Plant Circular RNA Database

Detail information of POPTR_0017s04760_circ_g.2

			
						 General Information
					
						CircRNA Name
						POPTR_0017s04760_circ_g.2
					
						ID in PlantcircBase
						pop_circ_003971
					
						Alias
						Chr17:1383750-1386270
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr17: 3659401-3661921  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0017s04760						
					
						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_0017s04760.1:7

General Information
CircRNA Name	POPTR_0017s04760_circ_g.2
ID in PlantcircBase	pop_circ_003971
Alias	Chr17:1383750-1386270
Organism	Populus trichocarpa
Position	chr17: 3659401-3661921 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0017s04760
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_0017s04760.1:7

			
						 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  
						
							AGACCCAGACCTTTCGGTTCAAAATATCTTGTTTTTCAAGCTCTTTTCGGATCCTTTTTTCATG
GGCTTCAACTTCACGAGCTATTCTTGCCTCCTCACTctcattatcatcacagagatatgcctgc
tcaacattccttttcttcagttgtggtccaaaacctgcagaaagaccgaattgccgcaatattt
caggccaa

									
								

					

						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
						
							CTCATTATCATCACAGAGATATGCCTGCTCAACATTCCTTTTCTTCAGTTGTGGTCCAAAACCT
GCAGAAAGACCGAATTGCCGCAATATTTCAGGCCAAGTTAATGGATTTAAGTGCCGCTGCCAGC
TACGTATATCAAAACCCCATGCATATGCCTGACACAGAAGCCAAAAATAATTTAGGATGAAAAA
AAGGAGCATAATTGAGGAGATCAAATTGCCACAGCAACACACAACAAAGAAGACTTACCCCTTC
AACAATCTGAGGATGTCCACCACCAGGATTAGCAGCACTGTTCTGATTTGGCCCCAGACTAGTT
GCCGGTGTCCTGGCAACATCTTCGATATCTTTAATGATGGATTTTAATAAAGAAATGTGTATCT
CGCCTAATAACCTTGGTTCCTGAAAGTAGAGGAAGCAGGAAAGACATCTGAATTCCACAAATGT
AGGGCAACCCTATATCAGATACCGGTCAGGAAAAGATTCACAGATACTTACATAATCATGAAAA
GCTTGGACAAACTCATCGAGAGTGAATGGCCATATCCCAAGAACATCCACAAAAGTGATTAAGA
ACCTCCAAACCTATAAATTTACAGTTTCATTCAAAATCTTTGAGAAGAACAAAAATAAGAAAAG
AAAGAAATGGCTGTGCATTTGGCATTCTAGAAGTGGTGGAATGATGAATTTTCCTTCCAAAAAA
