Plant Circular RNA Database

Detail information of POPTR_0019s08030_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0019s08030_circ_g.1
					
						ID in PlantcircBase
						pop_circ_004278
					
						Alias
						Chr19:8101753-8104336
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr19: 9350354-9352937  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0019s08030						
					
						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_0019s08030.2:2
POPTR_0019s08030.1:2

General Information
CircRNA Name	POPTR_0019s08030_circ_g.1
ID in PlantcircBase	pop_circ_004278
Alias	Chr19:8101753-8104336
Organism	Populus trichocarpa
Position	chr19: 9350354-9352937 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0019s08030
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_0019s08030.2:2 POPTR_0019s08030.1:2

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F: GCAATAGGGCTGCCTTTACG
 R: CTGACCAGGGGTAGTTGGAG
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	Yes 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	F: GCAATAGGGCTGCCTTTACG R: CTGACCAGGGGTAGTTGGAG 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  
						
							AAGGAACCATCACATTAGTTGGTTGAGGATGATGAAATTTACAAGTGCTACCAAACTTGCACTG
TCCTGTTCTTAAGTAATAAGCACACTCCATCTCATTcggacgtaaaggcagccctattgcactc
aagacacagtctggagcaggaattagcctctcccttggatggtggaatctacaaactgcaccaa
acttacag

									
								

					

						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: 621
Transcript exons: 9350354-9350680,9352644-9352937
CGGACGTAAAGGCAGCCCTATTGCACTCAAGACACAGTCTGGAGCAGGAATTAGCCTCTCCCTT
GGATGGTGGAATCTACAAACTGCACCAAACTTACAGTCTCCGGTCTTCATGTAAAACTGGCATT
CAGGCTGACCAGGTCTCTCAGGAAAAACACTCTCTCTTTGCAAGGCATAAAATCCCATGGGGAC
AGAATCAGAACGGTATGGAGAAAATGTCCCTTGAGATCCTGCATTGACTGATTCATTCTGGCGT
GAGGTTCCATATATCTGACTGTTTCCTGTTTGTTGCTGACTCTCTGGAGATGATACCGACCCAA
CCTGACCACTGTATGCATTCCAGCCAGGGACTGATACGACTCCCTGAGGTAGAATCAAAGGTGT
ATAATTTGAAGGAGCTTGCCAGCGTGGGCTGGTAATAAAAGATGCTCTTGACCAGTTTGTTGCA
AGTCCTCCTGGATAAGATTGCTGACCAGGGGTAGTTGGAGAATTGACAGTAGGGTAAACAGGAG
AGCCACGCAAAGGAACCATCACATTAGTTGGTTGAGGATGATGAAATTTACAAGTGCTACCAAA
CTTGCACTGTCCTGTTCTTAAGTAATAAGCACACTCCATCTCATT"
						
					

