Plant Circular RNA Database

Detail information of Niben101Scf01008g02005_circ_g.3

			
						 General Information
					
						CircRNA Name
						Niben101Scf01008g02005_circ_g.3
					
						ID in PlantcircBase
						nbe_circ_000300
					
						Alias
						NA
					
						Organism
						
							Nicotiana benthamiana						
					
						Position
						
							chrNiben101Scf01008: 216028-217458  JBrowse»						
					
						Reference genome
						
							Niben.genome.v1.0.1						
					
						Type  
						
							ie-circRNA							
									
						Identification method
						DCC
					
						Parent gene
						
							Niben101Scf01008g02005						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							Niben101Scf01008g02005_circ_g.2 Niben101Scf01008g02005_circ_g.1 						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						Exon boundary  
						
							No-No							"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  
						
							TT-TA							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
						Niben101Scf01008g02005.1:1

General Information
CircRNA Name	Niben101Scf01008g02005_circ_g.3
ID in PlantcircBase	nbe_circ_000300
Alias	NA
Organism	Nicotiana benthamiana
Position	chrNiben101Scf01008: 216028-217458 JBrowse»
Reference genome	Niben.genome.v1.0.1
Type	ie-circRNA
Identification method	DCC
Parent gene	Niben101Scf01008g02005
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	Niben101Scf01008g02005_circ_g.2 Niben101Scf01008g02005_circ_g.1
Support reads	NA
Tissues	leaf
Exon boundary	No-No "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	TT-TA 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	Niben101Scf01008g02005.1:1

			
						 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  
						
							TTTGGTTCATGAAGGAACACAACTTGCTATTGACTTTGCTTTTGTAAACTAATGTTGAAAATGG
TAGAAAATTATTAACTATGAGGCCGATAACATGATTagaaaagaattgaaaattgtacatactc
tttctatttctaacaattggggagattcgtcatcagttggaatccagcagtaataaattgaata
tagaaatt

						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
						
							AGAAAAGAATTGAAAATTGTACATACTCTTTCTATTTCTAACAATTGGGGAGATTCGTCATCAG
TTGGAATCCAGCAGTAATAAATTGAATATAGAAATTGGAGTTGTTAAGCGAGATGCTCATGTTT
TACCTATGCTGATTGCGGAGTGCTTTCCCTTGTTTTTTTTTCTCCTTTTAAATAATTTAAGAGG
CATCTTCCCTTTCCTAAGGTGGATTGTTAGTTCTTTTCTGCATTGTCTATGAGCTATCATCATG
CTTTCTATCTAATAACTGTTTGGTAAAATGGCTTTTTGGTGCCTATTAGATTATTGTTGAAACT
TGTTCGCTAAACTCAATTAAGTATGTGTTTTTTTGATAATTCAATCTAACGTTTTCTACTTCGA
TGTGCATTTCTGACTAATTTCTCGGCCCTATCTTCTGCTCATTGCATTCAGATGTCAGAACAAT
TGAATCAGGAATTATCTTTGTCTGGTAAGATACCTTCTGGTTTGTTTAATGCGATGTTTGGTCA
TAAGGGATGCTGGCAAAAGGATGCAGCATCGACAAAGCTTCTTGCCTTTGATGGTTGGTTTATT
ACCTTGTACAATATTGAGTTAGTGAGATCCCATCTAACACTATCTGAGCAAGTGAAGCAAGATG
TGCCTTCTTCATGGGATCCTTCTGCGCTTGCAGAGTAAGACCTTCCGCTCAATTGTTATTTGAA
TATCTATTTTGTTGTCCGTCAGAATAGTATACATACAAATCTGTGTACGTTCAAAATCTCAAGG
AAATCTGGTACATGCTCCTCTATGAAATTGGATGTAGGATGAATTGGATTCAGAAAGTTCTAAA
CTAACACACCTGCTGTTTTTCATAGAAAAGCATTTTCTCGTATTGTCATTGTGCGTTAAGTGTT
TGAGTGCAAACTAAGGAAAGGAAGCAAAAGAATAGAAGATCAAAGGGATGGATATGAAGAGAGA
GAGAGAGACTTTAGATTGTTTCTTTTGTTTGGTGAACTACAATAGGATATTATGGGAGGAATGT
TTTTGTTTCTTGGTTTGATTTCTTTCCTCTCCTCCTATGTAAGTCGAAGAAGGAGAAGATTCTA
TCCTATCTGTTTCTATACAAAACCACTGGCAATGCTTTCCGCCTTTTCTATCCAGTAGAAGTAG
CGAATTTATAAGGGAATGGAAAAAGAATGACCTATGAACTATAGGAGAGTCATTTATGGCCCTG
AAATTTGGACTCAGAAACAGCAGTGTTGTTATTTTAAGACAGTTGTTGAAAATTTTAATTTTTT
GTGCATTTGATTTTGATTTTATCTCCTTCACTCTGACCTTCTGTCCCTTCTTTTGGTTCATGAA
GGAACACAACTTGCTATTGACTTTGCTTTTGTAAACTAATGTTGAAAATGGTAGAAAATTATTA
ACTATGAGGCCGATAACATGATT

