Plant Circular RNA Database

Detail information of POPTR_0012s05450_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0012s05450_circ_g.1
					
						ID in PlantcircBase
						pop_circ_003123
					
						Alias
						Chr12:6018060-6020800
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr12: 5092507-5095247  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0012s05450						
					
						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_0012s05450.1:5
POPTR_0012s05450.2:5

General Information
CircRNA Name	POPTR_0012s05450_circ_g.1
ID in PlantcircBase	pop_circ_003123
Alias	Chr12:6018060-6020800
Organism	Populus trichocarpa
Position	chr12: 5092507-5095247 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0012s05450
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_0012s05450.1:5 POPTR_0012s05450.2:5

			
						 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  
						
							AACCAAAGTCCTCAAGCCAGCATCAGCATACTCGCCAATGTGCTCCCTGGTGGGCTCTTCAAAC
TCTCTTCCATCCCTTGCAAGTCTTTCAAACATGACActgcattccttcaaccccactgatacca
acaccaatatctgcttcttgaagcatcccaacatcatttgccccatcaccaattgctaatgttg
ttttacct

									
								

					

						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
						
							CTGCATTCCTTCAACCCCACTGATACCAACACCAATATCTGCTTCTTGAAGCATCCCAACATCA
TTTGCCCCATCACCAATTGCTAATGTTGTTTTACCTGTCTTACTTTTAACCAGTCTTGTAACCT
GCATTTATTAATATGACACCAGTTAGTTTAATTTTTTAGTGAAGTTGCTTCAGATAAGTCAATG
TCCAAATTCATTTCTCTCTCTCTCTCACCCACTCTTTAAATAATGCTACAATTATTCAAAGAAC
CAAATTATTTTCGTGAAGGCTAGCTCTAGGACTTTTTTTTTTCCCTGACATACCATAAGGCTTC
TTCTTTCACCATCTTTGCTGAATAATTAAAGAGAAGAAATTTAAAAGAAAACACAAATACTTGT
ATGCTTAACAATTCCTGTGGGCTTCTATGGGAAAGGACCTCTTTTCAATCACCAGTATTGGATA
AATATGAGGAAAAATTAATTATAATAAACAATCGAGGGCTAATCATTTACTTTTTGGCCAATGA
AGGAAATGAAATTATGTATACAGAGAATTGGTAGCAAGTAATTTTGATTAATAGCAGGTCTGGC
CAAAACTTTTATACGAAAATGTGACACCAGTAGTGCACTTCTGATAGAAGAAAGTTCTATGCAC
CACTTACATACTACGTCCTTTCTGTTATAGAGAATGAAGAACATAGGTTGAAAGAACATAATAA
CTTACAAGAGCTTTCTGTTTAGGAGATGATCGGCAGCAAATGACAGATGCACATCCAATAGCAA
