Plant Circular RNA Database

Detail information of POPTR_0001s13700_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0001s13700_circ_g.1
					
						ID in PlantcircBase
						pop_circ_000157
					
						Alias
						Chr01:4386347-4390225
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr1: 10786719-10790597  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0001s13700						
					
						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_0001s13700.1:5

General Information
CircRNA Name	POPTR_0001s13700_circ_g.1
ID in PlantcircBase	pop_circ_000157
Alias	Chr01:4386347-4390225
Organism	Populus trichocarpa
Position	chr1: 10786719-10790597 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0001s13700
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_0001s13700.1:5

			
						 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  
						
							TTGAGTGGGCCTTAAGCCCAATTCTCAGTCATGGAGTCAGTATAAATTTCCGTGACATTAATGG
GTGGACCGCTCTCCACTGGGCTGCTCATTTTGGAAGggaaaaccgtctcctggatctgctgcac
agctatcacccatattctcttatagtcctggcactaatactagtcagactcaaggatctacctc
tgcaatta

									
								

					

						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
						
							GGAAAACCGTCTCCTGGATCTGCTGCACAGCTATCACCCATATTCTCTTATAGTCCTGGCACTA
ATACTAGTCAGACTCAAGGATCTACCTCTGCAATTAGTAGTGTATATGAACCATACCAGAGTTT
TTCCAGTCCAGCATCTGTAGATGTTAGCTCTGGATTAGGTATCAAGGACAATGAGGTGGGTAGG
ACAGCAGAGTTTACTAGTTCTGCTAATAAGGAGGTTACTCAATTTTTCCGAAGGCTGGAGGAGC
AGTTGAGTTTGAATGAGGACAGCGCTGAAGAAATTGGCCCATTTGGTGCTGAAGAGGGAGCCAT
AAATGATACAAAAATTCTGGAATATGTAAATAACATCTCCAAAGAGGATCAATCTAAGAATTTA
CTTCATGGATCACTGTATATTGTTGATTATCAATCTTATGGTGGACTTGCTGGAAATCAACTAG
AGAGAAACAATCTTGCACCTCTTCAGGATGCAGGTTTGTTTTGTCTTTATTCGGTGCTTGTACT
CATTTAAACATGACATTCTTCTTCTGCTAGTTTATCGAAGCTGCATTATGTCTGGCTGCATTTA
ATTTTATTTGAATCATTTCATTTGTATCCTTATGTCATGTTTAGTATTGGTAATCGTCTTTTTT
TCTATATCTGACATTAGTTTCTTATTCGTTTCATTAGTTTCATTCAATTTTATTCAGTGTCGCT
GGCTTAAAATTTTGCAAGTCCAATTCTTGAGTGCAATGTTTTGTTTGCTATTGTTCTGGGTTTC
AGTTTTATTAATTTCTATGACTTAGCTCAGGTGGTCATAAATGGCTGGGTTGTCTTATATCCGT
GGTTCAAATCTTACCTGTTGAGAGAGAGGCATACCAGAGATTCCAGAAGAGGTTTTATTTGACA
GACAGTTCGTGAGTAAAACTCTCACATAATACTCGAATAAAATAAGGGAAAATAAAATTCCCTC
ACAGATGAAGTCCAATGGATTTGTTTTGGTATGATGGTCAATAAATGGTTGAGAGGAATACTAG
AGTCGTGATTGGAAGGTGAATACAATATACATCATTCTGATTCTGTAATTGTCCCAATGTAAAT
TCGAGATTGTGGACCTGATACTTGTCTTTCTTACAGCATATGTTGTAGTTCTATTAGAATCACA
ATTGTGTTGAAAAGGGAAAAGAATTTCCAATGTCATCAGATGTTGAGGCTTGATGAGGTTGAGG
CACTGGGTTTCATTACTCATCAAGTTACTATTCGGGATATTTCACACTAACTTGTACATGGCCT
CTGAGAATTAATGGATTAAAAGTGATCTTTTGATCATGGATGGAGAGGTTATTCATCTTCCAAG
