Plant Circular RNA Database

Detail information of POPTR_0019s09540_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0019s09540_circ_g.1
					
						ID in PlantcircBase
						pop_circ_004294
					
						Alias
						Chr19:10051654-10053609
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr19: 11132012-11133967  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0019s09540						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							POPTR_0019s09540_circ_g.2 						
					
						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_0019s09540.1:3

General Information
CircRNA Name	POPTR_0019s09540_circ_g.1
ID in PlantcircBase	pop_circ_004294
Alias	Chr19:10051654-10053609
Organism	Populus trichocarpa
Position	chr19: 11132012-11133967 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0019s09540
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	POPTR_0019s09540_circ_g.2
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_0019s09540.1:3

			
						 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  
						
							TTCGCGGACTTTGACAAAGGAAAGTGCATGTCATTGAACACATATGTAATGAGATTGTTCCCAA
CAGCAGCAATTCCCATCATCTCAAAAGCCTGAAGCCctgaacttttcagtatgaagcaagttgc
tggcatcagttgacgttgctgggacgtggcttgacacattgttgtggcagccatgaagcatctg
tgcgttcg

									
								

					

						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
						
							CTGAACTTTTCAGTATGAAGCAAGTTGCTGGCATCAGTTGACGTTGCTGGGACGTGGCTTGACA
CATTGTTGTGGCAGCCATGAAGCATCTGTGCGTTCGAGGGACAGATTTGCTTTCTTTTTGTTAT
TGCAGCAACAAAAACCTAATGAAGAGAATAGAAAATTAATCAAAGAATTAAAGGAGACAAACAA
TTGTAGACATATATTGAAAAATTAAAAATAACAAAGCAGGTAGATCATGGGCGGTGGCATGTAT
ATGGTGATGCCAACTAGCTTTTTTTTTATTTTTTTTATTCAGGAATAAAAAACGAGGCGCAGGA
TGCGATGATCCTTGAATCAGATGTGTATCAAGGACATGGTGCATGAAGTCATAACATAGATCAC
TAAGCTGTATGCCCTTTATATTAAATAAAGCTAATTGTAATATTAAATATTAAGGATTAATGTT
ATTTTAATCAGGGAAAGGAAACCAGACATAGCCTTTGATTAGTCAAATTATATGCACTAGTTTA
GTTCTATAGTCACAAAGATTGAATCTGAACCAAGAAAAGAAACAACAAATAAAACCTGAGCCAC
AGAAAAATTACAAAAGATGTTGAATTATCAGGCAAAAGGAAAATCTGATAGCAATTGGAGAGAA
AGAAACTGGTGGATATATAGTTAATCAAAAGTAAAAAAAAAAAAAAAAACAACTTTTAATCTCC
ACACACACTTTTCTATTTTAAAGCAAGAGGGAGAGGGATGGACTTAGGTTCAGGTTAAGCTTAA
ATCAAAGGGGGGAAAAGAGTTAAGTAGGAAAAGCAGACTTGCATGCTTTTTGCTCACAACCCAG
AGGTAAAAAGCCTTCCTAACTTGTAAAATTAAACATAAAAAGTCTATAAAGCATTCAAAGTTAA
AGAAGTAAGGAAAATGAGATTACCTGAGCAAATGGAGTGAAGATACTTCCTTTAGGAGGCTTGT
TCCTGTACGAAAATGAACCTGAAATCAAGCAAATCAATCCTACAGCCATGGCAGCAGCAGAGAC
TCCAAAACCAACATCCATTCCTGAATGGGTTTGGACCCAAACAAGAACTGTTAGGGCAATAAGC
TCTCCAATGCAGAAAGCAAAATAGGCTACATTGAAGTAGGTGGAGAGCTTCTTGGATTGCTTGG
GGTCTTCCTTCTTGAACTGGTCTGCCCCGTGAGAAATTATGTTTGGTTTTAGACATCCACTTCC
TAGAGCCACCAAGTAGAGCGCCAAAAAGAATATCAAAGCCTTGTAGCCCTTGGCTTCCACACAG
TCAACTCCATCAGATACCATATCACAGCTAGGTGGCCTCAACTGCGGGAGATGGGCTTGAACGG
ACAATAATATGAAACCCTGTAGCATGGGGGGGGGATTAATGGTGGTGAATACTTCGAAGAAGAA
TGATTGAATATTTTTCATGTGGGAATTTCTTAGCTCCTTCGGGGCCAGAAAACAATTATAGGAA
AATAATAAAAAAGAATACAACATGGGGATTCTTCTAAATATATATATAAGAATGGAATGACGAG
GATATTCAACTTATGCGGGATGTTCAATAGATTTCTTATTTACGGTAAGATTATTTTGAAGGAT
AAAAAAATATAGGTGCCTCTATATTTCTAGACAGACAAAAGAATCTTAGATAGGCAACTTGTAG
ATAGTGTTTGAGTTTTAAAAGATTTAGACAGTACAAAATAAAAGATAATGTCGGAAGAAAAAAG
GAGTACTTACAGAGAGCTCCACAAACCCAAAGATCAGCATGGTCCAAAAGCTCCCAAGGTAAGA
ATCTGAGAGGAACCCACCAAGGAGGGATAGGAGGAAGACAGTTCCTACGAAGTTCGTGACTATG
TTCGCGGACTTTGACAAAGGAAAGTGCATGTCATTGAACACATATGTAATGAGATTGTTCCCAA
CAGCAGCAATTCCCATCATCTCAAAAGCCTGAAGCC
						
