Plant Circular RNA Database

Detail information of POPTR_0018s11270_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0018s11270_circ_g.1
					
						ID in PlantcircBase
						pop_circ_004176
					
						Alias
						Chr18:13116028-13118057
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr18: 12066112-12068142  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0018s11270						
					
						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_0018s11270.1:5

General Information
CircRNA Name	POPTR_0018s11270_circ_g.1
ID in PlantcircBase	pop_circ_004176
Alias	Chr18:13116028-13118057
Organism	Populus trichocarpa
Position	chr18: 12066112-12068142 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0018s11270
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_0018s11270.1:5

			
						 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  
						
							GGTTGCTAGTTATGTTAGTAGAGAGGATGGGAAGACACCCTCAAGTTCAGGGCCTACAAGTCGT
AGTTGCTATTCTTTCTGCATGTGTCCTGGTGGACAGggtggtgcaggtacttggagtgatggaa
agctagtaactagaattggaaggaacagtgacagtgttttggcggtgagaaccattcctcatat
ttctgatc

									
								

					

						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
						
							GGTGGTGCAGGTACTTGGAGTGATGGAAAGCTAGTAACTAGAATTGGAAGGAACAGTGACAGTG
TTTTGGCGGTGAGAACCATTCCTCATATTTCTGATCTAATCTCCTATGCATTGCTTTTGCACTA
TACGTACTATCTTTTACAGATATTAGCTCTTCTACTATATCCGTGATTTCCTGGTTGGTTGTCT
CACAAATGCTTGCCTGTGTTTTTTTTGTTTTTAATAAGAAGCTTACATACGGTTTTATTGGAAG
ATACAATTACAGGTCCAATTTATTCATGCATGTTTATAACTTGATATAATTTCCTTTTGAGAGC
TGCATTTTAGTATGAATAAAGTTCTTTGATTATTAACCGGGTGGTTGCAGAATTAGCTGTCATC
ATGAAGATGTGGGTTTTCCAGTTACAAGATCATTATTATTCAAATTAATAGGTTAAACTACTTG
CAGAACTGCTAGGAAAAAATGTTCATGTCTTTCCCCATATTGCCTATTTATTTTTGCATTTCTT
CTTCTTTTCATTCTTACTTTTATTTGTTGAATCCTGCTAAACAAAATTTATAAACAAGTTCTAC
TTTTAGTTTCAGCAATTGTACGAGGTACTAATATTTATGTAAATCTCAGGTTATGAAAACTCTG
GTTCACTTTGGAGCCCCGGAAAACATCTTGATTGATGGAAAGCCTCATTTGGGAACTGATAGGC
TGGTTCCATTGCTCCGCAACTTTCGCCAAAATCTACAGGACCAGGGTGTAAGTTGCTGATTCAG
CATTTGCCTATCTGAAACAAGTTGTTGATTGTGTTTCTTTACTACCGTTTTCCACTCTGTTAAC
ATCCAGAAAACTATACTGCCTTAGGTTTCAATCAAGTTTGGGACAAGGGTAGATGATCTGATAA
TAGAGGATGGTCATGTTGTGGGTGTCAAAGTTTCCGATTCAAAGGACAAACAGAAGCTGGATTG
CCAAAAGTTGGGATTTGATGCTGTCATTCTGGCTGTGGGCCATTCTGCTCGTGATATATATCAC
ATGCTTCTTTCCCATGATATTGATTTGATGCCAAAAGATTTTGCTGTGAGTTCAGAATCCTTTT
CTCCTTTATCTATCGTGTAATAAAAAACTTGACAATGAGTGGCCATCCATTCGCTACTTTGGTC
CACCAAATTACTTTAAACAGAACACACCATTTATTCATGGTGTATATCAAGGAAGTAAGCTTCT
GTTTGGCCACTGGATTAGGCATGTTTGGTCATCAGTTGACCATAATAAGAGCCAAAATCAAATT
GACTTCCTTTGTTACTTGATGAGAGCTTCATTAATGGTCAATTCAGGGTAGAAGTGCATGATTT
GTTTTCGTCTAGACAGTGTAATCAGCATCGAATTTTCTTATAAATTTTGTGAAGTGATTTTTGG
CAGTGCTTCTATGGTGCCATTTCTGATCTGAAATAGGTCACTTAAATCGACTTTCAGCAAAATT
GCACAAAAAAAAACCTAGGGTTAAAAATTCATTTTATTTCTTGTCTGTTACAGTTCAGCATGAA
TATCTTTAATTCTTTTGTCTTTATTATGTGACATCCATGCTGTGGTTATTGATGTTCTGCTCGA
TTCTTATTTTTAACTTGGCATCTTGAGACTTTCCTGCCATTGTCATAGTAAGTTACTTGGTTGA
ACAGGTTGGTTTGCGGATTGAACACCCCCAAGAGCTAATAAACAGTGTACAGGTTGGTTAAGTA
TCTCTTTTCCTATTCTATAATGTAGATGAATTGATAATTGGCTTGACTTATCATGATATTTCAC
TTCTGTTCTAAAACATGATTCATCCAATAGCATTCTTTCTGTTCTGTTCTTGCAACTCAATTTA
TACAAATTTGCAGTATTCTAGTCTGGGCACTGAAGTTCATAGAGGACGGGGGAAAATACCAGTG
GCAGATTACAAGGTTGCTAGTTATGTTAGTAGAGAGGATGGGAAGACACCCTCAAGTTCAGGGC
CTACAAGTCGTAGTTGCTATTCTTTCTGCATGTGTCCTGGTGGACAG
						
