Plant Circular RNA Database

Detail information of POPTR_0018s08370_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0018s08370_circ_g.1
					
						ID in PlantcircBase
						pop_circ_004130
					
						Alias
						Chr18:4524970-4525594
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr18: 9313074-9313698  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0018s08370						
					
						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_0018s08370.1:2

General Information
CircRNA Name	POPTR_0018s08370_circ_g.1
ID in PlantcircBase	pop_circ_004130
Alias	Chr18:4524970-4525594
Organism	Populus trichocarpa
Position	chr18: 9313074-9313698 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0018s08370
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_0018s08370.1:2

			
						 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  
						
							CTGGCACCGTAAGTGCTGGAAAGTCCAGTGCACTGAGATTGGTGGGAGCTGACACAGTCTTCGA
GTTCGTAGTCTGATTGAAACCACCATCAACTTGGAGctgttcaaggtatgcattccttatacgt
gcatgatcacgagcttcttcccgcatctcagaatacatgcttgctgccatctcaacaatgttaa
tggaaata

						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
						
							CTGTTCAAGGTATGCATTCCTTATACGTGCATGATCACGAGCTTCTTCCCGCATCTCAGAATAC
ATGCTTGCTGCCATCTCAACAATGTTAATGGAAATATACACAGGAAAGGCATTCCCACATTAAA
AAGTTTCATAAACTAAGTAATTTTGTTGACCAAGGAATATTACCCACTGCTTCTCCAGTTTCAA
GCCAGACAGGAGCTGCTTGACCTGACCCACGACTTTGCGACCTATCTGCATAAATGCCTCTCCC
ATGACCACCACTATAAGCACTAGCCAAAACATGGGAACTTCTGCTTGAGCCAACAGTTGAATCA
GCAGAACCATTTCTGTCATGGTTCCACATACTAGAATCTTGAGAAGCCAATTTCCTGACAGCTG
ATGCAAAATCCACAGCACCTCTAGATGAAAAGGAAGCACCAGACTTGAATACAAGCATGTTGTC
TTTGTTAGAAGATCGATAAGGAATGCCAGCTTGCTGAAGATCATCTCCAGCATATTTTGAAGGA
CCATTCTGATTATCTGGCACCGTAAGTGCTGGAAAGTCCAGTGCACTGAGATTGGTGGGAGCTG
ACACAGTCTTCGAGTTCGTAGTCTGATTGAAACCACCATCAACTTGGAG

Sequences
Splice junction sequence	CTGGCACCGTAAGTGCTGGAAAGTCCAGTGCACTGAGATTGGTGGGAGCTGACACAGTCTTCGA GTTCGTAGTCTGATTGAAACCACCATCAACTTGGAGctgttcaaggtatgcattccttatacgt gcatgatcacgagcttcttcccgcatctcagaatacatgcttgctgccatctcaacaatgttaa tggaaata
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	CTGTTCAAGGTATGCATTCCTTATACGTGCATGATCACGAGCTTCTTCCCGCATCTCAGAATAC ATGCTTGCTGCCATCTCAACAATGTTAATGGAAATATACACAGGAAAGGCATTCCCACATTAAA AAGTTTCATAAACTAAGTAATTTTGTTGACCAAGGAATATTACCCACTGCTTCTCCAGTTTCAA GCCAGACAGGAGCTGCTTGACCTGACCCACGACTTTGCGACCTATCTGCATAAATGCCTCTCCC ATGACCACCACTATAAGCACTAGCCAAAACATGGGAACTTCTGCTTGAGCCAACAGTTGAATCA GCAGAACCATTTCTGTCATGGTTCCACATACTAGAATCTTGAGAAGCCAATTTCCTGACAGCTG ATGCAAAATCCACAGCACCTCTAGATGAAAAGGAAGCACCAGACTTGAATACAAGCATGTTGTC TTTGTTAGAAGATCGATAAGGAATGCCAGCTTGCTGAAGATCATCTCCAGCATATTTTGAAGGA CCATTCTGATTATCTGGCACCGTAAGTGCTGGAAAGTCCAGTGCACTGAGATTGGTGGGAGCTG ACACAGTCTTCGAGTTCGTAGTCTGATTGAAACCACCATCAACTTGGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.24438744