					

			
		

Sequences
Splice junction sequence	TTCGCGGACTTTGACAAAGGAAAGTGCATGTCATTGAACACATATGTAATGAGATTGTTCCCAA CAGCAGCAATTCCCATCATCTCAAAAGCCTGAAGCCctgaacttttcagtatgaagcaagttgc tggcatcagttgacgttgctgggacgtggcttgacacattgttgtggcagccatgaagcatctg tgcgttcg
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	CTGAACTTTTCAGTATGAAGCAAGTTGCTGGCATCAGTTGACGTTGCTGGGACGTGGCTTGACA CATTGTTGTGGCAGCCATGAAGCATCTGTGCGTTCGAGGGACAGATTTGCTTTCTTTTTGTTAT TGCAGCAACAAAAACCTAATGAAGAGAATAGAAAATTAATCAAAGAATTAAAGGAGACAAACAA TTGTAGACATATATTGAAAAATTAAAAATAACAAAGCAGGTAGATCATGGGCGGTGGCATGTAT ATGGTGATGCCAACTAGCTTTTTTTTTATTTTTTTTATTCAGGAATAAAAAACGAGGCGCAGGA TGCGATGATCCTTGAATCAGATGTGTATCAAGGACATGGTGCATGAAGTCATAACATAGATCAC TAAGCTGTATGCCCTTTATATTAAATAAAGCTAATTGTAATATTAAATATTAAGGATTAATGTT ATTTTAATCAGGGAAAGGAAACCAGACATAGCCTTTGATTAGTCAAATTATATGCACTAGTTTA GTTCTATAGTCACAAAGATTGAATCTGAACCAAGAAAAGAAACAACAAATAAAACCTGAGCCAC AGAAAAATTACAAAAGATGTTGAATTATCAGGCAAAAGGAAAATCTGATAGCAATTGGAGAGAA AGAAACTGGTGGATATATAGTTAATCAAAAGTAAAAAAAAAAAAAAAAACAACTTTTAATCTCC ACACACACTTTTCTATTTTAAAGCAAGAGGGAGAGGGATGGACTTAGGTTCAGGTTAAGCTTAA ATCAAAGGGGGGAAAAGAGTTAAGTAGGAAAAGCAGACTTGCATGCTTTTTGCTCACAACCCAG AGGTAAAAAGCCTTCCTAACTTGTAAAATTAAACATAAAAAGTCTATAAAGCATTCAAAGTTAA AGAAGTAAGGAAAATGAGATTACCTGAGCAAATGGAGTGAAGATACTTCCTTTAGGAGGCTTGT TCCTGTACGAAAATGAACCTGAAATCAAGCAAATCAATCCTACAGCCATGGCAGCAGCAGAGAC TCCAAAACCAACATCCATTCCTGAATGGGTTTGGACCCAAACAAGAACTGTTAGGGCAATAAGC TCTCCAATGCAGAAAGCAAAATAGGCTACATTGAAGTAGGTGGAGAGCTTCTTGGATTGCTTGG GGTCTTCCTTCTTGAACTGGTCTGCCCCGTGAGAAATTATGTTTGGTTTTAGACATCCACTTCC TAGAGCCACCAAGTAGAGCGCCAAAAAGAATATCAAAGCCTTGTAGCCCTTGGCTTCCACACAG TCAACTCCATCAGATACCATATCACAGCTAGGTGGCCTCAACTGCGGGAGATGGGCTTGAACGG ACAATAATATGAAACCCTGTAGCATGGGGGGGGGATTAATGGTGGTGAATACTTCGAAGAAGAA TGATTGAATATTTTTCATGTGGGAATTTCTTAGCTCCTTCGGGGCCAGAAAACAATTATAGGAA AATAATAAAAAAGAATACAACATGGGGATTCTTCTAAATATATATATAAGAATGGAATGACGAG GATATTCAACTTATGCGGGATGTTCAATAGATTTCTTATTTACGGTAAGATTATTTTGAAGGAT AAAAAAATATAGGTGCCTCTATATTTCTAGACAGACAAAAGAATCTTAGATAGGCAACTTGTAG ATAGTGTTTGAGTTTTAAAAGATTTAGACAGTACAAAATAAAAGATAATGTCGGAAGAAAAAAG GAGTACTTACAGAGAGCTCCACAAACCCAAAGATCAGCATGGTCCAAAAGCTCCCAAGGTAAGA ATCTGAGAGGAACCCACCAAGGAGGGATAGGAGGAAGACAGTTCCTACGAAGTTCGTGACTATG TTCGCGGACTTTGACAAAGGAAAGTGCATGTCATTGAACACATATGTAATGAGATTGTTCCCAA CAGCAGCAATTCCCATCATCTCAAAAGCCTGAAGCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.098628954