					

			
		

Sequences
Splice junction sequence	GGTTGCTAGTTATGTTAGTAGAGAGGATGGGAAGACACCCTCAAGTTCAGGGCCTACAAGTCGT AGTTGCTATTCTTTCTGCATGTGTCCTGGTGGACAGggtggtgcaggtacttggagtgatggaa agctagtaactagaattggaaggaacagtgacagtgttttggcggtgagaaccattcctcatat ttctgatc
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	GGTGGTGCAGGTACTTGGAGTGATGGAAAGCTAGTAACTAGAATTGGAAGGAACAGTGACAGTG TTTTGGCGGTGAGAACCATTCCTCATATTTCTGATCTAATCTCCTATGCATTGCTTTTGCACTA TACGTACTATCTTTTACAGATATTAGCTCTTCTACTATATCCGTGATTTCCTGGTTGGTTGTCT CACAAATGCTTGCCTGTGTTTTTTTTGTTTTTAATAAGAAGCTTACATACGGTTTTATTGGAAG ATACAATTACAGGTCCAATTTATTCATGCATGTTTATAACTTGATATAATTTCCTTTTGAGAGC TGCATTTTAGTATGAATAAAGTTCTTTGATTATTAACCGGGTGGTTGCAGAATTAGCTGTCATC ATGAAGATGTGGGTTTTCCAGTTACAAGATCATTATTATTCAAATTAATAGGTTAAACTACTTG CAGAACTGCTAGGAAAAAATGTTCATGTCTTTCCCCATATTGCCTATTTATTTTTGCATTTCTT CTTCTTTTCATTCTTACTTTTATTTGTTGAATCCTGCTAAACAAAATTTATAAACAAGTTCTAC TTTTAGTTTCAGCAATTGTACGAGGTACTAATATTTATGTAAATCTCAGGTTATGAAAACTCTG GTTCACTTTGGAGCCCCGGAAAACATCTTGATTGATGGAAAGCCTCATTTGGGAACTGATAGGC TGGTTCCATTGCTCCGCAACTTTCGCCAAAATCTACAGGACCAGGGTGTAAGTTGCTGATTCAG CATTTGCCTATCTGAAACAAGTTGTTGATTGTGTTTCTTTACTACCGTTTTCCACTCTGTTAAC ATCCAGAAAACTATACTGCCTTAGGTTTCAATCAAGTTTGGGACAAGGGTAGATGATCTGATAA TAGAGGATGGTCATGTTGTGGGTGTCAAAGTTTCCGATTCAAAGGACAAACAGAAGCTGGATTG CCAAAAGTTGGGATTTGATGCTGTCATTCTGGCTGTGGGCCATTCTGCTCGTGATATATATCAC ATGCTTCTTTCCCATGATATTGATTTGATGCCAAAAGATTTTGCTGTGAGTTCAGAATCCTTTT CTCCTTTATCTATCGTGTAATAAAAAACTTGACAATGAGTGGCCATCCATTCGCTACTTTGGTC CACCAAATTACTTTAAACAGAACACACCATTTATTCATGGTGTATATCAAGGAAGTAAGCTTCT GTTTGGCCACTGGATTAGGCATGTTTGGTCATCAGTTGACCATAATAAGAGCCAAAATCAAATT GACTTCCTTTGTTACTTGATGAGAGCTTCATTAATGGTCAATTCAGGGTAGAAGTGCATGATTT GTTTTCGTCTAGACAGTGTAATCAGCATCGAATTTTCTTATAAATTTTGTGAAGTGATTTTTGG CAGTGCTTCTATGGTGCCATTTCTGATCTGAAATAGGTCACTTAAATCGACTTTCAGCAAAATT GCACAAAAAAAAACCTAGGGTTAAAAATTCATTTTATTTCTTGTCTGTTACAGTTCAGCATGAA TATCTTTAATTCTTTTGTCTTTATTATGTGACATCCATGCTGTGGTTATTGATGTTCTGCTCGA TTCTTATTTTTAACTTGGCATCTTGAGACTTTCCTGCCATTGTCATAGTAAGTTACTTGGTTGA ACAGGTTGGTTTGCGGATTGAACACCCCCAAGAGCTAATAAACAGTGTACAGGTTGGTTAAGTA TCTCTTTTCCTATTCTATAATGTAGATGAATTGATAATTGGCTTGACTTATCATGATATTTCAC TTCTGTTCTAAAACATGATTCATCCAATAGCATTCTTTCTGTTCTGTTCTTGCAACTCAATTTA TACAAATTTGCAGTATTCTAGTCTGGGCACTGAAGTTCATAGAGGACGGGGGAAAATACCAGTG GCAGATTACAAGGTTGCTAGTTATGTTAGTAGAGAGGATGGGAAGACACCCTCAAGTTCAGGGC CTACAAGTCGTAGTTGCTATTCTTTCTGCATGTGTCCTGGTGGACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.110632595

