGW KVVASFEGNFPNRIKQLPLDRHFDINNVKRIVLEADGYQPYLISPEKGLRSLIKGVLELAKEPS KLCVDEVHRVLVDIVSSAANATPGLGRYPPFKREVVAIASSALDGFKNEAKKMVVALVDMERAF VPPQHFIRLVQRRMDRQRREDELKNKSSKKAVDAEQSILNRASVQQSGGSLKSMKDKSNQQDKD AQEGSALKTAGPGGEITAGFLLKKSGKTNGWSKRWFVLNEKSGKLGYTKKQEERHFRGVITLEI SDYVQHNDAILLVVIPATQAPEISSSRALRIAKEYDAESTRTVGVISKIDQAATESKALAAVQA LLLNQGPPKTSDIPWVALIGQSVSIASAQSASAPENSLETAWRAESESLKSILTGAPPSKLGRV ALVDALAGQIRSRMKLRLPNLLSGLQGKSQIVQDELVGLGEQMVSSSEGTRALALELCREFEDK FLLHLMGGEGNGWKVVASFEGNFPNRIKQLPLDRHFDINNVKRIVLEADGYQPYLISPEKGLRS LIKGVLELAKEPSKLCVDEVHRVLVDIVSSAANATPGLGRYPPFKREVVAIASSALDGFKNEAK KMVVALVDMERAFVPPQHFIRLVQRRMDRQRREDELKNKSSKKAVDAEQSILNRASVQQSGGSL KSMKDKSNQQDKDAQEGSALKTAGPGGEITAGFLLKKSGKTNGWSKRWFVLNEKSGKLGYTKKQ EERHFRGVITLEISDYVQHNDAILLVVIPATQAPEISSSRALRIAKEYDAESTRTVGVISKIDQ AATESKALAAVQALLLNQGPPKTSDIPWVALIGQSVSIASAQSASAPENSLETAWRAESESLKS ILTGAPPSKLGRVALVDALAGQIRSRMKLRLPNLLSGLQGKSQIVQDELVGLGEQMVSSSEGTR ALALELCREFEDKFLLHLMGGEGNGWKVVASFEGNFPNRIKQLPLDRHFDINNVKRIVLEADGY QPYLISPEKGLRSLIKGVLELAKEPSKLCVDEVHRVLVDIVSSAANATPGLGRYPPFKREVVAI ASSALDGFKNEAKKMVVALVDMERAFVPPQHFIRLVQRRMDRQRREDELKNKSSKKAVDAEQSI LNRASVQQSGGSLKSMKDKSNQQDKDAQEGSALKTAGPGGEITAGFLLKKSGKTNGWSKRWFVL NEKSGKLGYTKKQEERHFRGVITLEISDYVQHNDAILLVVIPATQAPEISSSRALRIAKEYDAE STRTVGVISKIDQAATESKALAAVQALLLNQGPPKTSDIPWVALIGQSVSIASAQSASAPENSL ETAWRAESESLKSILTGAPPSKLGRVALVDALAGQIRSRMKLRLPNLLSGLQGKSQIVQDELVG LGEQMVSSSEGTRALALELCREFEDKFLLHLMGGEGNGWKVVASFEGNFPNRIKQLPLDRHFDI NNVKRIVLEADGYQPYLISPEKGLRSLIKGVLELAKEPSKLCVDEVHRVLVDIVSSAANATPGL GRYPPFKREVVAIASSALDGFKNEAKKMVVALVDMERAFVPPQHFIRLVQRRMDRQRREDELKN KSSKKAVDAEQSILNRASVQQSGGSLKSMKDKSNQQDKDAQEGSALKTAGPGGEITAGFLLKKS GKTNGWSKRWFVLNEKSGKLGYTKKQEERHFRGVITLE(+) MKKVASLVTPKSKKKDTSVGLLLWRSVIMFSTMMLFC*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0004s23690_circ_g.2

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