Plant Circular RNA Database

Detail information of POPTR_0004s16820_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0004s16820_circ_g.1
					
						ID in PlantcircBase
						pop_circ_001350
					
						Alias
						Chr04:18141224-18142379
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr4: 17156342-17157497  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0004s16820						
					
						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_0004s16820.1:2

General Information
CircRNA Name	POPTR_0004s16820_circ_g.1
ID in PlantcircBase	pop_circ_001350
Alias	Chr04:18141224-18142379
Organism	Populus trichocarpa
Position	chr4: 17156342-17157497 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0004s16820
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_0004s16820.1:2

			
						 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  
						
							TGTTGTGTTCAGAGTTTACTGATGCTTTATCACCAGAGAGTGAAGCCAACCGATGCTCTAGGAG
AGTCACCTTGTCTTGCAATTCTTTGTTCTCGGAACActtcaaccgaacaactaggggctcttcc
ttgggagtttcatcaacttgtgatgcatccaaatcttctctctctttcaggatgctattacgat
caacttca

						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
						
							CTTCAACCGAACAACTAGGGGCTCTTCCTTGGGAGTTTCATCAACTTGTGATGCATCCAAATCT
TCTCTCTCTTTCAGGATGCTATTACGATCAACTTCAACACCATTTGTTTTAGGATCACTAGTGT
GATCTATACCATCACTATGCCTTTCATCAGCATTCATCCCAAAGATAGCACTATCCTCTCTCTT
TAACTTCGCAACAAGCACCCACATGTTTGCTAAGTCATTTTCCAGAGCCCCCTCCCTTTTTTTT
GCCTCTTCACACTTTTTCCTGTATTCATCTTCTATGAATTCCTTTTCAGCCAAGGCTGCCTCCA
GTGCCGCTTCGCGTTGTTTTCTTGCCTGCAGTTCCCTTTTCAAATCATCTGGATCAAGATTCCA
CGACTCAAAGTCATCAGAATGCATTCCTGAAAAATCATTTCCTCTGCCAGAGAACCGCCCCTTC
CTCCCATGTCTTATGCCATCATTAAACTTGCGGTTAACTCCATTAACTGATTGCATGCCAGCAC
CTCTAGAATGCACAGATTCTCGAGCAGCCAGCAATTCTTTTTCCAATTTTGCATTCTGTAATGA
GAGCTTTGTCACTTCACCAGCTAAATTTTTCAGCTCAACTGCAGCAGCAGAGGCCAGTTCCTTT
GCATAAGAAGCTTCTTCGGACAATTTCTGATTTTGCACCCGCAATCCACTATTCTCCTCTGAAA
TCTGAACCTGTCCAATCTTTAGCTTTTCATTCTCAATCTCCTGCTCAGATAAAAACAAAAGCAT
GTTTCTTAGCTGTAAGTAAAAACTTGGAATTACTTTGTTAGAAGTTAGAACTACCAGCTGGTAT
CAACTTTTTGCTTATGTTTTTGACACTATAGAACAGTAATAATCCTATTTCCATATGAGATGTT
TGAACTAAAACCCCTAGTTCAACTAGAAATAAAAACAATGACCACAACCAAAATAGAGTTATTT
TCAATAAGCCCATCCAAGATTTATTAGGTTGTAGTATATTGGTGATCACCTGGGACTGAACTTT
CTTTTTCAATTCATCCACATATTCTTCAGACATGTTGTGTTCAGAGTTTACTGATGCTTTATCA
CCAGAGAGTGAAGCCAACCGATGCTCTAGGAGAGTCACCTTGTCTTGCAATTCTTTGTTCTCGG
AACA