GCTCCAGAAACAGGTTCTTGACATCATCTTCGATAGCATAAGTGAGTGATTTGCCATCAATTAT
CAAAGCCAGTGCCTCAGAAGTTTCACTTGATGCAGTAAGCAGCGCCTTCCCTTCATTCATCTGA
TGGACGACGCTTGCCTTGAGAGCCTGCATAGTTGGCAAGGTCCAATGAACTTTTTTATTGCAAA
ATAAGAGTTATTCTGACCAGAAATGAAATCTCTGTCATACTATTTCTTTTAGAACACATCCTGT
AGACAAATTATATTGATGTCATCACAGCAACTGCGAAACTGCTTTACTGGCACGATAGAAACAA
GCTAATCCAATCTTCTCCACATGATAATTATAGCTCTATAAAATTCTCTTATTAATATCATATC
ATTATTCTTAATTCATTTTAGCTAACAAAATGAGAAGGATATTTCTCAGCTTGGAAGTGAGGGG
ATCATACATTCATGCATATGAATTAATAGATAAGAGGGAGATCTCGGAGAAATCACATTTGGAA
CTTTCTCCTGCAAACTGTTAGACCAAGATGACGTGAGGATATATGTGCTTTTCAAGGTTTTGGA
CATGTTCAGTTAGACTAAGGGGAAATTTATATTGACCAGCAGCTAGAGTTGGACCAGATGTAGC
TAAAGGAAAAAAAGGAAATGAAATAACTTAGATGTAGACATTGGATGAGTTGTGGGAAGACTAC
TATACCAGTAAAAACTAGAAACGATAAACAGTCTCAGTGTCTGGAGAGAGCTTTTTTGAAATTA
CTAGACTGGAAAAGTCAAAAAAAAAATTATTTTGTATTTTGCATAGAGGAGATCAAGAATTCTG
GAACATCTATGTGATGGAAATTGTTAATACAGTAAGGGATTTCCTAAAACTCTTTAGAATGTAC
TCCCTTCACATTCAAGTAGTCCACATAGAAAAGATACTAGTGGGTCATCCTCTCTAAGACTTGG
TCCCTTATTGTGGTTCTGCTGTTCGCATCTGAGATTGCAGCACTAGCTGCGAAGAGTTAGGATG
ATTTCCTCTTCCTACCGTTATCAAATATATATCACTACATTGCTTCTATGCATCATTAACTGAA
CTTTCTATTGATCTAAAGAGTCACTGAAAGAGAACAGCAGATGAAATCAGAAATTACCGTAACA
CCAGCAGCTTTGTCCTCCATTTTCTCTAGAGCTTTGTTTTCTGGAGTATCTGAACTGATTATTA
TTTGCTTCATCCCTTGTCTGAGTAAACTACAGGCAAAGCTGCAAGATTCAACATCAATTATGAT
GTATTAGTATACAGGATTAAACATCTATTAGACAGAAAATGACGTCCACTCAAACATACCCAAT
ATTGATGGCTGTCTCCATCTTATCTCCTGTTAAAACCCATATTTTTATTCCCGCTTGTGCAAGC
TTGTCAATACACTCAGGAACCTGTTCAGAAAAAACATTCAATTTCAAACACTTCGGCTAATTTT
TAAAGTAACTAAATATACATAACCATTTTTAGTTCAGAATAGAACAAAACAATTTCTTTAGGAT
TCAAAAGAGAAATAATACTGATGAACGTTTATTAGTTTAGATGAAGAATAGAGCTCTTTGAATG
ATGACACTCCAAACAAGTTGCTATGGAATAGCAAGCCAAATGATTTCTTATCAACTATACTAAA
AATCAACATTCCTAGAATTTTTTTAGACCCACCCCATTCTGAAGTTTGTCCTCAACAGCTGTAG
CACCAAGAAGAATCAAATCCCTCTCAATCTTTTCAGCTACTTCTTCAATCATATCCTCACGATC
TGCACTTAATGAGTTTTTTGCCTCAGTAAATTCATGATTGAACTCATCATATTCTTCCTCATCA
AGTTCACGATATGCAAGAACCAAAGTCCTCAAGCCAGCATCAGCATACTCGCCAATGTGCTCCC
TGGTGGGCTCTTCAAACTCTCTTCCATCCCTTGCAAGTCTTTCAAACATGACA
						