GTCCACATTTTGTTCAATATGATCCTTTTATTTTAGTTGTGGTCTGACCACCAATTATTCTCTT
GTTCTTTGAAAACCTGGAATTTTGGACTTTTGGCAACCAGCTTGCTACCTCCTGAAAACACTTC
TTGGAGATTCTTTAGTCATTCCTTGCTAGTGTTACTCCATGCTTGTTCTTGCATTGGTGCTGTA
AATGGAAACTACGAGATCTACTAAGTTTTTGTTTAGGTATCTGCCTTCATTTCTTCATTGATGT
ATAAATAAGATATAATAGGAAAGGAAGCAATAAAGAGCTGCTGATGGCTTTATGGTTTTTAGGT
GATAGTGGCGCTTACCAGCAACCATATTCACATTATTATACAGATGGAAGTGAAGAACCCCTTC
CCTGGAATGAAGGGATTGAGTCCTATAAGACTTCATCAGGCATTGAGTACCAGGTGAAATATAT
GGACACTGTAAATGGGCATATAGCTTTCTGTTACCTCTTTGATATCCTCTTATATTATGGTTGT
ATTGTTTATGGATGGCTGTATTTTTCAACAGGAAAAGACCAAGTCCTCTTTAAGTACAGAACCA
GCTCAAGAGCAAGAAAACTCTTATTGGATAAATTTCAATGAACCCAATGTCAGAAACTGTATGA
TATCTTATTCCCTTAATAGTGATTGACATTTTAATTTTCAGCATCTAATGAACTTGCATCAAGC
TTTTAACATTTTTTCATATTACCAGCTTCTTTGTTGCTGCCTCAAGAAGTTGAAAATTTTGAAC
TCCCTGCATATTCTTCTGTGATAGAAACACATGAAAACAATTCCAACTTCTATGCAATGCTATA
TGACCAAGACCATCTTGGAATACCCAATGAAGCAGATTCAAATTTGACAGTTGCACAGCAGCAG
AAGTTTACTATCCATGAAATATCCCCAGAATGGGGTTATGCCACTGAGGCTACAAAGGTATGAG
TCATCAGATTCCATGAACTGCTATGCTCTTTACAACATTTCTCATTATTCATTCATTGAGATGG
CAGTATTATTCCAAGAATGGAACTGTTGTGTAGTTTGAAGAATGTACAAACTCATTAATATGCA
TGTTAAAATAGGCTGCTCCTTCAGTGCATCGTGACATACTTCTAATTCGATAGTACAGTTTTCC
TTGTTTCTGGATGTGTTCATCCATTTCTTTTGCTTTTATGCTTTCACAGATGCATCCATCTGAC
ACCATGTCATGTGAGATGTGACTAGTTTTATGCTACCTGACTGCCTATTTGCAACCATCCTCAT
TCTTCACCAGGATAGAAGGAAATGGAGGAAACAAATCTCTTATAACTTATTCCTAGTTTATGAT
CTGGCTAAATTGGTTCCTGAATTCAATGAAGAAAGGTTTTAAGAAATTAGAAAAACATGACTAT
ATATTCCAGGACACTGAGGTGCTTGAATGCAGCATGTACTCCATGATCATGTTGCAAATAAATT
ATAAAATCAGTGCAGGACCAGAATCATCTTATGCTTGTCTGATGCCAATTCTAAGTGATAGATT
GCTGCACTCTCTTTCTAGGCTAAGAGTAATTCAAAATTTCATGGACAGCAATCCCAACCCTGGT
TCTGATTGGTACCATTTGAAAAACCAGATAAGACTATTTACTGGAAGTTCAATTGTCCTTCCTA
ATAACTTGATGTTTTGGTGAACCTTCTTTGAACTACCAATTCGCTTGCAAACTAAACAGCAAGG
ATCTCATAAACCTTCCTGATGCACCACTGGACTTCTCTTATGCATTGTTTTGAGGAGTTTTTTC
TTTTTAGATCTCAATTAAGAAATTCAAGTCCAAATTTTCAAGCCTTGATTCTCAATGCAGGTCA
TCATTGTTGGATCGTTTCTCTGTGACCCATCGGAGTCTTCATGGATGTGCATGTTCGGTGACAT
TGAGGTTCCTCTTCAAATCATTCAAGAAGGTGTCATTCGTTGTGAGTGTCCTCCCCACCATCCC
GGAAAGGTCACTCTCTGCATTACTTCTGGCAATCGGGAGTCCTGCAGTGAGATCAGAGGCTTTG
AGTACCGAGCTAAGGATAGTAGTTGTGCTCACTGTATCTTATCCCAGACAGAAGCTACTAAGAG
TCCAGATGAGCTATTGTTACTTTTCAGATTTGTGCAGATGCTTCTGTCTGATTATTCTTTGCAG
AGAGGAGACTCTGTAGAAATGGGAATTCATCTTCTGAGAGAATTGAAGGCTGATGATGATACAT
GGGGTGATATCATAGAGGCTCTCTTAGTTGGCAGTGGAACTTCATCCATGACAGTCGATTGGCT
TCTGCAACAACTTCTGAATGACAAGCTGCAGCAGTGGCTTTCCTCCAAGTCTCAGGAAGGACAT
GATCAACCTGGGTGTTCATTTTCCAAGAAAGAGCAAGGGATCATTCACATGGTTGCTGGGTTAG
GCTTTGAGTGGGCCTTAAGCCCAATTCTCAGTCATGGAGTCAGTATAAATTTCCGTGACATTAA
TGGGTGGACCGCTCTCCACTGGGCTGCTCATTTTGGAAG
						
