Plant Circular RNA Database

Detail information of POPTR_0016s14250_circ_g.2

			
						 General Information
					
						CircRNA Name
						POPTR_0016s14250_circ_g.2
					
						ID in PlantcircBase
						pop_circ_003924
					
						Alias
						Chr16:13848592|13849970
					
						Organism
						
							Populus trichocarpa						
					
						Position
						
							chr16: 13501142-13502520  JBrowse»						
					
						Reference genome
						
							Populus trichocarpa genome v3.0 						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							POPTR_0016s14250						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							POPTR_0016s14250_circ_g.1 						
					
						Support reads
						NA
					
						Tissues
						stem cambium
					
						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_0016s14250.1:2

General Information
CircRNA Name	POPTR_0016s14250_circ_g.2
ID in PlantcircBase	pop_circ_003924
Alias	Chr16:13848592\|13849970
Organism	Populus trichocarpa
Position	chr16: 13501142-13502520 JBrowse»
Reference genome	Populus trichocarpa genome v3.0
Type	e-circRNA
Identification method	find_circ
Parent gene	POPTR_0016s14250
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	POPTR_0016s14250_circ_g.1
Support reads	NA
Tissues	stem cambium
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_0016s14250.1:2

			
						 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  
						
							CCAGATGTCATTGAGATGACTTTTGTTCCTATCGCAGATCTCCTTGTTGGGGTGCCTGGAAAGG
AGCATCTGAGTCGTGCAATTGCTCTATATCTTGAATcttcattgaaaattttgggacgcatgtt
atcacttctgtaactattggtggtaaggatgtgatatatgttaaacaacaccagtcatcgcctt
tgtcaacc

									
								

					

						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: 410
Transcript exons: 13501142-13501367,13502337-13502520
CTTCATTGAAAATTTTGGGACGCATGTTATCACTTCTGTAACTATTGGTGGTAAGGATGTGATA
TATGTTAAACAACACCAGTCATCGCCTTTGTCAACCATGGAGATTAAACACTACGTGCAGGATA
TTGGAAATCAGAGGTTCTCTGACACAGAGGGCCATATGAGCTCAGGTCCAATGAAACTCAAGGA
TAAGGCTAGTCCCATGATTTCTCCTTATTTCTTTGATGTTACTGTCATTTTCCGCAGGAGGGGA
GGAGATGATCTGGAGCAAAATCATATCCGATGGGCAAGAACTGTAGAGTCATCTCCAGATGTCA
TTGAGATGACTTTTGTTCCTATCGCAGATCTCCTTGTTGGGGTGCCTGGAAAGGAGCATCTGAG
TCGTGCAATTGCTCTATATCTTGAAT"
						
					