						Genomic sequence
						
							CGGACGTAAAGGCAGCCCTATTGCACTCAAGACACAGTCTGGAGCAGGAATTAGCCTCTCCCTT
GGATGGTGGAATCTACAAACTGCACCAAACTTACAGTCTCCGGTCTTCATGTAAAACTGGCATT
CAGGCTGACCAGGTCTCTCAGGAAAAACACTCTCTCTTTGCAAGGCATAAAATCCCATGGGGAC
AGAATCAGAACGGTATGGAGAAAATGTCCCTTGAGATCCTGCATTGACTGATTCATTCTGGCGT
GAGGTTCCATATATCTGACTGTTTCCTGTTTGTTGCTGACTCTCTGGAGATGATACCGACCCAA
CCTGACCCTGGAAAATAGTTCAACAAGCATGTCACATTTCTTGATACTCAACTCATGCACACAG
AAAGCTTAGCAAGTGAATGTCAACTGCAAAACAAAAGAGCATTAATAAAAATTCATTATGCCCT
TGATGCAGCTGTAAAAGCAGATGTCAGAGCCTCCTACAAATTCATTATTGGACCACAGCCCAAA
ATAACTCCAGAAACATTTGGAAATGTTCTAATTGCACCTAAACCAATCTTAGAGATCAAGATGA
CGTATTTGTTGGTCTCGTTTAAACTCCATATAGATGCCAAGATTTTCAGAGGATAATACTAGTT
ACGTAAATAGCTTAGTTTAAATGCACTAGCTAAAGATTGGTCACACTTTCGTGGAAACATTTAA
CTGTCATTTCATTTTGCTCTTTGGAAATCTTGATACTTTCATAGTTTTGCAGCTATGGCTGGAT
ATTTTAGAAACTTCCCTGCAATTTGTAATCCCAAAATGGTATTATGCCATACATTAAAATCCAA
ATGGCAAGATTTCCTCTTGATGCAAAAAAATCGTGTGCCTTAAGGCATAGCAGACTGCCAGACA
CCTCTAAAATAACCAACATTAATTGCACACTCAAAGCTGGGGAACAAGCAATTGCACGCTCAAT
GCTGAGGGGTTTACAGAACTTAAGAGAAAAAAAAATTATTTGGAGGGGCTAGATCAGAATATTA
TAGGGGCCAATATGAAAAATATTCTAATTTTCGAGGACTACAGTCAGCTTGGTAGGCATGGCAC
CCTCATGAAAGACGTAATCGCCAGCCCTAAGCACATGGAATATTGAAGAAAAAAAACAAATTTA
TTTGGAGGCTAGACTAGAATATTATAGGGACCAATATGAAAAATATTCTGATTTTCAGGACTAC
AGTCAGCTTGGTAGGCTTGGCACCCTCGTGAATGACATAAACACCAGCCCTATGCACATGAAAT
ATTGAAATTTCACTCAATAAAGTTTCCTAAAGTTTTCAGCAACTCTGCCACAACATCTATCATA
AAAAATACCAAAAACACCTACCTCCAAGTCCGAGATCCCAAAACAAACACTAGTACCTTTTACC
CCAAATAAGCAGAGTCACCCCATCACCATCACTAGTACTCATCACCAGCCAACCCCAATCAACT
TCGACCAAGCTTCAGCTCCAGACTCATCCCCTAATGCAACTAAGGGTAGCTGATACTTCCAAGT
TCAGATGTCCCAGAATATAAAATAACCAAAAAATTTTGCAAAACAGAAAATATCTGAATAAGGC
TACTAAAAGATTTTTCCGATCACAGTTGAAAGCAAAGCTTGTCAATCACTATTTATATAAAACT
AGCAAATTGTACAAAAAGCTGAGCGAATTTAATGTTTGAAAAGAAATACAAGTACCAAAAAGAT
GTAAATGTGCAACATCAACAACTAAGTACTATGAGTGAAGAACCATTTTCTCATACACAAAAGA
CACGCTAATTAAATCAGCCAAAAAAAATAATCAGTGGAAACAGCTTGGATCCAAGATTTAAGAC
TTTGGTTGGGGGAAGACATTTCATTTGATATTTTGGTGGATTCGGTTTCTGATCAAGCTAATTG
GCACTGGAGGATATGTAAAACCGATCCCAACTAGTTTGTGATTCTTTGTTGTTGTTGGGTACTA
GAAAAAAGTACTTGACATGTTAAGAAATCTCTTTTGACTTTCAGGGAAGAAAGAAACAAAAATT
TCCTTCTTAGGAATGAAACTATTAAATTTGGAAGACGAGAACCAGATATATCATCTTTATGGAG
GGAAAAAGCTTTCCATCCTTAAAGGGGATAAAATATGTTAGGAAAAATCTTTAGAGATAGAATT
ATTAAGGGAGGGGGAGAGCTGCCCTCATTGTGTGATCCAAGTCCAGTAGCCTCCAAAGTAACCA
AAAAATTGTACTTGATTGTATTCTCTGACAAAAGATAAAGAGGAGCTTACACTGTATGCATTCC
AGCCAGGGACTGATACGACTCCCTGAGGTAGAATCAAAGGTGTATAATTTGAAGGAGCTTGCCA
GCGTGGGCTGGTAATAAAAGATGCTCTTGACCAGTTTGTTGCAAGTCCTCCTGGATAAGATTGC
TGACCAGGGGTAGTTGGAGAATTGACAGTAGGGTAAACAGGAGAGCCACGCAAAGGAACCATCA
CATTAGTTGGTTGAGGATGATGAAATTTACAAGTGCTACCAAACTTGCACTGTCCTGTTCTTAA
GTAATAAGCACACTCCATCTCATT
						