Sequences
Splice junction sequence	TTTGGTTCATGAAGGAACACAACTTGCTATTGACTTTGCTTTTGTAAACTAATGTTGAAAATGG TAGAAAATTATTAACTATGAGGCCGATAACATGATTagaaaagaattgaaaattgtacatactc tttctatttctaacaattggggagattcgtcatcagttggaatccagcagtaataaattgaata tagaaatt
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	AGAAAAGAATTGAAAATTGTACATACTCTTTCTATTTCTAACAATTGGGGAGATTCGTCATCAG TTGGAATCCAGCAGTAATAAATTGAATATAGAAATTGGAGTTGTTAAGCGAGATGCTCATGTTT TACCTATGCTGATTGCGGAGTGCTTTCCCTTGTTTTTTTTTCTCCTTTTAAATAATTTAAGAGG CATCTTCCCTTTCCTAAGGTGGATTGTTAGTTCTTTTCTGCATTGTCTATGAGCTATCATCATG CTTTCTATCTAATAACTGTTTGGTAAAATGGCTTTTTGGTGCCTATTAGATTATTGTTGAAACT TGTTCGCTAAACTCAATTAAGTATGTGTTTTTTTGATAATTCAATCTAACGTTTTCTACTTCGA TGTGCATTTCTGACTAATTTCTCGGCCCTATCTTCTGCTCATTGCATTCAGATGTCAGAACAAT TGAATCAGGAATTATCTTTGTCTGGTAAGATACCTTCTGGTTTGTTTAATGCGATGTTTGGTCA TAAGGGATGCTGGCAAAAGGATGCAGCATCGACAAAGCTTCTTGCCTTTGATGGTTGGTTTATT ACCTTGTACAATATTGAGTTAGTGAGATCCCATCTAACACTATCTGAGCAAGTGAAGCAAGATG TGCCTTCTTCATGGGATCCTTCTGCGCTTGCAGAGTAAGACCTTCCGCTCAATTGTTATTTGAA TATCTATTTTGTTGTCCGTCAGAATAGTATACATACAAATCTGTGTACGTTCAAAATCTCAAGG AAATCTGGTACATGCTCCTCTATGAAATTGGATGTAGGATGAATTGGATTCAGAAAGTTCTAAA CTAACACACCTGCTGTTTTTCATAGAAAAGCATTTTCTCGTATTGTCATTGTGCGTTAAGTGTT TGAGTGCAAACTAAGGAAAGGAAGCAAAAGAATAGAAGATCAAAGGGATGGATATGAAGAGAGA GAGAGAGACTTTAGATTGTTTCTTTTGTTTGGTGAACTACAATAGGATATTATGGGAGGAATGT TTTTGTTTCTTGGTTTGATTTCTTTCCTCTCCTCCTATGTAAGTCGAAGAAGGAGAAGATTCTA TCCTATCTGTTTCTATACAAAACCACTGGCAATGCTTTCCGCCTTTTCTATCCAGTAGAAGTAG CGAATTTATAAGGGAATGGAAAAAGAATGACCTATGAACTATAGGAGAGTCATTTATGGCCCTG AAATTTGGACTCAGAAACAGCAGTGTTGTTATTTTAAGACAGTTGTTGAAAATTTTAATTTTTT GTGCATTTGATTTTGATTTTATCTCCTTCACTCTGACCTTCTGTCCCTTCTTTTGGTTCATGAA GGAACACAACTTGCTATTGACTTTGCTTTTGTAAACTAATGTTGAAAATGGTAGAAAATTATTA ACTATGAGGCCGATAACATGATT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS

Conservation Information
Conserved circRNAs	NA
PMCS

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	NA
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Guria et al., 2019

circRNA

Detail information of Niben101Scf01008g02005_circ_g.3

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