Sequences
Splice junction sequence	TGTTGTGTTCAGAGTTTACTGATGCTTTATCACCAGAGAGTGAAGCCAACCGATGCTCTAGGAG AGTCACCTTGTCTTGCAATTCTTTGTTCTCGGAACActtcaaccgaacaactaggggctcttcc ttgggagtttcatcaacttgtgatgcatccaaatcttctctctctttcaggatgctattacgat caacttca
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	CTTCAACCGAACAACTAGGGGCTCTTCCTTGGGAGTTTCATCAACTTGTGATGCATCCAAATCT TCTCTCTCTTTCAGGATGCTATTACGATCAACTTCAACACCATTTGTTTTAGGATCACTAGTGT GATCTATACCATCACTATGCCTTTCATCAGCATTCATCCCAAAGATAGCACTATCCTCTCTCTT TAACTTCGCAACAAGCACCCACATGTTTGCTAAGTCATTTTCCAGAGCCCCCTCCCTTTTTTTT GCCTCTTCACACTTTTTCCTGTATTCATCTTCTATGAATTCCTTTTCAGCCAAGGCTGCCTCCA GTGCCGCTTCGCGTTGTTTTCTTGCCTGCAGTTCCCTTTTCAAATCATCTGGATCAAGATTCCA CGACTCAAAGTCATCAGAATGCATTCCTGAAAAATCATTTCCTCTGCCAGAGAACCGCCCCTTC CTCCCATGTCTTATGCCATCATTAAACTTGCGGTTAACTCCATTAACTGATTGCATGCCAGCAC CTCTAGAATGCACAGATTCTCGAGCAGCCAGCAATTCTTTTTCCAATTTTGCATTCTGTAATGA GAGCTTTGTCACTTCACCAGCTAAATTTTTCAGCTCAACTGCAGCAGCAGAGGCCAGTTCCTTT GCATAAGAAGCTTCTTCGGACAATTTCTGATTTTGCACCCGCAATCCACTATTCTCCTCTGAAA TCTGAACCTGTCCAATCTTTAGCTTTTCATTCTCAATCTCCTGCTCAGATAAAAACAAAAGCAT GTTTCTTAGCTGTAAGTAAAAACTTGGAATTACTTTGTTAGAAGTTAGAACTACCAGCTGGTAT CAACTTTTTGCTTATGTTTTTGACACTATAGAACAGTAATAATCCTATTTCCATATGAGATGTT TGAACTAAAACCCCTAGTTCAACTAGAAATAAAAACAATGACCACAACCAAAATAGAGTTATTT TCAATAAGCCCATCCAAGATTTATTAGGTTGTAGTATATTGGTGATCACCTGGGACTGAACTTT CTTTTTCAATTCATCCACATATTCTTCAGACATGTTGTGTTCAGAGTTTACTGATGCTTTATCA CCAGAGAGTGAAGCCAACCGATGCTCTAGGAGAGTCACCTTGTCTTGCAATTCTTTGTTCTCGG AACA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.20682802

Conservation Information
Conserved circRNAs	NA
PMCS	0.20682802

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							17157398-17156468(+)
17156915-17156454(+)
17157400-17156344(-)
						
					