					

			
		

Sequences
Splice junction sequence	AAGGAACCATCACATTAGTTGGTTGAGGATGATGAAATTTACAAGTGCTACCAAACTTGCACTG TCCTGTTCTTAAGTAATAAGCACACTCCATCTCATTcggacgtaaaggcagccctattgcactc aagacacagtctggagcaggaattagcctctcccttggatggtggaatctacaaactgcaccaa acttacag
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: 621 Transcript exons: 9350354-9350680,9352644-9352937 CGGACGTAAAGGCAGCCCTATTGCACTCAAGACACAGTCTGGAGCAGGAATTAGCCTCTCCCTT GGATGGTGGAATCTACAAACTGCACCAAACTTACAGTCTCCGGTCTTCATGTAAAACTGGCATT CAGGCTGACCAGGTCTCTCAGGAAAAACACTCTCTCTTTGCAAGGCATAAAATCCCATGGGGAC AGAATCAGAACGGTATGGAGAAAATGTCCCTTGAGATCCTGCATTGACTGATTCATTCTGGCGT GAGGTTCCATATATCTGACTGTTTCCTGTTTGTTGCTGACTCTCTGGAGATGATACCGACCCAA CCTGACCACTGTATGCATTCCAGCCAGGGACTGATACGACTCCCTGAGGTAGAATCAAAGGTGT ATAATTTGAAGGAGCTTGCCAGCGTGGGCTGGTAATAAAAGATGCTCTTGACCAGTTTGTTGCA AGTCCTCCTGGATAAGATTGCTGACCAGGGGTAGTTGGAGAATTGACAGTAGGGTAAACAGGAG AGCCACGCAAAGGAACCATCACATTAGTTGGTTGAGGATGATGAAATTTACAAGTGCTACCAAA CTTGCACTGTCCTGTTCTTAAGTAATAAGCACACTCCATCTCATT"
Genomic sequence	CGGACGTAAAGGCAGCCCTATTGCACTCAAGACACAGTCTGGAGCAGGAATTAGCCTCTCCCTT GGATGGTGGAATCTACAAACTGCACCAAACTTACAGTCTCCGGTCTTCATGTAAAACTGGCATT CAGGCTGACCAGGTCTCTCAGGAAAAACACTCTCTCTTTGCAAGGCATAAAATCCCATGGGGAC AGAATCAGAACGGTATGGAGAAAATGTCCCTTGAGATCCTGCATTGACTGATTCATTCTGGCGT GAGGTTCCATATATCTGACTGTTTCCTGTTTGTTGCTGACTCTCTGGAGATGATACCGACCCAA CCTGACCCTGGAAAATAGTTCAACAAGCATGTCACATTTCTTGATACTCAACTCATGCACACAG AAAGCTTAGCAAGTGAATGTCAACTGCAAAACAAAAGAGCATTAATAAAAATTCATTATGCCCT TGATGCAGCTGTAAAAGCAGATGTCAGAGCCTCCTACAAATTCATTATTGGACCACAGCCCAAA ATAACTCCAGAAACATTTGGAAATGTTCTAATTGCACCTAAACCAATCTTAGAGATCAAGATGA CGTATTTGTTGGTCTCGTTTAAACTCCATATAGATGCCAAGATTTTCAGAGGATAATACTAGTT ACGTAAATAGCTTAGTTTAAATGCACTAGCTAAAGATTGGTCACACTTTCGTGGAAACATTTAA CTGTCATTTCATTTTGCTCTTTGGAAATCTTGATACTTTCATAGTTTTGCAGCTATGGCTGGAT ATTTTAGAAACTTCCCTGCAATTTGTAATCCCAAAATGGTATTATGCCATACATTAAAATCCAA ATGGCAAGATTTCCTCTTGATGCAAAAAAATCGTGTGCCTTAAGGCATAGCAGACTGCCAGACA