TGAACTCCTCCAAAGATTTATTATTCCCAAGTCCAAAAAAAACAAGAGAATGTGCCTAGAAACC
CTCTATAGTGGGATTTATACAAATAGGTGGCATAGATATTCTTGCTTGAGAAAAAGGACACCAT
AACAATAGCAACCACAAGAAACAATAAAATCAACCTTCAACTATGTAAAGGAGAAGTGAGATTT
TGGGTTGACAAGAGGGATTGGTTTTAAAGGAGACAAAATAAAACAATGCATTGATGATGAGATA
ATACATATTAACAAGTAATAAAAACTCATTTTATCTCAATTCATTAACACCACCTACCGCACAT
ATGGTATTTTCAAAATAATTACTTGAAAATTCATCACCCATCTGCCTACAGAAACCCTGTTATT
CATTATGATTCACAGCTATGCATGAGAAAGAGAGTGAAATGTCCCAACAAACTGATTTTTATGC
CTACTTGAAGCAAAATACAATGGCAGGGGAACACTGAAAGAGAGTAATATTTGTCCTCAATGAA
GCAGCAAAAAAACACAGGAAACAAAATGATTTTTTAACCAACTTAAATCAAAATACAAATGACA
CACAAAGGATCAATATCTGAAATAAAAGCATAAAATGATATTAAAATATGACTCAAAGAAAAAC
TAAAATTTCCAAATTCCTTCTGTTTTCTATAGAGCAGCCGTCACATTCCACAAAATAATGGCAA
ATATGAGATGAGATTATGCACCATGGATGCAACATAAGTGTGCAAAGAAGTTCTGTGATCATTT
ACTTAAGAGAGTGTTCTGTCGCATACTTGCATTCCAGTCTTAACTACTACCATCCTTCCAGGAC
AGGTAGAGAGGAACAAGAAATAGGAAGAACTACAGAAACTCACCATAAGAAGATTTCCTATATT
CTCCTCAGAACCATTCCAGGGTTGAATAAGAAAAGGCCTCTTTAAAAGCACAGATTTGGGAGGG
AACTTGGTCAGCTTATCTGAAAAGCAATTTAACATGTCAAGCTCGAGTGTAATGAAAATTGACC
AACAATAAATCAAGATAAATGCATGAGCCTCGTAAAACATTTAAGGAAAAAATTGCACGGCAGT
AAATCTTCCAAGGCTGTGACTTAATATTTTGCAATGGTATCAGAACGGTTTCCTTGATCAAACT
AGACATTACCAACCTCGAAATAAATCTAGATTTTGCAAAGTTTCAAAGTCCAACGGAATTATAG
AAGGTAACCCCTTGCTGGAGGCAGCTAGCTCCATGAGTTCCAAACGTTCATCCTCGACAAGCTC
CAGTGATTCTTTAGCCATCCTACGTGCAATTGCCCTCTCACTAGCAGCTTTCTGCCTTGCTGCC
TCCCTTTGTCTACGCAATTCTTCCTTTTGCCTCATTTTCTCAACCTGAGTACATAAATGAAAAA
AAAAAAAAAGTGCCCCATTTATCCTCAGAGGCAAGATATAAAAGGACGGTCTTAAATAGGGTAT
CTGAACCTACTCTGATAGACTCCTTCTGCAAGAATTTTTCCCTGCGCTCCAGTTCACGCCTTTG
CTCCCTCTGGTGTCTCTCTACTTCTCGCTGCTTTTCACGCAACAACCTTTCTTCTTCCTTCCGC
CTTTCACGGTCATGTCTTTCCATTTCTTTCCTTATTTGCTCTTCTCTCTGAACATACAAGTGAC
ATAACACTGTCAGTATGACCTTATAGATTTGAAAAGGAAAGGCTTGTATGGTAAGACCCAGACC
TTTCGGTTCAAAATATCTTGTTTTTCAAGCTCTTTTCGGATCCTTTTTTCATGGGCTTCAACTT
CACGAGCTATTCTTGCCTCCTCACT
						
