Plant Circular RNA Database

Detail information of POPTR_0012s05780_circ_g.2

			
						 General Information
					
						CircRNA Name
						POPTR_0012s05780_circ_g.2
					
						ID in PlantcircBase
						pop_circ_003129
					
						Alias
						Chr12:6512493-6514499
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr12: 5594480-5596517  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0012s05780						
					
						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_0012s05780.1:5

General Information
CircRNA Name	POPTR_0012s05780_circ_g.2
ID in PlantcircBase	pop_circ_003129
Alias	Chr12:6512493-6514499
Organism	Populus trichocarpa
Position	chr12: 5594480-5596517 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0012s05780
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_0012s05780.1:5

			
						 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  
						
							CTTTCACCGGCCTCAAGATAGACTTGGCAGCTTCTCTAGCACAGGATCAAAAATGGCTGGGTGG
CATCTTTACAGGACACCGCAAAGGACAGTTGCTATGgttagctctgtccgtatgctgtctggtg
aacgtgtccttactgctgcacatgatggaactgttaagatgtgggatgttcgaactgatacttg
tgtggcaa

									
								

					

						Assembled circRNA sequence  
						
							Yes
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
						
							Transcript length: 666
Transcript exons: 5594480-5594661,5594762-5594833,5594919-5595079,5595293-
5595334,5596309-5596517
GTTAGCTCTGTCCGTATGCTGTCTGGTGAACGTGTCCTTACTGCTGCACATGATGGAACTGTTA
AGATGTGGGATGTTCGAACTGATACTTGTGTGGCAACAGTTGGCCGTTGCTCTAGTGCAGTCCT
ATGCATGGAGTATGATGATTCCACTGGAATTCTTGCTGCTGCTGGTAGAGATGCGGTTGCAAAC
ATATGGGATATCCGTGCTGGTAGGCAGATGCACAAGCTTTTAGGCCACACAAAATGGATTCGGT
CAATTAGAATGGTTGGAGACACACTGATTACTGGTAGTGATGATTGGACTGCCAGAGTGTGGTC
TGTTTCACGAGGAACATGCGATGCTGTTCTAGCCTGCCATGCTGGTCCAATATTATGCGTTGAA
TATTCCATGTCAGACAGAGGAATAATAACAGGTTCAACTGATGGACTTCTCCGGTTTTGGGAAA
ATGAGGAGGGAGGCATAAGATGCGTGAAGAATGTTACCATTCATTCAGCTCCTATATTATCCAT
CAATGCTGGGGAACACTGGTTGGGAATTGGCGCAGCTGACAATTCTATGTCTCTCTTTCACCGG
CCTCAAGATAGACTTGGCAGCTTCTCTAGCACAGGATCAAAAATGGCTGGGTGGCATCTTTACA
GGACACCGCAAAGGACAGTTGCTATG"
						
					