					

			
		

Sequences
Splice junction sequence	AACCAAAGTCCTCAAGCCAGCATCAGCATACTCGCCAATGTGCTCCCTGGTGGGCTCTTCAAAC TCTCTTCCATCCCTTGCAAGTCTTTCAAACATGACActgcattccttcaaccccactgatacca acaccaatatctgcttcttgaagcatcccaacatcatttgccccatcaccaattgctaatgttg ttttacct
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	CTGCATTCCTTCAACCCCACTGATACCAACACCAATATCTGCTTCTTGAAGCATCCCAACATCA TTTGCCCCATCACCAATTGCTAATGTTGTTTTACCTGTCTTACTTTTAACCAGTCTTGTAACCT GCATTTATTAATATGACACCAGTTAGTTTAATTTTTTAGTGAAGTTGCTTCAGATAAGTCAATG TCCAAATTCATTTCTCTCTCTCTCTCACCCACTCTTTAAATAATGCTACAATTATTCAAAGAAC CAAATTATTTTCGTGAAGGCTAGCTCTAGGACTTTTTTTTTTCCCTGACATACCATAAGGCTTC TTCTTTCACCATCTTTGCTGAATAATTAAAGAGAAGAAATTTAAAAGAAAACACAAATACTTGT ATGCTTAACAATTCCTGTGGGCTTCTATGGGAAAGGACCTCTTTTCAATCACCAGTATTGGATA AATATGAGGAAAAATTAATTATAATAAACAATCGAGGGCTAATCATTTACTTTTTGGCCAATGA AGGAAATGAAATTATGTATACAGAGAATTGGTAGCAAGTAATTTTGATTAATAGCAGGTCTGGC CAAAACTTTTATACGAAAATGTGACACCAGTAGTGCACTTCTGATAGAAGAAAGTTCTATGCAC CACTTACATACTACGTCCTTTCTGTTATAGAGAATGAAGAACATAGGTTGAAAGAACATAATAA CTTACAAGAGCTTTCTGTTTAGGAGATGATCGGCAGCAAATGACAGATGCACATCCAATAGCAA GCTCCAGAAACAGGTTCTTGACATCATCTTCGATAGCATAAGTGAGTGATTTGCCATCAATTAT CAAAGCCAGTGCCTCAGAAGTTTCACTTGATGCAGTAAGCAGCGCCTTCCCTTCATTCATCTGA TGGACGACGCTTGCCTTGAGAGCCTGCATAGTTGGCAAGGTCCAATGAACTTTTTTATTGCAAA ATAAGAGTTATTCTGACCAGAAATGAAATCTCTGTCATACTATTTCTTTTAGAACACATCCTGT AGACAAATTATATTGATGTCATCACAGCAACTGCGAAACTGCTTTACTGGCACGATAGAAACAA GCTAATCCAATCTTCTCCACATGATAATTATAGCTCTATAAAATTCTCTTATTAATATCATATC ATTATTCTTAATTCATTTTAGCTAACAAAATGAGAAGGATATTTCTCAGCTTGGAAGTGAGGGG ATCATACATTCATGCATATGAATTAATAGATAAGAGGGAGATCTCGGAGAAATCACATTTGGAA CTTTCTCCTGCAAACTGTTAGACCAAGATGACGTGAGGATATATGTGCTTTTCAAGGTTTTGGA CATGTTCAGTTAGACTAAGGGGAAATTTATATTGACCAGCAGCTAGAGTTGGACCAGATGTAGC TAAAGGAAAAAAAGGAAATGAAATAACTTAGATGTAGACATTGGATGAGTTGTGGGAAGACTAC TATACCAGTAAAAACTAGAAACGATAAACAGTCTCAGTGTCTGGAGAGAGCTTTTTTGAAATTA CTAGACTGGAAAAGTCAAAAAAAAAATTATTTTGTATTTTGCATAGAGGAGATCAAGAATTCTG GAACATCTATGTGATGGAAATTGTTAATACAGTAAGGGATTTCCTAAAACTCTTTAGAATGTAC TCCCTTCACATTCAAGTAGTCCACATAGAAAAGATACTAGTGGGTCATCCTCTCTAAGACTTGG TCCCTTATTGTGGTTCTGCTGTTCGCATCTGAGATTGCAGCACTAGCTGCGAAGAGTTAGGATG ATTTCCTCTTCCTACCGTTATCAAATATATATCACTACATTGCTTCTATGCATCATTAACTGAA CTTTCTATTGATCTAAAGAGTCACTGAAAGAGAACAGCAGATGAAATCAGAAATTACCGTAACA CCAGCAGCTTTGTCCTCCATTTTCTCTAGAGCTTTGTTTTCTGGAGTATCTGAACTGATTATTA TTTGCTTCATCCCTTGTCTGAGTAAACTACAGGCAAAGCTGCAAGATTCAACATCAATTATGAT GTATTAGTATACAGGATTAAACATCTATTAGACAGAAAATGACGTCCACTCAAACATACCCAAT ATTGATGGCTGTCTCCATCTTATCTCCTGTTAAAACCCATATTTTTATTCCCGCTTGTGCAAGC TTGTCAATACACTCAGGAACCTGTTCAGAAAAAACATTCAATTTCAAACACTTCGGCTAATTTT TAAAGTAACTAAATATACATAACCATTTTTAGTTCAGAATAGAACAAAACAATTTCTTTAGGAT TCAAAAGAGAAATAATACTGATGAACGTTTATTAGTTTAGATGAAGAATAGAGCTCTTTGAATG ATGACACTCCAAACAAGTTGCTATGGAATAGCAAGCCAAATGATTTCTTATCAACTATACTAAA AATCAACATTCCTAGAATTTTTTTAGACCCACCCCATTCTGAAGTTTGTCCTCAACAGCTGTAG CACCAAGAAGAATCAAATCCCTCTCAATCTTTTCAGCTACTTCTTCAATCATATCCTCACGATC TGCACTTAATGAGTTTTTTGCCTCAGTAAATTCATGATTGAACTCATCATATTCTTCCTCATCA AGTTCACGATATGCAAGAACCAAAGTCCTCAAGCCAGCATCAGCATACTCGCCAATGTGCTCCC TGGTGGGCTCTTCAAACTCTCTTCCATCCCTTGCAAGTCTTTCAAACATGACA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.121432871