Conservation Information
Conserved circRNAs	NA
PMCS	0.098628954

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11132095-11133954(-)
11133952-11133954(-)
						
						Potential amino acid sequence
						
							MAATTMCQATSQQRQLMPATCFILKSSGLQAFEMMGIAAVGNNLITYVFNDMHFPLSKSANIVT
NFVGTVFLLSLLGGFLSDSYLGSFWTMLIFGFVELSGFILLSVQAHLPQLRPPSCDMVSDGVDC
VEAKGYKALIFFLALYLVALGSGCLKPNIISHGADQFKKEDPKQSKKLSTYFNVAYFAFCIGEL
IALTVLVWVQTHSGMDVGFGVSAAAMAVGLICLISGSFSYRNKPPKGSIFTPFAQVFVAAITKR
KQICPSNAQMLHGCHNNVSSHVPATSTDASNLLHTEKFRASGF*(-)
MMGIAAVGNNLITYVFNDMHFPLSKSANIVTNFVGTVFLLSLLGGFLSDSYLGSFWTMLIFGFV
ELSGFILLSVQAHLPQLRPPSCDMVSDGVDCVEAKGYKALIFFLALYLVALGSGCLKPNIISHG
ADQFKKEDPKQSKKLSTYFNVAYFAFCIGELIALTVLVWVQTHSGMDVGFGVSAAAMAVGLICL
ISGSFSYRNKPPKGSIFTPFAQVFVAAITKRKQICPSNAQMLHGCHNNVSSHVPATSTDASNLL
HTEKFRASGF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11132095-11133954(-) 11133952-11133954(-)
Potential amino acid sequence	MAATTMCQATSQQRQLMPATCFILKSSGLQAFEMMGIAAVGNNLITYVFNDMHFPLSKSANIVT NFVGTVFLLSLLGGFLSDSYLGSFWTMLIFGFVELSGFILLSVQAHLPQLRPPSCDMVSDGVDC VEAKGYKALIFFLALYLVALGSGCLKPNIISHGADQFKKEDPKQSKKLSTYFNVAYFAFCIGEL IALTVLVWVQTHSGMDVGFGVSAAAMAVGLICLISGSFSYRNKPPKGSIFTPFAQVFVAAITKR KQICPSNAQMLHGCHNNVSSHVPATSTDASNLLHTEKFRASGF(-) MMGIAAVGNNLITYVFNDMHFPLSKSANIVTNFVGTVFLLSLLGGFLSDSYLGSFWTMLIFGFV ELSGFILLSVQAHLPQLRPPSCDMVSDGVDCVEAKGYKALIFFLALYLVALGSGCLKPNIISHG ADQFKKEDPKQSKKLSTYFNVAYFAFCIGELIALTVLVWVQTHSGMDVGFGVSAAAMAVGLICL ISGSFSYRNKPPKGSIFTPFAQVFVAAITKRKQICPSNAQMLHGCHNNVSSHVPATSTDASNLL HTEKFRASGF(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0019s09540_circ_g.1

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