CCTCTAAAATAACCAACATTAATTGCACACTCAAAGCTGGGGAACAAGCAATTGCACGCTCAAT GCTGAGGGGTTTACAGAACTTAAGAGAAAAAAAAATTATTTGGAGGGGCTAGATCAGAATATTA TAGGGGCCAATATGAAAAATATTCTAATTTTCGAGGACTACAGTCAGCTTGGTAGGCATGGCAC CCTCATGAAAGACGTAATCGCCAGCCCTAAGCACATGGAATATTGAAGAAAAAAAACAAATTTA TTTGGAGGCTAGACTAGAATATTATAGGGACCAATATGAAAAATATTCTGATTTTCAGGACTAC AGTCAGCTTGGTAGGCTTGGCACCCTCGTGAATGACATAAACACCAGCCCTATGCACATGAAAT ATTGAAATTTCACTCAATAAAGTTTCCTAAAGTTTTCAGCAACTCTGCCACAACATCTATCATA AAAAATACCAAAAACACCTACCTCCAAGTCCGAGATCCCAAAACAAACACTAGTACCTTTTACC CCAAATAAGCAGAGTCACCCCATCACCATCACTAGTACTCATCACCAGCCAACCCCAATCAACT TCGACCAAGCTTCAGCTCCAGACTCATCCCCTAATGCAACTAAGGGTAGCTGATACTTCCAAGT TCAGATGTCCCAGAATATAAAATAACCAAAAAATTTTGCAAAACAGAAAATATCTGAATAAGGC TACTAAAAGATTTTTCCGATCACAGTTGAAAGCAAAGCTTGTCAATCACTATTTATATAAAACT AGCAAATTGTACAAAAAGCTGAGCGAATTTAATGTTTGAAAAGAAATACAAGTACCAAAAAGAT GTAAATGTGCAACATCAACAACTAAGTACTATGAGTGAAGAACCATTTTCTCATACACAAAAGA CACGCTAATTAAATCAGCCAAAAAAAATAATCAGTGGAAACAGCTTGGATCCAAGATTTAAGAC TTTGGTTGGGGGAAGACATTTCATTTGATATTTTGGTGGATTCGGTTTCTGATCAAGCTAATTG GCACTGGAGGATATGTAAAACCGATCCCAACTAGTTTGTGATTCTTTGTTGTTGTTGGGTACTA GAAAAAAGTACTTGACATGTTAAGAAATCTCTTTTGACTTTCAGGGAAGAAAGAAACAAAAATT TCCTTCTTAGGAATGAAACTATTAAATTTGGAAGACGAGAACCAGATATATCATCTTTATGGAG GGAAAAAGCTTTCCATCCTTAAAGGGGATAAAATATGTTAGGAAAAATCTTTAGAGATAGAATT ATTAAGGGAGGGGGAGAGCTGCCCTCATTGTGTGATCCAAGTCCAGTAGCCTCCAAAGTAACCA AAAAATTGTACTTGATTGTATTCTCTGACAAAAGATAAAGAGGAGCTTACACTGTATGCATTCC AGCCAGGGACTGATACGACTCCCTGAGGTAGAATCAAAGGTGTATAATTTGAAGGAGCTTGCCA GCGTGGGCTGGTAATAAAAGATGCTCTTGACCAGTTTGTTGCAAGTCCTCCTGGATAAGATTGC TGACCAGGGGTAGTTGGAGAATTGACAGTAGGGTAAACAGGAGAGCCACGCAAAGGAACCATCA CATTAGTTGGTTGAGGATGATGAAATTTACAAGTGCTACCAAACTTGCACTGTCCTGTTCTTAA GTAATAAGCACACTCCATCTCATT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.414088935

Conservation Information
Conserved circRNAs	NA
PMCS	0.414088935

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9352933-9350356(-)
						