Conservation Information
Conserved circRNAs	NA
PMCS	0.24438744

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9313517-9313076(-)
9313092-9313096(-)
						
						Potential amino acid sequence
						
							MLVFKSGASFSSRGAVDFASAVRKLASQDSSMWNHDRNGSADSTVGSSRSSHVLASAYSGGHGR
GIYADRSQSRGSGQAAPVWLETGEAVASMYSEMREEARDHARIRNAYLEQLQVDGGFNQTTNSK
TVSAPTNLSALDFPALTVPDNQNGPSKYAGDDLQQAGIPYRSSNKDNMLVFKSGASFSSRGAVD
FASAVRKLASQDSSMWNHDRNGSADSTVGSSRSSHVLASAYSGGHGRGIYADRSQSRGSGQAAP
VWLETGEAVASMYSEMREEARDHARIRNAYLEQLQVDGGFNQTTNSKTVSAPTNLSALDFPALT
VPDNQNGPSKYAGDDLQQAGIPYRSSNKDNMLVFKSGASFSSRGAVDFASAVRKLASQDSSMWN
HDRNGSADSTVGSSRSSHVLASAYSGGHGRGIYADRSQSRGSGQAAPVWLETGEAVASMYSEMR
EEARDHARIRNAYLEQLQVDGGFNQTTNSKTVSAPTNLSALDFPALTVPDNQNGPSKYAGDDLQ
QAGIPYRSSNKDNMLVFKSGASFSSRGAVDFASAVRKLASQDSSMWNHDRNGSADSTVGSSRSS
HVLASAYSGGHGRGIYADRSQSRGSGQAAPVWLETGEAVASMYSEMREEARDHARIRNAYLEQ(
-)
MHTLNSSKLMVVSIRLRTRRLCQLPPISVHWTFQHLRCQIIRMVLQNMLEMIFSKLAFLIDLLT
KTTCLYSSLVLPFHLEVLWILHQLSGNWLLKILVCGTMTEMVLLIQLLAQAEVPMFWLVLIVVV
MGEAFMQIGRKVVGQVKQLLSGLKLEKQWQACILRCGKKLVIMHV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9313517-9313076(-) 9313092-9313096(-)
Potential amino acid sequence	MLVFKSGASFSSRGAVDFASAVRKLASQDSSMWNHDRNGSADSTVGSSRSSHVLASAYSGGHGR GIYADRSQSRGSGQAAPVWLETGEAVASMYSEMREEARDHARIRNAYLEQLQVDGGFNQTTNSK TVSAPTNLSALDFPALTVPDNQNGPSKYAGDDLQQAGIPYRSSNKDNMLVFKSGASFSSRGAVD FASAVRKLASQDSSMWNHDRNGSADSTVGSSRSSHVLASAYSGGHGRGIYADRSQSRGSGQAAP VWLETGEAVASMYSEMREEARDHARIRNAYLEQLQVDGGFNQTTNSKTVSAPTNLSALDFPALT VPDNQNGPSKYAGDDLQQAGIPYRSSNKDNMLVFKSGASFSSRGAVDFASAVRKLASQDSSMWN HDRNGSADSTVGSSRSSHVLASAYSGGHGRGIYADRSQSRGSGQAAPVWLETGEAVASMYSEMR EEARDHARIRNAYLEQLQVDGGFNQTTNSKTVSAPTNLSALDFPALTVPDNQNGPSKYAGDDLQ QAGIPYRSSNKDNMLVFKSGASFSSRGAVDFASAVRKLASQDSSMWNHDRNGSADSTVGSSRSS HVLASAYSGGHGRGIYADRSQSRGSGQAAPVWLETGEAVASMYSEMREEARDHARIRNAYLEQ( -) MHTLNSSKLMVVSIRLRTRRLCQLPPISVHWTFQHLRCQIIRMVLQNMLEMIFSKLAFLIDLLT KTTCLYSSLVLPFHLEVLWILHQLSGNWLLKILVCGTMTEMVLLIQLLAQAEVPMFWLVLIVVV MGEAFMQIGRKVVGQVKQLLSGLKLEKQWQACILRCGKKLVIMHV*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0018s08370_circ_g.1

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