Conservation Information
Conserved circRNAs	NA
PMCS	0.110632595

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							12066741-12068139(+)
12068055-12066142(+)
						
						Potential amino acid sequence
						
							MKTLVHFGAPENILIDGKPHLGTDRLVPLLRNFRQNLQDQGVSIKFGTRVDDLIIEDGHVVGVK
VSDSKDKQKLDCQKLGFDAVILAVGHSARDIYHMLLSHDIDLMPKDFAVGLRIEHPQELINSVQ
YSSLGTEVHRGRGKIPVADYKVASYVSREDGKTPSSSGPTSRSCYSFCMCPGGQGGAGTWSDGK
LVTRIGRNSDSVLAVMKTLVHFGAPENILIDGKPHLGTDRLVPLLRNFRQNLQDQGVSIKFGTR
VDDLIIEDGHVVGVKVSDSKDKQKLDCQKLGFDAVILAVGHSARDIYHMLLSHDIDLMPKDFAV
GLRIEHPQELINSVQYSSLGTEVHRGRGKIPVADYKVASYVSREDGKTPSSSGPTSRSCYSFCM
CPGGQGGAGTWSDGKLVTRIGRNSDSVLAVMKTLVHFGAPENILIDGKPHLGTDRLVPLLRNFR
QNLQDQGVSIKFGTRVDDLIIEDGHVVGVKVSDSKDKQKLDCQKLGFDAVILAVGHSARDIYHM
LLSHDIDLMPKDFAVGLRIEHPQELINSVQYSSLGTEVHRGRGKIPVADYKVASYVSREDGKTP
SSSGPTSRSCYSFCMCPGGQGGAGTWSDGKLVTRIGRNSDSVLAVMKTLVHFGAPENILIDGKP
HLGTDRLVPLLRNFRQNLQDQGVSIKFGTRVDDLIIEDGHVVGVKVSDSKDKQKLDCQKLGFDA
VILAVGHSARDIYHMLLSHDIDLMPKDFAVGLRIEHPQELINSVQYSSLGTEVHRGRGKIPVAD
YKVASYVSREDGKTPSSSGPTSRSCYSFCMCPGGQ(+)
MLVERMGRHPQVQGLQVVVAILSACVLVDRVVQVLGVMES*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	12066741-12068139(+) 12068055-12066142(+)
Potential amino acid sequence	MKTLVHFGAPENILIDGKPHLGTDRLVPLLRNFRQNLQDQGVSIKFGTRVDDLIIEDGHVVGVK VSDSKDKQKLDCQKLGFDAVILAVGHSARDIYHMLLSHDIDLMPKDFAVGLRIEHPQELINSVQ YSSLGTEVHRGRGKIPVADYKVASYVSREDGKTPSSSGPTSRSCYSFCMCPGGQGGAGTWSDGK LVTRIGRNSDSVLAVMKTLVHFGAPENILIDGKPHLGTDRLVPLLRNFRQNLQDQGVSIKFGTR VDDLIIEDGHVVGVKVSDSKDKQKLDCQKLGFDAVILAVGHSARDIYHMLLSHDIDLMPKDFAV GLRIEHPQELINSVQYSSLGTEVHRGRGKIPVADYKVASYVSREDGKTPSSSGPTSRSCYSFCM CPGGQGGAGTWSDGKLVTRIGRNSDSVLAVMKTLVHFGAPENILIDGKPHLGTDRLVPLLRNFR QNLQDQGVSIKFGTRVDDLIIEDGHVVGVKVSDSKDKQKLDCQKLGFDAVILAVGHSARDIYHM LLSHDIDLMPKDFAVGLRIEHPQELINSVQYSSLGTEVHRGRGKIPVADYKVASYVSREDGKTP SSSGPTSRSCYSFCMCPGGQGGAGTWSDGKLVTRIGRNSDSVLAVMKTLVHFGAPENILIDGKP HLGTDRLVPLLRNFRQNLQDQGVSIKFGTRVDDLIIEDGHVVGVKVSDSKDKQKLDCQKLGFDA VILAVGHSARDIYHMLLSHDIDLMPKDFAVGLRIEHPQELINSVQYSSLGTEVHRGRGKIPVAD YKVASYVSREDGKTPSSSGPTSRSCYSFCMCPGGQ(+) MLVERMGRHPQVQGLQVVVAILSACVLVDRVVQVLGVMES*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0018s11270_circ_g.1

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