						Genomic sequence
						
							GTTAGCTCTGTCCGTATGCTGTCTGGTGAACGTGTCCTTACTGCTGCACATGATGGAACTGTTA
AGATGTGGGATGTTCGAACTGATACTTGTGTGGCAACAGTTGGCCGTTGCTCTAGTGCAGTCCT
ATGCATGGAGTATGATGATTCCACTGGAATTCTTGCTGCTGCTGGTAGAGATGCGTATGTACTT
TGAACTTACAAATGCTACAGCATGTTTTTTTGAATCTTTATTCTGTTACTGACTACTGAAAACC
AACCTGCTCAACACTTGCATTACTAGGGTTGCAAACATATGGGATATCCGTGCTGGTAGGCAGA
TGCACAAGCTTTTAGGCCACACAAAATGGATTCGGTGAGCTGAGCAGAGTATTTTTCTTCTGTT
TATGATAACTGTTAATTACAGTTGTGAAGGAGCTATTTGTCTGTCCATCATGTAGGTCAATTAG
AATGGTTGGAGACACACTGATTACTGGTAGTGATGATTGGACTGCCAGAGTGTGGTCTGTTTCA
CGAGGAACATGCGATGCTGTTCTAGCCTGCCATGCTGGTCCAATATTATGCGTTGAATATTCCA
TGTCAGACAGAGGAATAATAACAGGTAAATAAATAATAACAGGTAAATAATATCTTTTACTTTT
TTTTTTGTTCAGATTCAATTGCATTTACCTTGTGCTCCTATGGTATTTATCATTTATTTGAAGG
GCTACGTGATATCTTAATCGAATGAATGTTAAAGATTCATACTGAAATATGTTTCAAGTGCCAA
CATGAACTGCTGAAGATATGTACTGACTTGAGATATCCTTTTCAGGTTCAACTGATGGACTTCT
CCGGTTTTGGGAAAATGAGGAGGGTAAGAGCAGTAATATTTTCTTGCCAAGTTGAACTTCCTAT
CCTTTTATTTTTGTTTTTTGAGCTGTTCTATGTTTGGCCCTGTTAAGACGTAATTTTTCCAACT
TGAGAGTCTCATCTGACTTGCATCAGAGGATATTATATCATGAAGGAGTTGTCCATACATGGGC
CAATAACATCTCTCTGTTTCATTTAATTTAGGAAGTAATGCAGTGTTTGTCCACAAAATACCAG
TATCGTGTCTCAGAATTTTTAAGGAACACATGTATTTTAATGGATGTAATTGTGGTTATACTAT
ACTTACCAAGCTCTACCAGCTAATAAGCACTTAATGTTTCATTCATGTTTATTGTTGCATATTG
CAAACAATACCATTTTGACTTTTTCTTGTTCTAATTTTCTCCTTTTATTTTTCTATCCCCCTCT
ATTTGGCATTGACATGTTGTAAGTGCAAGTATGGCATTTACTTAATCCTTAATCTAAGAGGATT
TTTTTCCATTTCTATTTGTTTTATTTTTTTACATATACTATGTATGTGAATGTCTTTTATGTAC
TTATATTGAGAGGTCAATTAAAATAATTTGATACCAGTGCAGTCCATATCAATGGTAAAAACAT
AATGCCTACCCACGTTTGGTTTGTGAATTTTTTTTTTGGAATTGCAACATATTTTGCCTGTAGT
CTTACCTTGGTAATGGTTGAAAGCCAAGCAACAAAAAAAGCCTTTTGACCATTCTTCCTTTAAA
ATTTAACAGTTTCTATACTTTGTACAAGGGTATCATTTCTGCATGGCCTGCTTTCAGTGTCTTG
CATGATATGTCATATGGCACAAGAAAAAAGTTTGTATTTTCATTTTTCCAATTAAATTTCTCAC
GTCCCTCCTCTCCATTTACAAATCATTTTTCTGATTAAAATTTTCTTGTCCGTCCTTTCCTTTG
AGCACCACTGATATCATTTTTAACATAATGTGTGCAGGAGGCATAAGATGCGTGAAGAATGTTA
CCATTCATTCAGCTCCTATATTATCCATCAATGCTGGGGAACACTGGTTGGGAATTGGCGCAGC
TGACAATTCTATGTCTCTCTTTCACCGGCCTCAAGATAGACTTGGCAGCTTCTCTAGCACAGGA
TCAAAAATGGCTGGGTGGCATCTTTACAGGACACCGCAAAGGACAGTTGCTATG
						
					

			
		