Conservation Information
Conserved circRNAs	NA
PMCS	0.121432871

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5095101-5092526(+)
5095186-5092590(+)
5095245-5095238(-)
5092582-5095238(-)
						
						Potential amino acid sequence
						
							MIELIIFFLIKFTICKNQSPQASISILANVLPGGLFKLSSIPCKSFKHDTAFLQPH*(+)
MCSLVGSSNSLPSLASLSNMTLHSFNPTDTNTNICFLKHPNIICPITNC*(+)
MFERLARDGREFEEPTREHIGEYADAGLRTLVLAYRELDEEEYDEFNHEFTEAKNSLSADREDM
IEEVAEKIERDLILLGATAVEDKLQNGVPECIDKLAQAGIKIWVLTGDKMETAINIGFACSLLR
QGMKQIIISSDTPENKALEKMEDKAAGVTALKASVVHQMNEGKALLTASSETSEALALIIDGKS
LTYAIEDDVKNLFLELAIGCASVICCRSSPKQKALVTRLVKSKTGKTTLAIGDGANDVGMLQEA
DIGVGISGVEGMQCHV*(-)
MGQMMLGCFKKQILVLVSVGLKECSVMFERLARDGREFEEPTREHIGEYADAGLRTLVLAYREL
DEEEYDEFNHEFTEAKNSLSADREDMIEEVAEKIERDLILLGATAVEDKLQNGVPECIDKLAQA
GIKIWVLTGDKMETAINIGFACSLLRQGMKQIIISSDTPENKALEKMEDKAAGVTALKASVVHQ
MNEGKALLTASSETSEALALIIDGKSLTYAIEDDVKNLFLELAIGCASVICCRSSPKQKALVTR
LVKSKTGKTTLAIGDGANDVGMLQEADIGVGISGVEGMQCHV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5095101-5092526(+) 5095186-5092590(+) 5095245-5095238(-) 5092582-5095238(-)
Potential amino acid sequence	MIELIIFFLIKFTICKNQSPQASISILANVLPGGLFKLSSIPCKSFKHDTAFLQPH(+) MCSLVGSSNSLPSLASLSNMTLHSFNPTDTNTNICFLKHPNIICPITNC(+) MFERLARDGREFEEPTREHIGEYADAGLRTLVLAYRELDEEEYDEFNHEFTEAKNSLSADREDM IEEVAEKIERDLILLGATAVEDKLQNGVPECIDKLAQAGIKIWVLTGDKMETAINIGFACSLLR QGMKQIIISSDTPENKALEKMEDKAAGVTALKASVVHQMNEGKALLTASSETSEALALIIDGKS LTYAIEDDVKNLFLELAIGCASVICCRSSPKQKALVTRLVKSKTGKTTLAIGDGANDVGMLQEA DIGVGISGVEGMQCHV(-) MGQMMLGCFKKQILVLVSVGLKECSVMFERLARDGREFEEPTREHIGEYADAGLRTLVLAYREL DEEEYDEFNHEFTEAKNSLSADREDMIEEVAEKIERDLILLGATAVEDKLQNGVPECIDKLAQA GIKIWVLTGDKMETAINIGFACSLLRQGMKQIIISSDTPENKALEKMEDKAAGVTALKASVVHQ MNEGKALLTASSETSEALALIIDGKSLTYAIEDDVKNLFLELAIGCASVICCRSSPKQKALVTR LVKSKTGKTTLAIGDGANDVGMLQEADIGVGISGVEGMQCHV(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0012s05450_circ_g.1

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