Plant Circular RNA Database

Detail information of Niben101Scf01068g05007_circ_g.2

			
						 General Information
					
						CircRNA Name
						Niben101Scf01068g05007_circ_g.2
					
						ID in PlantcircBase
						nbe_circ_000338
					
						Alias
						NA
					
						Organism
						
							Nicotiana benthamiana						
					
						Position
						
							chrNiben101Scf01068: 564777-566525  JBrowse»						
					
						Reference genome
						
							Niben.genome.v1.0.1						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						DCC
					
						Parent gene
						
							Niben101Scf01068g05007						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							Niben101Scf01068g05007_circ_g.7 Niben101Scf01068g05007_circ_g.8 Niben101Scf01068g05007_circ_g.9 Niben101Scf01068g05007_circ_g.10 Niben101Scf01068g05007_circ_g.11 Niben101Scf01068g05007_circ_g.12 Niben101Scf01068g05007_circ_g.13 Niben101Scf01068g05007_circ_g.14 Niben101Scf01068g05007_circ_g.15 Niben101Scf01068g05007_circ_g.16 Niben101Scf01068g05007_circ_g.17 Niben101Scf01068g05007_circ_g.18 Niben101Scf01068g05007_circ_g.19 Niben101Scf01068g05007_circ_g.20 Niben101Scf01068g05007_circ_g.21 Niben101Scf01068g05007_circ_g.1 Niben101Scf01068g05007_circ_g.3 Niben101Scf01068g05007_circ_g.22 Niben101Scf01068g05007_circ_g.4 Niben101Scf01068g05007_circ_g.23 Niben101Scf01068g05007_circ_g.24 Niben101Scf01068g05007_circ_g.25 Niben101Scf01068g05007_circ_g.26 Niben101Scf01068g05007_circ_g.27 Niben101Scf01068g05007_circ_g.28 Niben101Scf01068g05007_circ_g.5 Niben101Scf01068g05007_circ_g.6 Niben101Scf01068g05007_circ_g.29 Niben101Scf01068g05007_circ_g.30 Niben101Scf01068g05007_circ_g.31 Niben101Scf01068g05007_circ_g.32 Niben101Scf01068g05007_circ_g.33 Niben101Scf01068g05007_circ_g.34 Niben101Scf01068g05007_circ_g.35 Niben101Scf01068g05007_circ_g.36 Niben101Scf01068g05007_circ_g.37 Niben101Scf01068g05007_circ_g.38 						
					
						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  
						
							AT-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
						Niben101Scf01068g05007.1:2

General Information
CircRNA Name	Niben101Scf01068g05007_circ_g.2
ID in PlantcircBase	nbe_circ_000338
Alias	NA
Organism	Nicotiana benthamiana
Position	chrNiben101Scf01068: 564777-566525 JBrowse»
Reference genome	Niben.genome.v1.0.1
Type	ei-circRNA
Identification method	DCC
Parent gene	Niben101Scf01068g05007
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	Niben101Scf01068g05007_circ_g.7 Niben101Scf01068g05007_circ_g.8 Niben101Scf01068g05007_circ_g.9 Niben101Scf01068g05007_circ_g.10 Niben101Scf01068g05007_circ_g.11 Niben101Scf01068g05007_circ_g.12 Niben101Scf01068g05007_circ_g.13 Niben101Scf01068g05007_circ_g.14 Niben101Scf01068g05007_circ_g.15 Niben101Scf01068g05007_circ_g.16 Niben101Scf01068g05007_circ_g.17 Niben101Scf01068g05007_circ_g.18 Niben101Scf01068g05007_circ_g.19 Niben101Scf01068g05007_circ_g.20 Niben101Scf01068g05007_circ_g.21 Niben101Scf01068g05007_circ_g.1 Niben101Scf01068g05007_circ_g.3 Niben101Scf01068g05007_circ_g.22 Niben101Scf01068g05007_circ_g.4 Niben101Scf01068g05007_circ_g.23 Niben101Scf01068g05007_circ_g.24 Niben101Scf01068g05007_circ_g.25 Niben101Scf01068g05007_circ_g.26 Niben101Scf01068g05007_circ_g.27 Niben101Scf01068g05007_circ_g.28 Niben101Scf01068g05007_circ_g.5 Niben101Scf01068g05007_circ_g.6 Niben101Scf01068g05007_circ_g.29 Niben101Scf01068g05007_circ_g.30 Niben101Scf01068g05007_circ_g.31 Niben101Scf01068g05007_circ_g.32 Niben101Scf01068g05007_circ_g.33 Niben101Scf01068g05007_circ_g.34 Niben101Scf01068g05007_circ_g.35 Niben101Scf01068g05007_circ_g.36 Niben101Scf01068g05007_circ_g.37 Niben101Scf01068g05007_circ_g.38
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	AT-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	Niben101Scf01068g05007.1:2