Sequences
Splice junction sequence	CTTTCACCGGCCTCAAGATAGACTTGGCAGCTTCTCTAGCACAGGATCAAAAATGGCTGGGTGG CATCTTTACAGGACACCGCAAAGGACAGTTGCTATGgttagctctgtccgtatgctgtctggtg aacgtgtccttactgctgcacatgatggaactgttaagatgtgggatgttcgaactgatacttg tgtggcaa
Assembled circRNA sequence	Yes 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	Transcript length: 666 Transcript exons: 5594480-5594661,5594762-5594833,5594919-5595079,5595293- 5595334,5596309-5596517 GTTAGCTCTGTCCGTATGCTGTCTGGTGAACGTGTCCTTACTGCTGCACATGATGGAACTGTTA AGATGTGGGATGTTCGAACTGATACTTGTGTGGCAACAGTTGGCCGTTGCTCTAGTGCAGTCCT ATGCATGGAGTATGATGATTCCACTGGAATTCTTGCTGCTGCTGGTAGAGATGCGGTTGCAAAC ATATGGGATATCCGTGCTGGTAGGCAGATGCACAAGCTTTTAGGCCACACAAAATGGATTCGGT CAATTAGAATGGTTGGAGACACACTGATTACTGGTAGTGATGATTGGACTGCCAGAGTGTGGTC TGTTTCACGAGGAACATGCGATGCTGTTCTAGCCTGCCATGCTGGTCCAATATTATGCGTTGAA TATTCCATGTCAGACAGAGGAATAATAACAGGTTCAACTGATGGACTTCTCCGGTTTTGGGAAA ATGAGGAGGGAGGCATAAGATGCGTGAAGAATGTTACCATTCATTCAGCTCCTATATTATCCAT CAATGCTGGGGAACACTGGTTGGGAATTGGCGCAGCTGACAATTCTATGTCTCTCTTTCACCGG CCTCAAGATAGACTTGGCAGCTTCTCTAGCACAGGATCAAAAATGGCTGGGTGGCATCTTTACA GGACACCGCAAAGGACAGTTGCTATG"
Genomic sequence	GTTAGCTCTGTCCGTATGCTGTCTGGTGAACGTGTCCTTACTGCTGCACATGATGGAACTGTTA AGATGTGGGATGTTCGAACTGATACTTGTGTGGCAACAGTTGGCCGTTGCTCTAGTGCAGTCCT ATGCATGGAGTATGATGATTCCACTGGAATTCTTGCTGCTGCTGGTAGAGATGCGTATGTACTT TGAACTTACAAATGCTACAGCATGTTTTTTTGAATCTTTATTCTGTTACTGACTACTGAAAACC AACCTGCTCAACACTTGCATTACTAGGGTTGCAAACATATGGGATATCCGTGCTGGTAGGCAGA TGCACAAGCTTTTAGGCCACACAAAATGGATTCGGTGAGCTGAGCAGAGTATTTTTCTTCTGTT TATGATAACTGTTAATTACAGTTGTGAAGGAGCTATTTGTCTGTCCATCATGTAGGTCAATTAG AATGGTTGGAGACACACTGATTACTGGTAGTGATGATTGGACTGCCAGAGTGTGGTCTGTTTCA