						Genomic sequence
						
							CTTCATTGAAAATTTTGGGACGCATGTTATCACTTCTGTAACTATTGGTGGTAAGGATGTGATA
TATGTTAAACAACACCAGTCATCGCCTTTGTCAACCATGGAGATTAAACACTACGTGCAGGATA
TTGGAAATCAGAGGTTCTCTGACACAGAGGGCCATATGAGCTCAGGTCCAATGAAACTCAAGGA
TAAGGCTAGTCCCATGATTTCTCCTTATTTCTTTGTCCACCTTCGTTAACATGCCCTTACTTCT
TGATCACCTGTGACTTATACCAGATTATTCTTGATTTAGCAGGGTGGTGATTCAGGTATATTTA
ACAGCCAAGGGATATACCCTCAGCCAACTAGTGCGCCGTATCTTACTGGGAAAGAAGTATGTAG
AAGCCAATCTTTCTCTTTTCTTTTCCTTTTCTTTTCTTAGAATTGCCCTTTTATCTCACTGAAA
TTTTGATGTTAAATGTTCTCTTTGTTGAACTGTTTTATGATGCCTTTTGTTGTCATTTTAATGA
ATTCAAGATTTCTTTATATGACGATGCAAAGTATCTACATCCAAACATAATTTCCCTGAACATG
TTAACCAAATGCAACAACTGAGCATTCGAGGTTTTACTCCATCTGTTGGTCTTGTAGTTCCCAG
TCCAGTTCCTTCTTTAAATTTGCTCTGTGTATTGTAACTATGTTTTCTATTATTGATTAGTTGA
AATTGGAATAAATTTCATGTTGTTATCATTTTTCTTTGAAAAGTTTTGCTTGCCAATATGTCTT
GTATTTTCCATATTTGTTCCTTGTTTGGATTTTGCCTTTTCATAGCAATCCCATTGCAACGATG
TTTTCCTGTACGAATCAGTTGGATCTGGAATGAATTAACAATGGGTTTTGATGTTTTTGTCAAA
AACGTTTTCTTGCTATTGTTGTCATGATTTTATCAGGAAAAAAAGGATCACTCGTATTCTATCT
CAGTTTATTGCATTTAAGAAGTTGCCACGGGTGGCTAACTCTTGTATTTGCATGAATGCAGTCT
GCATTCTCTTTTTGTCAATAGATTATTTACATACAGTTAAATAATGTGTAAGGCTTATGTTCTA
GAACTTTACATACAGTTAAATAATGTGTAAGGCTTATGTTCTAGAACTTGCTCCGATAAATTTA
TCGGCAGGTCTAAAAATTTGTTCTGTTATTCTTCTATATGCAGGATGTTACTGTCATTTTCCGC
AGGAGGGGAGGAGATGATCTGGAGCAAAATCATATCCGATGGGCAAGAACTGTAGAGTCATCTC
CAGATGTCATTGAGATGACTTTTGTTCCTATCGCAGATCTCCTTGTTGGGGTGCCTGGAAAGGA
GCATCTGAGTCGTGCAATTGCTCTATATCTTGAAT
						
					

			
		