			
						 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  
						
							AATATTATTTAAGATATAACTCTGCAGAGCAGTAAACTAAGCATTACTAATAAATCTACATATC
CTCAACACGTACGCAAATTCAAACAGACTGATTATAagtcggtgatattgctcagcctgctttc
tacttttccgaaccaaaactcgagaatcagggcccatcccactgcaagaaaaaagtaaataaca
ttggtact

									
								

					

						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
						
							AGTCGGTGATATTGCTCAGCCTGCTTTCTACTTTTCCGAACCAAAACTCGAGAATCAGGGCCCA
TCCCACTGCAAGAAAAAAGTAAATAACATTGGTACTAGAGAGATAGCCGGAGGTAATGCAATAA
CCATAATTAACCAAGCAAGCATCCTCTGGAAGGATATATCATAGAACTAAGACCTTTTGCAAGG
CATATATTGATGCTGTACTGATATTCTTAGATAATTTAGGACAAGAGGTAGCACCAACAGCAAA
ACATCAGCTCTCAAAGGTTCCATCCTTCGATGTGTAACAAGTTTTTACTAATCAGTACTAGAGA
ATAGCTACTCTCAGTCCGGTGTTTTCTCAAACATCATTGTAATACTTAGTATAAGGAGCAATAA
TGAAGGAAATTAGGATCCTCTTATTTCACAATTCAGAAGGAACTTTTCTTTCCATAGTCAACTT
AGCTTTATAAAATGTAAATCCACAACTCTTTATGAGCAAATTTCCGATCAAGTTTCTCTACAAC
TTAAATAAATTTTTTCTTGATTATGGTTCTAAAACAAAAGCATATTCCTAGCAAACTGGTTGAA
TTTTAGGTAAAGCATCTCAGCACTATGTTAGTGCTGCTGTGTGTTGCAAAAAAAATTCTTAATT
AAAAAATATCAAATAGCATACTCATTCCAACATTTCTACAGGATCCACATCCAGTAGTTAGATC
AACAAAGAATCTTTTGATGGAGATCCATGACAATGCATCCCAGCTATCAATTCCAATCATTCCA
CTTCTTTATTTTAATCGCATATGATTTAAAGGAATTACAACCAATCTGTTGGAACTAAGGTATA
GTTGAATGATCGAATGATTGAATAAAATGTGATCTACTACTTTTATTTGTTACTCTATTACATA
AAACTTGCCCCATTCAAACTGTCAGTATGAGGCCATTTAAATGAGCCTCAGCGATTATTTTTCA
TCAGGAGTTGCTTATCATTGTGACTACAGACACAGAGGTATCTATGTATTCATCACTTGAAATT
AAGGATAATTAACTTGATTTGCATTTTTATTTCAAGGAAACTTGGCTAATGAGTCCAGAATTCA
TAAATAAAAGAGAGAGAAAAGAACTCGCTATAGGTCAATTGACTTGGCAAACAGGAAAGAAATT
CACTGGGTCCATTGTGATTCACATACCAAGAGCACAGCCAGAATTATTTCTTTAGTCAATGAAT
ACCGGTCCATTCTATTGACATGAATCTTAAACTATAACATCATTAAACGAACTAAAGAAAGAGC
CAACCCGAACAGCATAGTTTTATGTCTAACATATAACAGAATGTACCTGTAGACAACTCCAATA
TTAGGTGTCAAAACCTGTATTTTCTGCACCTGTTGTGCATTTCAAAGAGTCAGGGATAGATAGC
ATAACTACAAGGACATCATTACATGACAGAGGTTAAGGAATGTCTAGCAAAAAAAAAATAGTTG
GAATCCCCATGCAGTCCCAAAACACCGAATGCTGTGAAACTTAGTGCTTATAGAAGTTCAATAA
TAAAGCATCAGTGTAATACATAGCAATGAACCACAGAAAATAAGAATTTAACAGTAAAGACTAT
AAACTTAAATGCACGTATGGCATGTTGTAACTTGGTGACTGCATTTGTGAATATTATTTAAGAT
ATAACTCTGCAGAGCAGTAAACTAAGCATTACTAATAAATCTACATATCCTCAACACGTACGCA
AATTCAAACAGACTGATTATA
						