CGAGGAACATGCGATGCTGTTCTAGCCTGCCATGCTGGTCCAATATTATGCGTTGAATATTCCA TGTCAGACAGAGGAATAATAACAGGTAAATAAATAATAACAGGTAAATAATATCTTTTACTTTT TTTTTTGTTCAGATTCAATTGCATTTACCTTGTGCTCCTATGGTATTTATCATTTATTTGAAGG GCTACGTGATATCTTAATCGAATGAATGTTAAAGATTCATACTGAAATATGTTTCAAGTGCCAA CATGAACTGCTGAAGATATGTACTGACTTGAGATATCCTTTTCAGGTTCAACTGATGGACTTCT CCGGTTTTGGGAAAATGAGGAGGGTAAGAGCAGTAATATTTTCTTGCCAAGTTGAACTTCCTAT CCTTTTATTTTTGTTTTTTGAGCTGTTCTATGTTTGGCCCTGTTAAGACGTAATTTTTCCAACT TGAGAGTCTCATCTGACTTGCATCAGAGGATATTATATCATGAAGGAGTTGTCCATACATGGGC CAATAACATCTCTCTGTTTCATTTAATTTAGGAAGTAATGCAGTGTTTGTCCACAAAATACCAG TATCGTGTCTCAGAATTTTTAAGGAACACATGTATTTTAATGGATGTAATTGTGGTTATACTAT ACTTACCAAGCTCTACCAGCTAATAAGCACTTAATGTTTCATTCATGTTTATTGTTGCATATTG CAAACAATACCATTTTGACTTTTTCTTGTTCTAATTTTCTCCTTTTATTTTTCTATCCCCCTCT ATTTGGCATTGACATGTTGTAAGTGCAAGTATGGCATTTACTTAATCCTTAATCTAAGAGGATT TTTTTCCATTTCTATTTGTTTTATTTTTTTACATATACTATGTATGTGAATGTCTTTTATGTAC TTATATTGAGAGGTCAATTAAAATAATTTGATACCAGTGCAGTCCATATCAATGGTAAAAACAT AATGCCTACCCACGTTTGGTTTGTGAATTTTTTTTTTGGAATTGCAACATATTTTGCCTGTAGT CTTACCTTGGTAATGGTTGAAAGCCAAGCAACAAAAAAAGCCTTTTGACCATTCTTCCTTTAAA ATTTAACAGTTTCTATACTTTGTACAAGGGTATCATTTCTGCATGGCCTGCTTTCAGTGTCTTG CATGATATGTCATATGGCACAAGAAAAAAGTTTGTATTTTCATTTTTCCAATTAAATTTCTCAC GTCCCTCCTCTCCATTTACAAATCATTTTTCTGATTAAAATTTTCTTGTCCGTCCTTTCCTTTG AGCACCACTGATATCATTTTTAACATAATGTGTGCAGGAGGCATAAGATGCGTGAAGAATGTTA CCATTCATTCAGCTCCTATATTATCCATCAATGCTGGGGAACACTGGTTGGGAATTGGCGCAGC TGACAATTCTATGTCTCTCTTTCACCGGCCTCAAGATAGACTTGGCAGCTTCTCTAGCACAGGA TCAAAAATGGCTGGGTGGCATCTTTACAGGACACCGCAAAGGACAGTTGCTATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							gar_circ_000378 						
					