					

			
		

Sequences
Splice junction sequence	TTGAGTGGGCCTTAAGCCCAATTCTCAGTCATGGAGTCAGTATAAATTTCCGTGACATTAATGG GTGGACCGCTCTCCACTGGGCTGCTCATTTTGGAAGggaaaaccgtctcctggatctgctgcac agctatcacccatattctcttatagtcctggcactaatactagtcagactcaaggatctacctc tgcaatta
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	GGAAAACCGTCTCCTGGATCTGCTGCACAGCTATCACCCATATTCTCTTATAGTCCTGGCACTA ATACTAGTCAGACTCAAGGATCTACCTCTGCAATTAGTAGTGTATATGAACCATACCAGAGTTT TTCCAGTCCAGCATCTGTAGATGTTAGCTCTGGATTAGGTATCAAGGACAATGAGGTGGGTAGG ACAGCAGAGTTTACTAGTTCTGCTAATAAGGAGGTTACTCAATTTTTCCGAAGGCTGGAGGAGC AGTTGAGTTTGAATGAGGACAGCGCTGAAGAAATTGGCCCATTTGGTGCTGAAGAGGGAGCCAT AAATGATACAAAAATTCTGGAATATGTAAATAACATCTCCAAAGAGGATCAATCTAAGAATTTA CTTCATGGATCACTGTATATTGTTGATTATCAATCTTATGGTGGACTTGCTGGAAATCAACTAG AGAGAAACAATCTTGCACCTCTTCAGGATGCAGGTTTGTTTTGTCTTTATTCGGTGCTTGTACT CATTTAAACATGACATTCTTCTTCTGCTAGTTTATCGAAGCTGCATTATGTCTGGCTGCATTTA ATTTTATTTGAATCATTTCATTTGTATCCTTATGTCATGTTTAGTATTGGTAATCGTCTTTTTT TCTATATCTGACATTAGTTTCTTATTCGTTTCATTAGTTTCATTCAATTTTATTCAGTGTCGCT GGCTTAAAATTTTGCAAGTCCAATTCTTGAGTGCAATGTTTTGTTTGCTATTGTTCTGGGTTTC AGTTTTATTAATTTCTATGACTTAGCTCAGGTGGTCATAAATGGCTGGGTTGTCTTATATCCGT GGTTCAAATCTTACCTGTTGAGAGAGAGGCATACCAGAGATTCCAGAAGAGGTTTTATTTGACA GACAGTTCGTGAGTAAAACTCTCACATAATACTCGAATAAAATAAGGGAAAATAAAATTCCCTC ACAGATGAAGTCCAATGGATTTGTTTTGGTATGATGGTCAATAAATGGTTGAGAGGAATACTAG AGTCGTGATTGGAAGGTGAATACAATATACATCATTCTGATTCTGTAATTGTCCCAATGTAAAT TCGAGATTGTGGACCTGATACTTGTCTTTCTTACAGCATATGTTGTAGTTCTATTAGAATCACA ATTGTGTTGAAAAGGGAAAAGAATTTCCAATGTCATCAGATGTTGAGGCTTGATGAGGTTGAGG CACTGGGTTTCATTACTCATCAAGTTACTATTCGGGATATTTCACACTAACTTGTACATGGCCT CTGAGAATTAATGGATTAAAAGTGATCTTTTGATCATGGATGGAGAGGTTATTCATCTTCCAAG GTCCACATTTTGTTCAATATGATCCTTTTATTTTAGTTGTGGTCTGACCACCAATTATTCTCTT GTTCTTTGAAAACCTGGAATTTTGGACTTTTGGCAACCAGCTTGCTACCTCCTGAAAACACTTC TTGGAGATTCTTTAGTCATTCCTTGCTAGTGTTACTCCATGCTTGTTCTTGCATTGGTGCTGTA AATGGAAACTACGAGATCTACTAAGTTTTTGTTTAGGTATCTGCCTTCATTTCTTCATTGATGT ATAAATAAGATATAATAGGAAAGGAAGCAATAAAGAGCTGCTGATGGCTTTATGGTTTTTAGGT GATAGTGGCGCTTACCAGCAACCATATTCACATTATTATACAGATGGAAGTGAAGAACCCCTTC CCTGGAATGAAGGGATTGAGTCCTATAAGACTTCATCAGGCATTGAGTACCAGGTGAAATATAT