					

			
		

Sequences
Splice junction sequence	AGACCCAGACCTTTCGGTTCAAAATATCTTGTTTTTCAAGCTCTTTTCGGATCCTTTTTTCATG GGCTTCAACTTCACGAGCTATTCTTGCCTCCTCACTctcattatcatcacagagatatgcctgc tcaacattccttttcttcagttgtggtccaaaacctgcagaaagaccgaattgccgcaatattt caggccaa
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	CTCATTATCATCACAGAGATATGCCTGCTCAACATTCCTTTTCTTCAGTTGTGGTCCAAAACCT GCAGAAAGACCGAATTGCCGCAATATTTCAGGCCAAGTTAATGGATTTAAGTGCCGCTGCCAGC TACGTATATCAAAACCCCATGCATATGCCTGACACAGAAGCCAAAAATAATTTAGGATGAAAAA AAGGAGCATAATTGAGGAGATCAAATTGCCACAGCAACACACAACAAAGAAGACTTACCCCTTC AACAATCTGAGGATGTCCACCACCAGGATTAGCAGCACTGTTCTGATTTGGCCCCAGACTAGTT GCCGGTGTCCTGGCAACATCTTCGATATCTTTAATGATGGATTTTAATAAAGAAATGTGTATCT CGCCTAATAACCTTGGTTCCTGAAAGTAGAGGAAGCAGGAAAGACATCTGAATTCCACAAATGT AGGGCAACCCTATATCAGATACCGGTCAGGAAAAGATTCACAGATACTTACATAATCATGAAAA GCTTGGACAAACTCATCGAGAGTGAATGGCCATATCCCAAGAACATCCACAAAAGTGATTAAGA ACCTCCAAACCTATAAATTTACAGTTTCATTCAAAATCTTTGAGAAGAACAAAAATAAGAAAAG AAAGAAATGGCTGTGCATTTGGCATTCTAGAAGTGGTGGAATGATGAATTTTCCTTCCAAAAAA TGAACTCCTCCAAAGATTTATTATTCCCAAGTCCAAAAAAAACAAGAGAATGTGCCTAGAAACC CTCTATAGTGGGATTTATACAAATAGGTGGCATAGATATTCTTGCTTGAGAAAAAGGACACCAT AACAATAGCAACCACAAGAAACAATAAAATCAACCTTCAACTATGTAAAGGAGAAGTGAGATTT TGGGTTGACAAGAGGGATTGGTTTTAAAGGAGACAAAATAAAACAATGCATTGATGATGAGATA ATACATATTAACAAGTAATAAAAACTCATTTTATCTCAATTCATTAACACCACCTACCGCACAT ATGGTATTTTCAAAATAATTACTTGAAAATTCATCACCCATCTGCCTACAGAAACCCTGTTATT CATTATGATTCACAGCTATGCATGAGAAAGAGAGTGAAATGTCCCAACAAACTGATTTTTATGC CTACTTGAAGCAAAATACAATGGCAGGGGAACACTGAAAGAGAGTAATATTTGTCCTCAATGAA GCAGCAAAAAAACACAGGAAACAAAATGATTTTTTAACCAACTTAAATCAAAATACAAATGACA CACAAAGGATCAATATCTGAAATAAAAGCATAAAATGATATTAAAATATGACTCAAAGAAAAAC TAAAATTTCCAAATTCCTTCTGTTTTCTATAGAGCAGCCGTCACATTCCACAAAATAATGGCAA ATATGAGATGAGATTATGCACCATGGATGCAACATAAGTGTGCAAAGAAGTTCTGTGATCATTT ACTTAAGAGAGTGTTCTGTCGCATACTTGCATTCCAGTCTTAACTACTACCATCCTTCCAGGAC AGGTAGAGAGGAACAAGAAATAGGAAGAACTACAGAAACTCACCATAAGAAGATTTCCTATATT CTCCTCAGAACCATTCCAGGGTTGAATAAGAAAAGGCCTCTTTAAAAGCACAGATTTGGGAGGG AACTTGGTCAGCTTATCTGAAAAGCAATTTAACATGTCAAGCTCGAGTGTAATGAAAATTGACC AACAATAAATCAAGATAAATGCATGAGCCTCGTAAAACATTTAAGGAAAAAATTGCACGGCAGT AAATCTTCCAAGGCTGTGACTTAATATTTTGCAATGGTATCAGAACGGTTTCCTTGATCAAACT AGACATTACCAACCTCGAAATAAATCTAGATTTTGCAAAGTTTCAAAGTCCAACGGAATTATAG AAGGTAACCCCTTGCTGGAGGCAGCTAGCTCCATGAGTTCCAAACGTTCATCCTCGACAAGCTC CAGTGATTCTTTAGCCATCCTACGTGCAATTGCCCTCTCACTAGCAGCTTTCTGCCTTGCTGCC TCCCTTTGTCTACGCAATTCTTCCTTTTGCCTCATTTTCTCAACCTGAGTACATAAATGAAAAA AAAAAAAAAGTGCCCCATTTATCCTCAGAGGCAAGATATAAAAGGACGGTCTTAAATAGGGTAT CTGAACCTACTCTGATAGACTCCTTCTGCAAGAATTTTTCCCTGCGCTCCAGTTCACGCCTTTG CTCCCTCTGGTGTCTCTCTACTTCTCGCTGCTTTTCACGCAACAACCTTTCTTCTTCCTTCCGC CTTTCACGGTCATGTCTTTCCATTTCTTTCCTTATTTGCTCTTCTCTCTGAACATACAAGTGAC ATAACACTGTCAGTATGACCTTATAGATTTGAAAAGGAAAGGCTTGTATGGTAAGACCCAGACC TTTCGGTTCAAAATATCTTGTTTTTCAAGCTCTTTTCGGATCCTTTTTTCATGGGCTTCAACTT CACGAGCTATTCTTGCCTCCTCACT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.115350126