						PMCS
						0.432163629

Conservation Information
Conserved circRNAs	gar_circ_000378
PMCS	0.432163629

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							5594496-5596514(+)
5596331-5594811(+)
5594532-5596466(-)
5596341-5596489(-)
						
					

						Potential amino acid sequence
						
							MLSGERVLTAAHDGTVKMWDVRTDTCVATVGRCSSAVLCMEYDDSTGILAAAGRDAVANIWDIR
AGRQMHKLLGHTKWIRSIRMVGDTLITGSDDWTARVWSVSRGTCDAVLACHAGPILCVEYSMSD
RGIITGSTDGLLRFWENEEGGIRCVKNVTIHSAPILSINAGEHWLGIGAADNSMSLFHRPQDRL
GSFSSTGSKMAGWHLYRTPQRTVAMVSSVRMLSGERVLTAAHDGTVKMWDVRTDTCVATVGRCS
SAVLCMEYDDSTGILAAAGRDAVANIWDIRAGRQMHKLLGHTKWIRSIRMVGDTLITGSDDWTA
RVWSVSRGTCDAVLACHAGPILCVEYSMSDRGIITGSTDGLLRFWENEEGGIRCVKNVTIHSAP
ILSINAGEHWLGIGAADNSMSLFHRPQDRLGSFSSTGSKMAGWHLYRTPQRTVAMVSSVRMLSG
ERVLTAAHDGTVKMWDVRTDTCVATVGRCSSAVLCMEYDDSTGILAAAGRDAVANIWDIRAGRQ
MHKLLGHTKWIRSIRMVGDTLITGSDDWTARVWSVSRGTCDAVLACHAGPILCVEYSMSDRGII
TGSTDGLLRFWENEEGGIRCVKNVTIHSAPILSINAGEHWLGIGAADNSMSLFHRPQDRLGSFS
STGSKMAGWHLYRTPQRTVAMVSSVRMLSGERVLTAAHDGTVKMWDVRTDTCVATVGRCSSAVL
CMEYDDSTGILAAAGRDAVANIWDIRAGRQMHKLLGHTKWIRSIRMVGDTLITGSDDWTARVWS
VSRGTCDAVLACHAGPILCVEYSMSDRGIITGSTDGLLRFWENEEGGIRCVKNVTIHSAPILSI
NAGEHWLGIGAADNSMSLFHRPQDRLGSFSSTGSKMAGWHLYRTPQRTVAM(+)
MLPFIQLLYYPSMLGNTGWELAQLTILCLSFTGLKIDLAASLAQDQKWLGGIFTGHRKGQLLWL
ALSVCCLVNVSLLLHMMELLRCGMFELILVWQQLAVALVQSYAWSMMIPLEFLLLLVEMRLQTY
GISVLVGRCTSF*(+)
MCSSKDTFTRQHTDRANHSNCPLRCPVKMPPSHF*(-)
MVTFFTHLMPPSSFSQNRRSPSVEPVIIPLSDMEYSTHNIGPAWQARTASHVPRETDHTLAVQS
SLPVISVSPTILIDRIHFVWPKSLCICLPARISHMFATASLPAAARIPVESSYSMHRTALEQRP
TVATQVSVRTSHILTVPSCAAVRTRSPDSIRTELTIATVLCGVL*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	5594496-5596514(+) 5596331-5594811(+) 5594532-5596466(-) 5596341-5596489(-)
Potential amino acid sequence	MLSGERVLTAAHDGTVKMWDVRTDTCVATVGRCSSAVLCMEYDDSTGILAAAGRDAVANIWDIR AGRQMHKLLGHTKWIRSIRMVGDTLITGSDDWTARVWSVSRGTCDAVLACHAGPILCVEYSMSD RGIITGSTDGLLRFWENEEGGIRCVKNVTIHSAPILSINAGEHWLGIGAADNSMSLFHRPQDRL GSFSSTGSKMAGWHLYRTPQRTVAMVSSVRMLSGERVLTAAHDGTVKMWDVRTDTCVATVGRCS SAVLCMEYDDSTGILAAAGRDAVANIWDIRAGRQMHKLLGHTKWIRSIRMVGDTLITGSDDWTA RVWSVSRGTCDAVLACHAGPILCVEYSMSDRGIITGSTDGLLRFWENEEGGIRCVKNVTIHSAP ILSINAGEHWLGIGAADNSMSLFHRPQDRLGSFSSTGSKMAGWHLYRTPQRTVAMVSSVRMLSG ERVLTAAHDGTVKMWDVRTDTCVATVGRCSSAVLCMEYDDSTGILAAAGRDAVANIWDIRAGRQ MHKLLGHTKWIRSIRMVGDTLITGSDDWTARVWSVSRGTCDAVLACHAGPILCVEYSMSDRGII TGSTDGLLRFWENEEGGIRCVKNVTIHSAPILSINAGEHWLGIGAADNSMSLFHRPQDRLGSFS STGSKMAGWHLYRTPQRTVAMVSSVRMLSGERVLTAAHDGTVKMWDVRTDTCVATVGRCSSAVL CMEYDDSTGILAAAGRDAVANIWDIRAGRQMHKLLGHTKWIRSIRMVGDTLITGSDDWTARVWS VSRGTCDAVLACHAGPILCVEYSMSDRGIITGSTDGLLRFWENEEGGIRCVKNVTIHSAPILSI NAGEHWLGIGAADNSMSLFHRPQDRLGSFSSTGSKMAGWHLYRTPQRTVAM(+) MLPFIQLLYYPSMLGNTGWELAQLTILCLSFTGLKIDLAASLAQDQKWLGGIFTGHRKGQLLWL ALSVCCLVNVSLLLHMMELLRCGMFELILVWQQLAVALVQSYAWSMMIPLEFLLLLVEMRLQTY GISVLVGRCTSF(+) MCSSKDTFTRQHTDRANHSNCPLRCPVKMPPSHF(-) MVTFFTHLMPPSSFSQNRRSPSVEPVIIPLSDMEYSTHNIGPAWQARTASHVPRETDHTLAVQS SLPVISVSPTILIDRIHFVWPKSLCICLPARISHMFATASLPAAARIPVESSYSMHRTALEQRP TVATQVSVRTSHILTVPSCAAVRTRSPDSIRTELTIATVLCGVL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0012s05780_circ_g.2

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