GGACACTGTAAATGGGCATATAGCTTTCTGTTACCTCTTTGATATCCTCTTATATTATGGTTGT ATTGTTTATGGATGGCTGTATTTTTCAACAGGAAAAGACCAAGTCCTCTTTAAGTACAGAACCA GCTCAAGAGCAAGAAAACTCTTATTGGATAAATTTCAATGAACCCAATGTCAGAAACTGTATGA TATCTTATTCCCTTAATAGTGATTGACATTTTAATTTTCAGCATCTAATGAACTTGCATCAAGC TTTTAACATTTTTTCATATTACCAGCTTCTTTGTTGCTGCCTCAAGAAGTTGAAAATTTTGAAC TCCCTGCATATTCTTCTGTGATAGAAACACATGAAAACAATTCCAACTTCTATGCAATGCTATA TGACCAAGACCATCTTGGAATACCCAATGAAGCAGATTCAAATTTGACAGTTGCACAGCAGCAG AAGTTTACTATCCATGAAATATCCCCAGAATGGGGTTATGCCACTGAGGCTACAAAGGTATGAG TCATCAGATTCCATGAACTGCTATGCTCTTTACAACATTTCTCATTATTCATTCATTGAGATGG CAGTATTATTCCAAGAATGGAACTGTTGTGTAGTTTGAAGAATGTACAAACTCATTAATATGCA TGTTAAAATAGGCTGCTCCTTCAGTGCATCGTGACATACTTCTAATTCGATAGTACAGTTTTCC TTGTTTCTGGATGTGTTCATCCATTTCTTTTGCTTTTATGCTTTCACAGATGCATCCATCTGAC ACCATGTCATGTGAGATGTGACTAGTTTTATGCTACCTGACTGCCTATTTGCAACCATCCTCAT TCTTCACCAGGATAGAAGGAAATGGAGGAAACAAATCTCTTATAACTTATTCCTAGTTTATGAT CTGGCTAAATTGGTTCCTGAATTCAATGAAGAAAGGTTTTAAGAAATTAGAAAAACATGACTAT ATATTCCAGGACACTGAGGTGCTTGAATGCAGCATGTACTCCATGATCATGTTGCAAATAAATT ATAAAATCAGTGCAGGACCAGAATCATCTTATGCTTGTCTGATGCCAATTCTAAGTGATAGATT GCTGCACTCTCTTTCTAGGCTAAGAGTAATTCAAAATTTCATGGACAGCAATCCCAACCCTGGT TCTGATTGGTACCATTTGAAAAACCAGATAAGACTATTTACTGGAAGTTCAATTGTCCTTCCTA ATAACTTGATGTTTTGGTGAACCTTCTTTGAACTACCAATTCGCTTGCAAACTAAACAGCAAGG ATCTCATAAACCTTCCTGATGCACCACTGGACTTCTCTTATGCATTGTTTTGAGGAGTTTTTTC TTTTTAGATCTCAATTAAGAAATTCAAGTCCAAATTTTCAAGCCTTGATTCTCAATGCAGGTCA TCATTGTTGGATCGTTTCTCTGTGACCCATCGGAGTCTTCATGGATGTGCATGTTCGGTGACAT TGAGGTTCCTCTTCAAATCATTCAAGAAGGTGTCATTCGTTGTGAGTGTCCTCCCCACCATCCC GGAAAGGTCACTCTCTGCATTACTTCTGGCAATCGGGAGTCCTGCAGTGAGATCAGAGGCTTTG AGTACCGAGCTAAGGATAGTAGTTGTGCTCACTGTATCTTATCCCAGACAGAAGCTACTAAGAG TCCAGATGAGCTATTGTTACTTTTCAGATTTGTGCAGATGCTTCTGTCTGATTATTCTTTGCAG AGAGGAGACTCTGTAGAAATGGGAATTCATCTTCTGAGAGAATTGAAGGCTGATGATGATACAT GGGGTGATATCATAGAGGCTCTCTTAGTTGGCAGTGGAACTTCATCCATGACAGTCGATTGGCT TCTGCAACAACTTCTGAATGACAAGCTGCAGCAGTGGCTTTCCTCCAAGTCTCAGGAAGGACAT GATCAACCTGGGTGTTCATTTTCCAAGAAAGAGCAAGGGATCATTCACATGGTTGCTGGGTTAG GCTTTGAGTGGGCCTTAAGCCCAATTCTCAGTCATGGAGTCAGTATAAATTTCCGTGACATTAA TGGGTGGACCGCTCTCCACTGGGCTGCTCATTTTGGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.103900256