						Potential amino acid sequence
						
							MLCSEFTDALSPESEANRCSRRVTLSCNSLFSEHFNRTTRGSSLGVSSTCDASKSSLSFRMLLR
STSTPFVLGSLV*(+)
MRALSLHQLNFSAQLQQQRPVPLHKKLLRTISDFAPAIHYSPLKSEPVQSLAFHSQSPAGTELS
FSIHPHILQTCCVQSLLMLYHQRVKPTDALGESPCLAILCSRNTSTEQLGALPWEFHQLVMHPN
LLSLSGCYYDQLQHHLF*(+)
MSEEYVDELKKKVQSQQEIENEKLKIGQVQISEENSGLRVQNQKLSEEASYAKELASAAAVELK
NLAGEVTKLSLQNAKLEKELLAARESVHSRGAGMQSVNGVNRKFNDGIRHGRKGRFSGRGNDFS
GMHSDDFESWNLDPDDLKRELQARKQREAALEAALAEKEFIEDEYRKKCEEAKKREGALENDLA
NMWVLVAKLKREDSAIFGMNADERHSDGIDHTSDPKTNGVEVDRNSILKEREDLDASQVDETPK
EEPLVVRLKCSENKELQDKVTLLEHRLASLSGDKASVNSEHNMSEEYVDELKKKVQSQQEIENE
KLKIGQVQISEENSGLRVQNQKLSEEASYAKELASAAAVELKNLAGEVTKLSLQNAKLEKELLA
ARESVHSRGAGMQSVNGVNRKFNDGIRHGRKGRFSGRGNDFSGMHSDDFESWNLDPDDLKRELQ
ARKQREAALEAALAEKEFIEDEYRKKCEEAKKREGALENDLANMWVLVAKLKREDSAIFGMNAD
ERHSDGIDHTSDPKTNGVEVDRNSILKEREDLDASQVDETPKEEPLVVRLKCSENKELQDKVTL
LEHRLASLSGDKASVNSEHNMSEEYVDELKKKVQSQQEIENEKLKIGQVQISEENSGLRVQNQK
LSEEASYAKELASAAAVELKNLAGEVTKLSLQNAKLEKELLAARESVHSRGAGMQSVNGVNRKF
NDGIRHGRKGRFSGRGNDFSGMHSDDFESWNLDPDDLKRELQARKQREAALEAALAEKEFIEDE
YRKKCEEAKKREGALENDLANMWVLVAKLKREDSAIFGMNADERHSDGIDHTSDPKTNGVEVDR
NSILKEREDLDASQVDETPKEEPLVVRLKCSENKELQDKVTLLEHRLASLSGDKASVNSEHNMS
EEYVDELKKKVQSQQEIENEKLKIGQVQISEENSGLRVQNQKLSEEASYAKELASAAAVELKNL
AGEVTKLSLQNAKLEKELLAARESVHSRGAGMQSVNGVNRKFNDGIRHGRKGRFSGRGNDFSGM
HSDDFESWNLDPDDLKRELQARKQREAALEAALAEKEFIEDEYRKKCEEAKKREGALENDLANM
WVLVAKLKREDSAIFGMNADERHSDGIDHTSDPKTNGVEVDRNSILKEREDLDASQVDETPKEE
PLVVRLK(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	17157398-17156468(+) 17156915-17156454(+) 17157400-17156344(-)
Potential amino acid sequence	MLCSEFTDALSPESEANRCSRRVTLSCNSLFSEHFNRTTRGSSLGVSSTCDASKSSLSFRMLLR STSTPFVLGSLV(+) MRALSLHQLNFSAQLQQQRPVPLHKKLLRTISDFAPAIHYSPLKSEPVQSLAFHSQSPAGTELS FSIHPHILQTCCVQSLLMLYHQRVKPTDALGESPCLAILCSRNTSTEQLGALPWEFHQLVMHPN LLSLSGCYYDQLQHHLF(+) MSEEYVDELKKKVQSQQEIENEKLKIGQVQISEENSGLRVQNQKLSEEASYAKELASAAAVELK NLAGEVTKLSLQNAKLEKELLAARESVHSRGAGMQSVNGVNRKFNDGIRHGRKGRFSGRGNDFS GMHSDDFESWNLDPDDLKRELQARKQREAALEAALAEKEFIEDEYRKKCEEAKKREGALENDLA NMWVLVAKLKREDSAIFGMNADERHSDGIDHTSDPKTNGVEVDRNSILKEREDLDASQVDETPK EEPLVVRLKCSENKELQDKVTLLEHRLASLSGDKASVNSEHNMSEEYVDELKKKVQSQQEIENE KLKIGQVQISEENSGLRVQNQKLSEEASYAKELASAAAVELKNLAGEVTKLSLQNAKLEKELLA ARESVHSRGAGMQSVNGVNRKFNDGIRHGRKGRFSGRGNDFSGMHSDDFESWNLDPDDLKRELQ ARKQREAALEAALAEKEFIEDEYRKKCEEAKKREGALENDLANMWVLVAKLKREDSAIFGMNAD ERHSDGIDHTSDPKTNGVEVDRNSILKEREDLDASQVDETPKEEPLVVRLKCSENKELQDKVTL LEHRLASLSGDKASVNSEHNMSEEYVDELKKKVQSQQEIENEKLKIGQVQISEENSGLRVQNQK LSEEASYAKELASAAAVELKNLAGEVTKLSLQNAKLEKELLAARESVHSRGAGMQSVNGVNRKF NDGIRHGRKGRFSGRGNDFSGMHSDDFESWNLDPDDLKRELQARKQREAALEAALAEKEFIEDE YRKKCEEAKKREGALENDLANMWVLVAKLKREDSAIFGMNADERHSDGIDHTSDPKTNGVEVDR NSILKEREDLDASQVDETPKEEPLVVRLKCSENKELQDKVTLLEHRLASLSGDKASVNSEHNMS EEYVDELKKKVQSQQEIENEKLKIGQVQISEENSGLRVQNQKLSEEASYAKELASAAAVELKNL AGEVTKLSLQNAKLEKELLAARESVHSRGAGMQSVNGVNRKFNDGIRHGRKGRFSGRGNDFSGM HSDDFESWNLDPDDLKRELQARKQREAALEAALAEKEFIEDEYRKKCEEAKKREGALENDLANM WVLVAKLKREDSAIFGMNADERHSDGIDHTSDPKTNGVEVDRNSILKEREDLDASQVDETPKEE PLVVRLK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0004s16820_circ_g.1

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