Plant Circular RNA Database

Detail information of POPTR_0013s09680_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0013s09680_circ_g.1
					
						ID in PlantcircBase
						pop_circ_003330
					
						Alias
						Chr13:9225130-9226366
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr13: 9538696-9539932  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0013s09680						
					
						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_0013s09680.2:3
POPTR_0013s09680.1:3

General Information
CircRNA Name	POPTR_0013s09680_circ_g.1
ID in PlantcircBase	pop_circ_003330
Alias	Chr13:9225130-9226366
Organism	Populus trichocarpa
Position	chr13: 9538696-9539932 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0013s09680
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_0013s09680.2:3 POPTR_0013s09680.1:3

			
						 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  
						
							CCTCTGTGTCATCAACATAACAGATGTTAATTAGATACTCGAGACCCATTAGCAGAGCAGTTAT
GTTCTCCTGCGTAGACTCCAGCACTTGAATATGAGActtatattgaacaagaacatcattatcc
ttcatggtttcacgaacaatattaccattttcatcttcaactatcaaaacctcctcaggtttag
ccatacga

						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
						
							CTTATATTGAACAAGAACATCATTATCCTTCATGGTTTCACGAACAATATTACCATTTTCATCT
TCAACTATCAAAACCTCCTCAGGTTTAGCCATACGACAGATCATAAGCATTCGCAACTTGGACA
TTGGAGTAGCATAAAGCTGCCTCCTCTGCAGAATTTGTGACCCTAAACCATCAACCATGCCATG
TAGCAAAGGCATCTGCAGATTCCGAGAATTGATAGTCTAGAATCAGTAATCTCCATGGAAGAAT
GGAAGTGTTAAACAAGAAACTTGTAACCGATTCATAATGATGAAAATGCAAGAATTTCTAATAT
CTGCACATTATATATGTAAAATGAGAAAACAATGAACTACATGAAGCAGATAAGATTGTCTAAA
AATATGAGCAGAGTGCAAGACATCGAACAAAATACACAAGAAAATTTTCAAACATCTAAAATAT
TGTCACACTTCTTATTGGATATTTACCCACATTTTTTTACTGAAAAATATGTGGGATAAGATAG
TATCCCACATGGGAAAAGGCATTTTGAAAAAGGGAGGAGAAGAAATACATAGTAATGGATATCC
TCCACAACAAACAAGAAAAAAAAAAACATCAATAAAACATGACAATACTATCTATATAAAAATC
GATCCATTAAAGAGACTCCTAGAAAATTTACAGCTACTTCAGGGTTGTCTGAAATATGGTGTAT
TTCACAAGAGATGCAAAGGGATAATGGTATGTGTTATTGTAAGGCAACGAAAAACAGAAGTCAG
AATTAGTAAAAGGAGAACCACAATGAGCAGAATGACACAATAGCTGAACACCACATTACTCCAC
TTGCCAACCACCATCTGGTAATAAATACATTCTACCTGCAGTCCCATCATGTTTACAGCCACTG
CAGGGTTGTCCAAATTATGGCGTGCCTCGAAAAGCTCCAAAACCAAGGAGTTCCAATAGTCCAA
GCAAACCTATAAAGCGTGCAAGGCAGCAAGACTAGTCATATTATCAGACTTGGAATTACATAAT
AATTCACATATACAGACATGCATACTACAACACCAGTACACGTGTGCACCCACACATACACATC
GAGAAAGATGAACGAGAGCAAGAGAAGGAAAATAACTTCACCTTAAAAACCTCTGTGTCATCAA
CATAACAGATGTTAATTAGATACTCGAGACCCATTAGCAGAGCAGTTATGTTCTCCTGCGTAGA
CTCCAGCACTTGAATATGAGA