Sequences
Splice junction sequence	CCAGATGTCATTGAGATGACTTTTGTTCCTATCGCAGATCTCCTTGTTGGGGTGCCTGGAAAGG AGCATCTGAGTCGTGCAATTGCTCTATATCTTGAATcttcattgaaaattttgggacgcatgtt atcacttctgtaactattggtggtaaggatgtgatatatgttaaacaacaccagtcatcgcctt tgtcaacc
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: 410 Transcript exons: 13501142-13501367,13502337-13502520 CTTCATTGAAAATTTTGGGACGCATGTTATCACTTCTGTAACTATTGGTGGTAAGGATGTGATA TATGTTAAACAACACCAGTCATCGCCTTTGTCAACCATGGAGATTAAACACTACGTGCAGGATA TTGGAAATCAGAGGTTCTCTGACACAGAGGGCCATATGAGCTCAGGTCCAATGAAACTCAAGGA TAAGGCTAGTCCCATGATTTCTCCTTATTTCTTTGATGTTACTGTCATTTTCCGCAGGAGGGGA GGAGATGATCTGGAGCAAAATCATATCCGATGGGCAAGAACTGTAGAGTCATCTCCAGATGTCA TTGAGATGACTTTTGTTCCTATCGCAGATCTCCTTGTTGGGGTGCCTGGAAAGGAGCATCTGAG TCGTGCAATTGCTCTATATCTTGAAT"
Genomic sequence	CTTCATTGAAAATTTTGGGACGCATGTTATCACTTCTGTAACTATTGGTGGTAAGGATGTGATA TATGTTAAACAACACCAGTCATCGCCTTTGTCAACCATGGAGATTAAACACTACGTGCAGGATA TTGGAAATCAGAGGTTCTCTGACACAGAGGGCCATATGAGCTCAGGTCCAATGAAACTCAAGGA TAAGGCTAGTCCCATGATTTCTCCTTATTTCTTTGTCCACCTTCGTTAACATGCCCTTACTTCT TGATCACCTGTGACTTATACCAGATTATTCTTGATTTAGCAGGGTGGTGATTCAGGTATATTTA ACAGCCAAGGGATATACCCTCAGCCAACTAGTGCGCCGTATCTTACTGGGAAAGAAGTATGTAG AAGCCAATCTTTCTCTTTTCTTTTCCTTTTCTTTTCTTAGAATTGCCCTTTTATCTCACTGAAA TTTTGATGTTAAATGTTCTCTTTGTTGAACTGTTTTATGATGCCTTTTGTTGTCATTTTAATGA ATTCAAGATTTCTTTATATGACGATGCAAAGTATCTACATCCAAACATAATTTCCCTGAACATG TTAACCAAATGCAACAACTGAGCATTCGAGGTTTTACTCCATCTGTTGGTCTTGTAGTTCCCAG TCCAGTTCCTTCTTTAAATTTGCTCTGTGTATTGTAACTATGTTTTCTATTATTGATTAGTTGA AATTGGAATAAATTTCATGTTGTTATCATTTTTCTTTGAAAAGTTTTGCTTGCCAATATGTCTT GTATTTTCCATATTTGTTCCTTGTTTGGATTTTGCCTTTTCATAGCAATCCCATTGCAACGATG TTTTCCTGTACGAATCAGTTGGATCTGGAATGAATTAACAATGGGTTTTGATGTTTTTGTCAAA AACGTTTTCTTGCTATTGTTGTCATGATTTTATCAGGAAAAAAAGGATCACTCGTATTCTATCT CAGTTTATTGCATTTAAGAAGTTGCCACGGGTGGCTAACTCTTGTATTTGCATGAATGCAGTCT GCATTCTCTTTTTGTCAATAGATTATTTACATACAGTTAAATAATGTGTAAGGCTTATGTTCTA GAACTTTACATACAGTTAAATAATGTGTAAGGCTTATGTTCTAGAACTTGCTCCGATAAATTTA TCGGCAGGTCTAAAAATTTGTTCTGTTATTCTTCTATATGCAGGATGTTACTGTCATTTTCCGC AGGAGGGGAGGAGATGATCTGGAGCAAAATCATATCCGATGGGCAAGAACTGTAGAGTCATCTC CAGATGTCATTGAGATGACTTTTGTTCCTATCGCAGATCTCCTTGTTGGGGTGCCTGGAAAGGA GCATCTGAGTCGTGCAATTGCTCTATATCTTGAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.524446809

Conservation Information
Conserved circRNAs	NA
PMCS	0.524446809

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							13501243-13501179(+)
13501168-13502389(-)
13501245-13502451(-)
						
						Potential amino acid sequence
						
							MEIKHYVQDIGNQRFSDTEGHMSSGPMKLKDKASPMISPYFFDVTVIFRRRGGDDLEQNHIRWA
RTVESSPDVIEMTFVPIADLLVGVPGKEHLSRAIALYLESSLKILGRMLSLL*(+)
MRPKIFNEDSRYRAIARLRCSFPGTPTRRSAIGTKVISMTSGDDSTVLAHRI*(-)
MVDKGDDWCCLTYITSLPPIVTEVITCVPKFSMKIQDIEQLHDSDAPFQAPQQGDLR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	13501243-13501179(+) 13501168-13502389(-) 13501245-13502451(-)
Potential amino acid sequence	MEIKHYVQDIGNQRFSDTEGHMSSGPMKLKDKASPMISPYFFDVTVIFRRRGGDDLEQNHIRWA RTVESSPDVIEMTFVPIADLLVGVPGKEHLSRAIALYLESSLKILGRMLSLL(+) MRPKIFNEDSRYRAIARLRCSFPGTPTRRSAIGTKVISMTSGDDSTVLAHRI(-) MVDKGDDWCCLTYITSLPPIVTEVITCVPKFSMKIQDIEQLHDSDAPFQAPQQGDLR*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zheng et al., 2020

circRNA

Detail information of POPTR_0016s14250_circ_g.2

Address

Any questions?

Supported by