Conservation Information
Conserved circRNAs	NA
PMCS	0.103900256

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							10788888-10786863(+)
10790559-10786768(+)
10786761-10790557(-)
						
						Potential amino acid sequence
						
							MLYDQDHLGIPNEADSNLTVAQQQKFTIHEISPEWGYATEATKVIIVGSFLCDPSESSWMCMFG
DIEVPLQIIQEGVIRCECPPHHPGKVTLCITSGNRESCSEIRGFEYRAKDSSCAHCILSQTEAT
KSPDELLLLFRFVQMLLSDYSLQRGDSVEMGIHLLRELKADDDTWGDIIEALLVGSGTSSMTVD
WLLQQLLNDKLQQWLSSKSQEGHDQPGCSFSKKEQGIIHMVAGLGFEWALSPILSHGVSINFRD
INGWTALHWAAHFGRENRLLDLLHSYHPYSLIVLALILVRLKDLPLQLVVYMNHTRVFPVQHL*
(+)
MGGPLSTGLLILEGKTVSWICCTAITHILL*(+)
MGDSCAADPGDGFPFQNEQPSGERSTH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	10788888-10786863(+) 10790559-10786768(+) 10786761-10790557(-)
Potential amino acid sequence	MLYDQDHLGIPNEADSNLTVAQQQKFTIHEISPEWGYATEATKVIIVGSFLCDPSESSWMCMFG DIEVPLQIIQEGVIRCECPPHHPGKVTLCITSGNRESCSEIRGFEYRAKDSSCAHCILSQTEAT KSPDELLLLFRFVQMLLSDYSLQRGDSVEMGIHLLRELKADDDTWGDIIEALLVGSGTSSMTVD WLLQQLLNDKLQQWLSSKSQEGHDQPGCSFSKKEQGIIHMVAGLGFEWALSPILSHGVSINFRD INGWTALHWAAHFGRENRLLDLLHSYHPYSLIVLALILVRLKDLPLQLVVYMNHTRVFPVQHL* (+) MGGPLSTGLLILEGKTVSWICCTAITHILL(+) MGDSCAADPGDGFPFQNEQPSGERSTH(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0001s13700_circ_g.1

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