						Potential amino acid sequence
						
							MECAYYLRTGQCKFGSTCKFHHPQPTNVMVPLRGSPVYPTVNSPTTPGQQSYPGGLATNWSRAS
FITSPRWQAPSNYTPLILPQGVVSVPGWNAYSGQVGSVSSPESQQQTGNSQIYGTSRQNESVNA
GSQGTFSPYRSDSVPMGFYALQRESVFPERPGQPECQFYMKTGDCKFGAVCRFHHPRERLIPAP
DCVLSAIGLPLRPNEMECAYYLRTGQCKFGSTCKFHHPQPTNVMVPLRGSPVYPTVNSPTTPGQ
QSYPGGLATNWSRASFITSPRWQAPSNYTPLILPQGVVSVPGWNAYSGQVGSVSSPESQQQTGN
SQIYGTSRQNESVNAGSQGTFSPYRSDSVPMGFYALQRESVFPERPGQPECQFYMKTGDCKFGA
VCRFHHPRERLIPAPDCVLSAIGLPLRPNEMECAYYLRTGQCKFGSTCKFHHPQPTNVMVPLRG
SPVYPTVNSPTTPGQQSYPGGLATNWSRASFITSPRWQAPSNYTPLILPQGVVSVPGWNAYSGQ
VGSVSSPESQQQTGNSQIYGTSRQNESVNAGSQGTFSPYRSDSVPMGFYALQRESVFPERPGQP
ECQFYMKTGDCKFGAVCRFHHPRERLIPAPDCVLSAIGLPLRPNEMECAYYLRTGQCKFGSTCK
FHHPQPTNVMVPLRGSPVYPTVNSPTTPGQQSYPGGLATNWSRASFITSPRWQAPSNYTPLILP
QGVVSVPGWNAYSGQVGSVSSPESQQQTGNSQIYGTSRQNESVNAGSQGTFSPYRSDSVPMGFY
ALQRESVFPERPGQPECQFYMKTGDCKFGAVCRFHHPRERLIPAPDCVLSAIGLPLRP(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9352933-9350356(-)
Potential amino acid sequence	MECAYYLRTGQCKFGSTCKFHHPQPTNVMVPLRGSPVYPTVNSPTTPGQQSYPGGLATNWSRAS FITSPRWQAPSNYTPLILPQGVVSVPGWNAYSGQVGSVSSPESQQQTGNSQIYGTSRQNESVNA GSQGTFSPYRSDSVPMGFYALQRESVFPERPGQPECQFYMKTGDCKFGAVCRFHHPRERLIPAP DCVLSAIGLPLRPNEMECAYYLRTGQCKFGSTCKFHHPQPTNVMVPLRGSPVYPTVNSPTTPGQ QSYPGGLATNWSRASFITSPRWQAPSNYTPLILPQGVVSVPGWNAYSGQVGSVSSPESQQQTGN SQIYGTSRQNESVNAGSQGTFSPYRSDSVPMGFYALQRESVFPERPGQPECQFYMKTGDCKFGA VCRFHHPRERLIPAPDCVLSAIGLPLRPNEMECAYYLRTGQCKFGSTCKFHHPQPTNVMVPLRG SPVYPTVNSPTTPGQQSYPGGLATNWSRASFITSPRWQAPSNYTPLILPQGVVSVPGWNAYSGQ VGSVSSPESQQQTGNSQIYGTSRQNESVNAGSQGTFSPYRSDSVPMGFYALQRESVFPERPGQP ECQFYMKTGDCKFGAVCRFHHPRERLIPAPDCVLSAIGLPLRPNEMECAYYLRTGQCKFGSTCK FHHPQPTNVMVPLRGSPVYPTVNSPTTPGQQSYPGGLATNWSRASFITSPRWQAPSNYTPLILP QGVVSVPGWNAYSGQVGSVSSPESQQQTGNSQIYGTSRQNESVNAGSQGTFSPYRSDSVPMGFY ALQRESVFPERPGQPECQFYMKTGDCKFGAVCRFHHPRERLIPAPDCVLSAIGLPLRP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0019s08030_circ_g.1

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