Conservation Information
Conserved circRNAs	NA
PMCS	0.115350126

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							3661717-3659502(+)
3661354-3659663(+)
3661729-3659403(-)
						
					

						Potential amino acid sequence
						
							MSFHFFPYLLFSLSVQNILFFKLFSDPFFMGFNFTSYSCLLTLIIITEICLLNIPFLQLWSKTC
RKTELPQYFRPS*(+)
MSSKRSSSTSSSDSLAILRAIALSLAAFCLAASLCLRNSSFCLIFSTLIDSFCKNFSLRSSSRL
CSLWCLSTSRCFSRNNLSSSFRLSRSCLSISFLICSSLFRFKISCFSSSFRILFSWASTSRAIL
ASSLSLSSQRYACSTFLFFSCGPKPAERPNCRNISGQVNGFKCRCQLRISKPHAYAPSTI*(+)
MERHDRERRKEEERLLREKQREVERHQREQRRELERREKFLQKESIRVEKMRQKEELRRQREAA
RQKAASERAIARRMAKESLELVEDERLELMELAASSKGLPSIIPLDFETLQNLDLFRDKLTKFP
PKSVLLKRPFLIQPWNGSEENIGNLLMVWRFLITFVDVLGIWPFTLDEFVQAFHDYEPRLLGEI
HISLLKSIIKDIEDVARTPATSLGPNQNSAANPGGGHPQIVEGAYAWGFDIRSWQRHLNPLTWP
EILRQFGLSAGFGPQLKKRNVEQAYLCDDNESEEARIAREVEAHEKRIRKELEKQDILNRKREE
QIRKEMERHDRERRKEEERLLREKQREVERHQREQRRELERREKFLQKESIRVEKMRQKEELRR
QREAARQKAASERAIARRMAKESLELVEDERLELMELAASSKGLPSIIPLDFETLQNLDLFRDK
LTKFPPKSVLLKRPFLIQPWNGSEENIGNLLMVWRFLITFVDVLGIWPFTLDEFVQAFHDYEPR
LLGEIHISLLKSIIKDIEDVARTPATSLGPNQNSAANPGGGHPQIVEGAYAWGFDIRSWQRHLN
PLTWPEILRQFGLSAGFGPQLKKRNVEQAYLCDDNESEEARIAREVEAHEKRIRKELEKQDILN
RKREEQIRKEMERHDRERRKEEERLLREKQREVERHQREQRRELERREKFLQKESIRVEKMRQK
EELRRQREAARQKAASERAIARRMAKESLELVEDERLELMELAASSKGLPSIIPLDFETLQNLD
LFRDKLTKFPPKSVLLKRPFLIQPWNGSEENIGNLLMVWRFLITFVDVLGIWPFTLDEFVQAFH
DYEPRLLGEIHISLLKSIIKDIEDVARTPATSLGPNQNSAANPGGGHPQIVEGAYAWGFDIRSW
QRHLNPLTWPEILRQFGLSAGFGPQLKKRNVEQAYLCDDNESEEARIAREVEAHEKRIRKELEK
QDILNRKREEQIRKEMERHDRERRKEEERLLREKQREVERHQREQRRELERREKFLQKESIRVE
KMRQKEELRRQREAARQKAASERAIARRMAKESLELVEDERLELMELAASSKGLPSIIPLDFET
LQNLDLFRDKLTKFPPKSVLLKRPFLIQPWNGSEENIGNLLMVWRFLITFVDVLGIWPFTLDEF
VQAFHDYEPRLLGEIHISLLKSIIKDIEDVARTPATSLGPNQNSAANPGGGHPQIVEGAYAWGF