Sequences
Splice junction sequence	CCTCTGTGTCATCAACATAACAGATGTTAATTAGATACTCGAGACCCATTAGCAGAGCAGTTAT GTTCTCCTGCGTAGACTCCAGCACTTGAATATGAGActtatattgaacaagaacatcattatcc ttcatggtttcacgaacaatattaccattttcatcttcaactatcaaaacctcctcaggtttag ccatacga
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	CTTATATTGAACAAGAACATCATTATCCTTCATGGTTTCACGAACAATATTACCATTTTCATCT TCAACTATCAAAACCTCCTCAGGTTTAGCCATACGACAGATCATAAGCATTCGCAACTTGGACA TTGGAGTAGCATAAAGCTGCCTCCTCTGCAGAATTTGTGACCCTAAACCATCAACCATGCCATG TAGCAAAGGCATCTGCAGATTCCGAGAATTGATAGTCTAGAATCAGTAATCTCCATGGAAGAAT GGAAGTGTTAAACAAGAAACTTGTAACCGATTCATAATGATGAAAATGCAAGAATTTCTAATAT CTGCACATTATATATGTAAAATGAGAAAACAATGAACTACATGAAGCAGATAAGATTGTCTAAA AATATGAGCAGAGTGCAAGACATCGAACAAAATACACAAGAAAATTTTCAAACATCTAAAATAT TGTCACACTTCTTATTGGATATTTACCCACATTTTTTTACTGAAAAATATGTGGGATAAGATAG TATCCCACATGGGAAAAGGCATTTTGAAAAAGGGAGGAGAAGAAATACATAGTAATGGATATCC TCCACAACAAACAAGAAAAAAAAAAACATCAATAAAACATGACAATACTATCTATATAAAAATC GATCCATTAAAGAGACTCCTAGAAAATTTACAGCTACTTCAGGGTTGTCTGAAATATGGTGTAT TTCACAAGAGATGCAAAGGGATAATGGTATGTGTTATTGTAAGGCAACGAAAAACAGAAGTCAG AATTAGTAAAAGGAGAACCACAATGAGCAGAATGACACAATAGCTGAACACCACATTACTCCAC TTGCCAACCACCATCTGGTAATAAATACATTCTACCTGCAGTCCCATCATGTTTACAGCCACTG CAGGGTTGTCCAAATTATGGCGTGCCTCGAAAAGCTCCAAAACCAAGGAGTTCCAATAGTCCAA GCAAACCTATAAAGCGTGCAAGGCAGCAAGACTAGTCATATTATCAGACTTGGAATTACATAAT AATTCACATATACAGACATGCATACTACAACACCAGTACACGTGTGCACCCACACATACACATC GAGAAAGATGAACGAGAGCAAGAGAAGGAAAATAACTTCACCTTAAAAACCTCTGTGTCATCAA CATAACAGATGTTAATTAGATACTCGAGACCCATTAGCAGAGCAGTTATGTTCTCCTGCGTAGA CTCCAGCACTTGAATATGAGA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.130023161

Conservation Information
Conserved circRNAs	NA
PMCS	0.130023161

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9539928-9538860(+)
9538901-9538876(-)
9538720-9539895(-)
						
						Potential amino acid sequence
						
							MRLILNKNIIILHGFTNNITIFIFNYQNLLRFSHTTDHKHSQLGHWSSIKLPPLQNL*(+)
MPLLHGMVDGLGSQILQRRQLYATPMSKLRMLMICRMAKPEEVLIVEDENGNIVRETMKDNDVL
VQYKSHIQVLESTQENITALLMGLEYLINICYVDDTEVFKVCLDYWNSLVLELFEARHNLDNPA
VAVNMMGLQVEYAFATWHG*(-)
MMFLFNISLIFKCWSLRRRT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9539928-9538860(+) 9538901-9538876(-) 9538720-9539895(-)
Potential amino acid sequence	MRLILNKNIIILHGFTNNITIFIFNYQNLLRFSHTTDHKHSQLGHWSSIKLPPLQNL(+) MPLLHGMVDGLGSQILQRRQLYATPMSKLRMLMICRMAKPEEVLIVEDENGNIVRETMKDNDVL VQYKSHIQVLESTQENITALLMGLEYLINICYVDDTEVFKVCLDYWNSLVLELFEARHNLDNPA VAVNMMGLQVEYAFATWHG(-) MMFLFNISLIFKCWSLRRRT*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0013s09680_circ_g.1

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