Plant Circular RNA Database

Detail information of POPTR_0016s02120_circ_g.1

			
						 General Information
					
						CircRNA Name
						POPTR_0016s02120_circ_g.1
					
						ID in PlantcircBase
						pop_circ_003805
					
						Alias
						Chr16:1091167-1091900
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr16: 1021773-1022506  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							POPTR_0016s02120						
					
						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_0016s02120.1:3

General Information
CircRNA Name	POPTR_0016s02120_circ_g.1
ID in PlantcircBase	pop_circ_003805
Alias	Chr16:1091167-1091900
Organism	Populus trichocarpa
Position	chr16: 1021773-1022506 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	POPTR_0016s02120
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_0016s02120.1:3

			
						 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  
						
							GGTATGAATCCTTCAAGAGTCGAAGTGCAGCATGAGAGCCAATATACCCAGCACCTCCAGTCAC
TAAGACATGCGTTACGCCGAGCTCATGCTGGGAGAActgaggagtttgttctgtaatcggcatc
ttaacaggctcgccgtaagttgcacaagtgctagaataaatcaatgtcttcaccttatgtgctg
ccattgct

						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
						
							CTGAGGAGTTTGTTCTGTAATCGGCATCTTAACAGGCTCGCCGTAAGTTGCACAAGTGCTAGAA
TAAATCAATGTCTTCACCTTATGTGCTGCCATTGCTTCTAAAACTACCAAGGTATTTGATGTGA
TGTTGTGATAATATCTGCACAGCATGGTAAAAATTAATTCTAGAGACAACTGCTAGCAGATACA
TTGAGATGACAAAGAAGAACTGTACTTCTATGAAAAACAATTTAAGACAGTGACCGGATGCAAA
CAGTAGATTTAGCAAGATAAATGTTTGAAATTGAAGATTCGAAGTATACCTGAGAGGTTCCATT
GTACTTTCACCAACATATGCAACAGCAGCGAAATGCATCACAGCATCAAATGCATTTTCAGCAA
AGATTTTGTTTACAGCTTTTGCATCTCCCAAGTCTGCGTATATGAACTGTAACCGCCCAGGCTC
CGGAAATAGATCTTGGAGAACTTTAACAGCACCCAGATTCCCTCGAGAAAGATTGTCCTGACAG
AGAAGGCATAGAGATTATAAATCCATGAAATGACATAGTTAATTCAACATCAGAACTCATATGC
TTAGACCAAAAAGATTTCAAGTTTCCCGAATGAATTAAACATACCACTTTAGTTACACGGTATG
AATCCTTCAAGAGTCGAAGTGCAGCATGAGAGCCAATATACCCAGCACCTCCAGTCACTAAGAC
ATGCGTTACGCCGAGCTCATGCTGGGAGAA

Sequences
Splice junction sequence	GGTATGAATCCTTCAAGAGTCGAAGTGCAGCATGAGAGCCAATATACCCAGCACCTCCAGTCAC TAAGACATGCGTTACGCCGAGCTCATGCTGGGAGAActgaggagtttgttctgtaatcggcatc ttaacaggctcgccgtaagttgcacaagtgctagaataaatcaatgtcttcaccttatgtgctg ccattgct
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	CTGAGGAGTTTGTTCTGTAATCGGCATCTTAACAGGCTCGCCGTAAGTTGCACAAGTGCTAGAA TAAATCAATGTCTTCACCTTATGTGCTGCCATTGCTTCTAAAACTACCAAGGTATTTGATGTGA TGTTGTGATAATATCTGCACAGCATGGTAAAAATTAATTCTAGAGACAACTGCTAGCAGATACA TTGAGATGACAAAGAAGAACTGTACTTCTATGAAAAACAATTTAAGACAGTGACCGGATGCAAA CAGTAGATTTAGCAAGATAAATGTTTGAAATTGAAGATTCGAAGTATACCTGAGAGGTTCCATT GTACTTTCACCAACATATGCAACAGCAGCGAAATGCATCACAGCATCAAATGCATTTTCAGCAA AGATTTTGTTTACAGCTTTTGCATCTCCCAAGTCTGCGTATATGAACTGTAACCGCCCAGGCTC CGGAAATAGATCTTGGAGAACTTTAACAGCACCCAGATTCCCTCGAGAAAGATTGTCCTGACAG AGAAGGCATAGAGATTATAAATCCATGAAATGACATAGTTAATTCAACATCAGAACTCATATGC TTAGACCAAAAAGATTTCAAGTTTCCCGAATGAATTAAACATACCACTTTAGTTACACGGTATG AATCCTTCAAGAGTCGAAGTGCAGCATGAGAGCCAATATACCCAGCACCTCCAGTCACTAAGAC ATGCGTTACGCCGAGCTCATGCTGGGAGAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.196001374