DIRSWQRHLNPLTWPEILRQFGLSAGFGPQLKKRNVEQAYLCDDNE(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	3661717-3659502(+) 3661354-3659663(+) 3661729-3659403(-)
Potential amino acid sequence	MSFHFFPYLLFSLSVQNILFFKLFSDPFFMGFNFTSYSCLLTLIIITEICLLNIPFLQLWSKTC RKTELPQYFRPS(+) MSSKRSSSTSSSDSLAILRAIALSLAAFCLAASLCLRNSSFCLIFSTLIDSFCKNFSLRSSSRL CSLWCLSTSRCFSRNNLSSSFRLSRSCLSISFLICSSLFRFKISCFSSSFRILFSWASTSRAIL ASSLSLSSQRYACSTFLFFSCGPKPAERPNCRNISGQVNGFKCRCQLRISKPHAYAPSTI(+) MERHDRERRKEEERLLREKQREVERHQREQRRELERREKFLQKESIRVEKMRQKEELRRQREAA RQKAASERAIARRMAKESLELVEDERLELMELAASSKGLPSIIPLDFETLQNLDLFRDKLTKFP PKSVLLKRPFLIQPWNGSEENIGNLLMVWRFLITFVDVLGIWPFTLDEFVQAFHDYEPRLLGEI HISLLKSIIKDIEDVARTPATSLGPNQNSAANPGGGHPQIVEGAYAWGFDIRSWQRHLNPLTWP EILRQFGLSAGFGPQLKKRNVEQAYLCDDNESEEARIAREVEAHEKRIRKELEKQDILNRKREE QIRKEMERHDRERRKEEERLLREKQREVERHQREQRRELERREKFLQKESIRVEKMRQKEELRR QREAARQKAASERAIARRMAKESLELVEDERLELMELAASSKGLPSIIPLDFETLQNLDLFRDK LTKFPPKSVLLKRPFLIQPWNGSEENIGNLLMVWRFLITFVDVLGIWPFTLDEFVQAFHDYEPR LLGEIHISLLKSIIKDIEDVARTPATSLGPNQNSAANPGGGHPQIVEGAYAWGFDIRSWQRHLN PLTWPEILRQFGLSAGFGPQLKKRNVEQAYLCDDNESEEARIAREVEAHEKRIRKELEKQDILN RKREEQIRKEMERHDRERRKEEERLLREKQREVERHQREQRRELERREKFLQKESIRVEKMRQK EELRRQREAARQKAASERAIARRMAKESLELVEDERLELMELAASSKGLPSIIPLDFETLQNLD LFRDKLTKFPPKSVLLKRPFLIQPWNGSEENIGNLLMVWRFLITFVDVLGIWPFTLDEFVQAFH DYEPRLLGEIHISLLKSIIKDIEDVARTPATSLGPNQNSAANPGGGHPQIVEGAYAWGFDIRSW QRHLNPLTWPEILRQFGLSAGFGPQLKKRNVEQAYLCDDNESEEARIAREVEAHEKRIRKELEK QDILNRKREEQIRKEMERHDRERRKEEERLLREKQREVERHQREQRRELERREKFLQKESIRVE KMRQKEELRRQREAARQKAASERAIARRMAKESLELVEDERLELMELAASSKGLPSIIPLDFET LQNLDLFRDKLTKFPPKSVLLKRPFLIQPWNGSEENIGNLLMVWRFLITFVDVLGIWPFTLDEF VQAFHDYEPRLLGEIHISLLKSIIKDIEDVARTPATSLGPNQNSAANPGGGHPQIVEGAYAWGF DIRSWQRHLNPLTWPEILRQFGLSAGFGPQLKKRNVEQAYLCDDNE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0017s04760_circ_g.2

Address

Any questions?

Supported by