					

			
		

Sequences
Splice junction sequence	AATATTATTTAAGATATAACTCTGCAGAGCAGTAAACTAAGCATTACTAATAAATCTACATATC CTCAACACGTACGCAAATTCAAACAGACTGATTATAagtcggtgatattgctcagcctgctttc tacttttccgaaccaaaactcgagaatcagggcccatcccactgcaagaaaaaagtaaataaca ttggtact
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	AGTCGGTGATATTGCTCAGCCTGCTTTCTACTTTTCCGAACCAAAACTCGAGAATCAGGGCCCA TCCCACTGCAAGAAAAAAGTAAATAACATTGGTACTAGAGAGATAGCCGGAGGTAATGCAATAA CCATAATTAACCAAGCAAGCATCCTCTGGAAGGATATATCATAGAACTAAGACCTTTTGCAAGG CATATATTGATGCTGTACTGATATTCTTAGATAATTTAGGACAAGAGGTAGCACCAACAGCAAA ACATCAGCTCTCAAAGGTTCCATCCTTCGATGTGTAACAAGTTTTTACTAATCAGTACTAGAGA ATAGCTACTCTCAGTCCGGTGTTTTCTCAAACATCATTGTAATACTTAGTATAAGGAGCAATAA TGAAGGAAATTAGGATCCTCTTATTTCACAATTCAGAAGGAACTTTTCTTTCCATAGTCAACTT AGCTTTATAAAATGTAAATCCACAACTCTTTATGAGCAAATTTCCGATCAAGTTTCTCTACAAC TTAAATAAATTTTTTCTTGATTATGGTTCTAAAACAAAAGCATATTCCTAGCAAACTGGTTGAA TTTTAGGTAAAGCATCTCAGCACTATGTTAGTGCTGCTGTGTGTTGCAAAAAAAATTCTTAATT AAAAAATATCAAATAGCATACTCATTCCAACATTTCTACAGGATCCACATCCAGTAGTTAGATC AACAAAGAATCTTTTGATGGAGATCCATGACAATGCATCCCAGCTATCAATTCCAATCATTCCA CTTCTTTATTTTAATCGCATATGATTTAAAGGAATTACAACCAATCTGTTGGAACTAAGGTATA GTTGAATGATCGAATGATTGAATAAAATGTGATCTACTACTTTTATTTGTTACTCTATTACATA AAACTTGCCCCATTCAAACTGTCAGTATGAGGCCATTTAAATGAGCCTCAGCGATTATTTTTCA TCAGGAGTTGCTTATCATTGTGACTACAGACACAGAGGTATCTATGTATTCATCACTTGAAATT AAGGATAATTAACTTGATTTGCATTTTTATTTCAAGGAAACTTGGCTAATGAGTCCAGAATTCA TAAATAAAAGAGAGAGAAAAGAACTCGCTATAGGTCAATTGACTTGGCAAACAGGAAAGAAATT CACTGGGTCCATTGTGATTCACATACCAAGAGCACAGCCAGAATTATTTCTTTAGTCAATGAAT ACCGGTCCATTCTATTGACATGAATCTTAAACTATAACATCATTAAACGAACTAAAGAAAGAGC CAACCCGAACAGCATAGTTTTATGTCTAACATATAACAGAATGTACCTGTAGACAACTCCAATA TTAGGTGTCAAAACCTGTATTTTCTGCACCTGTTGTGCATTTCAAAGAGTCAGGGATAGATAGC ATAACTACAAGGACATCATTACATGACAGAGGTTAAGGAATGTCTAGCAAAAAAAAAATAGTTG GAATCCCCATGCAGTCCCAAAACACCGAATGCTGTGAAACTTAGTGCTTATAGAAGTTCAATAA TAAAGCATCAGTGTAATACATAGCAATGAACCACAGAAAATAAGAATTTAACAGTAAAGACTAT AAACTTAAATGCACGTATGGCATGTTGTAACTTGGTGACTGCATTTGTGAATATTATTTAAGAT ATAACTCTGCAGAGCAGTAAACTAAGCATTACTAATAAATCTACATATCCTCAACACGTACGCA AATTCAAACAGACTGATTATA

			
						 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 Niben101Scf01068g05007_circ_g.2

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