Conservation Information
Conserved circRNAs	NA
PMCS	0.196001374

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1022478-1021874(+)
1022411-1021789(+)
1022132-1021775(-)
						
						Potential amino acid sequence
						
							MRYAELMLGELRSLFCNRHLNRLAVSCTSARINQCLHLMCCHCF*(+)
MNPSRVEVQHESQYTQHLQSLRHALRRAHAGRTEEFVL*(+)
MHFAAVAYVGESTMEPLRYYHNITSNTLVVLEAMAAHKVKTLIYSSTCATYGEPVKMPITEQTP
QFSQHELGVTHVLVTGGAGYIGSHAALRLLKDSYRVTKVDNLSRGNLGAVKVLQDLFPEPGRLQ
FIYADLGDAKAVNKIFAENAFDAVMHFAAVAYVGESTMEPLRYYHNITSNTLVVLEAMAAHKVK
TLIYSSTCATYGEPVKMPITEQTPQFSQHELGVTHVLVTGGAGYIGSHAALRLLKDSYRVTKVD
NLSRGNLGAVKVLQDLFPEPGRLQFIYADLGDAKAVNKIFAENAFDAVMHFAAVAYVGESTMEP
LRYYHNITSNTLVVLEAMAAHKVKTLIYSSTCATYGEPVKMPITEQTPQFSQHELGVTHVLVTG
GAGYIGSHAALRLLKDSYRVTKVDNLSRGNLGAVKVLQDLFPEPGRLQFIYADLGDAKAVNKIF
AENAFDAVMHFAAVAYVGESTMEPLRYYHNITSNTLVVLEAMAAHKVKTLIYSSTCATYGEPVK
MPITEQTPQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1022478-1021874(+) 1022411-1021789(+) 1022132-1021775(-)
Potential amino acid sequence	MRYAELMLGELRSLFCNRHLNRLAVSCTSARINQCLHLMCCHCF(+) MNPSRVEVQHESQYTQHLQSLRHALRRAHAGRTEEFVL(+) MHFAAVAYVGESTMEPLRYYHNITSNTLVVLEAMAAHKVKTLIYSSTCATYGEPVKMPITEQTP QFSQHELGVTHVLVTGGAGYIGSHAALRLLKDSYRVTKVDNLSRGNLGAVKVLQDLFPEPGRLQ FIYADLGDAKAVNKIFAENAFDAVMHFAAVAYVGESTMEPLRYYHNITSNTLVVLEAMAAHKVK TLIYSSTCATYGEPVKMPITEQTPQFSQHELGVTHVLVTGGAGYIGSHAALRLLKDSYRVTKVD NLSRGNLGAVKVLQDLFPEPGRLQFIYADLGDAKAVNKIFAENAFDAVMHFAAVAYVGESTMEP LRYYHNITSNTLVVLEAMAAHKVKTLIYSSTCATYGEPVKMPITEQTPQFSQHELGVTHVLVTG GAGYIGSHAALRLLKDSYRVTKVDNLSRGNLGAVKVLQDLFPEPGRLQFIYADLGDAKAVNKIF AENAFDAVMHFAAVAYVGESTMEPLRYYHNITSNTLVVLEAMAAHKVKTLIYSSTCATYGEPVK MPITEQTPQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2021

circRNA

Detail information of POPTR_0016s02120_circ_g.1

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