Plant Circular RNA Database

Detail information of POPTR_0004s11320_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0004s11320_circ_g.1
					
						ID in PlantcircBase
						pop_circ_001297
					
						Alias
						Chr04:10378773-10384637
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr4: 9919013-9924863  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0004s11320						
					
						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_0004s11320.1:8

General Information
CircRNA Name	POPTR_0004s11320_circ_g.1
ID in PlantcircBase	pop_circ_001297
Alias	Chr04:10378773-10384637
Organism	Populus trichocarpa
Position	chr4: 9919013-9924863 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0004s11320
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_0004s11320.1:8

			
						 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  
						
							TTGATCAACATGTTGATGAAGACGTTTATGATACTCTGCAAATATTTTTGCTGCCTCATCACAT
TGCTGGTCGTAAGCCTCCAGCATGACCTGTTTGTGCcaaacctctcacgtacttgcaatcttcc
aagcacttttgggcattcaaagctgtagtcttaagctcaggtaaccatttctccacgacaattt
tctcttgc

						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	TTGATCAACATGTTGATGAAGACGTTTATGATACTCTGCAAATATTTTTGCTGCCTCATCACAT TGCTGGTCGTAAGCCTCCAGCATGACCTGTTTGTGCcaaacctctcacgtacttgcaatcttcc aagcacttttgggcattcaaagctgtagtcttaagctcaggtaaccatttctccacgacaattt tctcttgc
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
						0.111112244

Conservation Information
Conserved circRNAs	NA
PMCS	0.111112244

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9924774-9919065(+)
9924850-9919081(+)
9924852-9924824(-)
						
						Potential amino acid sequence
						
							MLMKTFMILCKYFCCLITLLVVSLQHDLFVPNLSRTCNLPSTFGHSKL*(+)
MTCLCQTSHVLAIFQALLGIQSCSLKLR*(+)
MLEAYDQQCDEAAKIFAEYHKRLHQHVDQARDAQRSSIDSSIEEVSSFSANSEKEAVYSTVKGT
KSADDVILIETTCERNIRKACESLAVYMVERIRNSFPAYEGSGIHLNTQSEAAKLAIDFDGEIP
DDVRTVIVNCLKNPPLLLQAITAYTSRLKTLVSREIEKTDVRADAELLRYKYENNRVMDVSSTD
TNSSLHHQLYGYGMIATDMTYRGSQNQLLERQKAHVQQFLATEDALNKAAEARDLCQKLLKRLH
GTGDEVSSNSIVSGGTTQNMSSLRQFELEVWAKEREAAGLRTSLNTLMSEIQRLNKLCAERKEA
EDSLRKNWKKIEEFDARRSELEAIYTTLLKFNTEDAAAFWKRQPLIAREYASITIIPACTIVVE
IANSAKDLIDKEVNAFSQCPDNSLYMLPSTSQALLESMGSNGSTGPEVAAAAEKNAALLTARAG
ARDPSAIPSICRVSAALQYPAGLEGSDAGLASVLESLEFCLKLRGSEASVLEDLAKAINLVHIR
HDLVESGHAVLNHAYRSQQEYERTTNFCLDLANEQEKIVVEKWLPELKTTALNAQKCLEDCKYV
RGLAQTGHAGGLRPAM*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9924774-9919065(+) 9924850-9919081(+) 9924852-9924824(-)
Potential amino acid sequence	MLMKTFMILCKYFCCLITLLVVSLQHDLFVPNLSRTCNLPSTFGHSKL(+) MTCLCQTSHVLAIFQALLGIQSCSLKLR(+) MLEAYDQQCDEAAKIFAEYHKRLHQHVDQARDAQRSSIDSSIEEVSSFSANSEKEAVYSTVKGT KSADDVILIETTCERNIRKACESLAVYMVERIRNSFPAYEGSGIHLNTQSEAAKLAIDFDGEIP DDVRTVIVNCLKNPPLLLQAITAYTSRLKTLVSREIEKTDVRADAELLRYKYENNRVMDVSSTD TNSSLHHQLYGYGMIATDMTYRGSQNQLLERQKAHVQQFLATEDALNKAAEARDLCQKLLKRLH GTGDEVSSNSIVSGGTTQNMSSLRQFELEVWAKEREAAGLRTSLNTLMSEIQRLNKLCAERKEA EDSLRKNWKKIEEFDARRSELEAIYTTLLKFNTEDAAAFWKRQPLIAREYASITIIPACTIVVE IANSAKDLIDKEVNAFSQCPDNSLYMLPSTSQALLESMGSNGSTGPEVAAAAEKNAALLTARAG ARDPSAIPSICRVSAALQYPAGLEGSDAGLASVLESLEFCLKLRGSEASVLEDLAKAINLVHIR HDLVESGHAVLNHAYRSQQEYERTTNFCLDLANEQEKIVVEKWLPELKTTALNAQKCLEDCKYV RGLAQTGHAGGLRPAM*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0004s11320_circ_g.1

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