Plant Circular RNA Database

Detail information of Os01g0908200_circ_g.7

			
						 General Information
					
						CircRNA Name
						Os01g0908200_circ_g.7
					
						ID in PlantcircBase
						osa_circ_005357
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 39547655-39547962  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, circseq_cup
					
						Parent gene
						
							Os01g0908200						
					
						Parent gene annotation
						
							Member of the Bric-a-Brac/Tramtrack/Broad (BTB) family, BT1/BT2 
ortholog, Negative regulation of nitrate uptake and nitrogen use
 efficiency (Os01t0908200-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						11/17
					
						Tissues
						root/shoot, root
					
						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
						Os01t0908200-01:1

General Information
CircRNA Name	Os01g0908200_circ_g.7
ID in PlantcircBase	osa_circ_005357
Alias	NA
Organism	Oryza sativa
Position	chr1: 39547655-39547962 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, circseq_cup
Parent gene	Os01g0908200
Parent gene annotation	Member of the Bric-a-Brac/Tramtrack/Broad (BTB) family, BT1/BT2 ortholog, Negative regulation of nitrate uptake and nitrogen use efficiency (Os01t0908200-01)
Parent gene strand	+
Alternative splicing	NA
Support reads	11/17
Tissues	root/shoot, root
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	Os01t0908200-01:1

			
						 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  
						
							GCACCAGCTGCCCGCGCTGCCAGCGCATGTGGCAGCTGCTCCGCCTCCACGCCGCCCTCTGCGA
CCTCCCCGACGGCCACTGCAACACCCCTCTCTGCATcggcggaggaagtggaggaggaagaggg
cggagcaaggggtctacgtggagctgagcgaggcgatggactgcctgagccacatctgcacgga
ggggtgca

						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: 308
Transcript exons: 39547655-39547962
CGGCGGAGGAAGTGGAGGAGGAAGAGGGCGGAGCAAGGGGTCTACGTGGAGCTGAGCGAGGCGA
TGGACTGCCTGAGCCACATCTGCACGGAGGGGTGCACGGAGGTCGGGCCGGTGGGGCGTGCGCC
GGCGGCGGCGCCGTGCCCGGCGTACGCGACGGCGTGCCGGGGACTGCAGCTGCTGATCCGCCAC
TTCTCCCGGTGCCACCGCACCAGCTGCCCGCGCTGCCAGCGCATGTGGCAGCTGCTCCGCCTCC
ACGCCGCCCTCTGCGACCTCCCCGACGGCCACTGCAACACCCCTCTCTGCAT
						
						Genomic sequence
						
							CGGCGGAGGAAGTGGAGGAGGAAGAGGGCGGAGCAAGGGGTCTACGTGGAGCTGAGCGAGGCGA
TGGACTGCCTGAGCCACATCTGCACGGAGGGGTGCACGGAGGTCGGGCCGGTGGGGCGTGCGCC
GGCGGCGGCGCCGTGCCCGGCGTACGCGACGGCGTGCCGGGGACTGCAGCTGCTGATCCGCCAC
TTCTCCCGGTGCCACCGCACCAGCTGCCCGCGCTGCCAGCGCATGTGGCAGCTGCTCCGCCTCC
ACGCCGCCCTCTGCGACCTCCCCGACGGCCACTGCAACACCCCTCTCTGCAT

Sequences
Splice junction sequence	GCACCAGCTGCCCGCGCTGCCAGCGCATGTGGCAGCTGCTCCGCCTCCACGCCGCCCTCTGCGA CCTCCCCGACGGCCACTGCAACACCCCTCTCTGCATcggcggaggaagtggaggaggaagaggg cggagcaaggggtctacgtggagctgagcgaggcgatggactgcctgagccacatctgcacgga ggggtgca
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: 308 Transcript exons: 39547655-39547962 CGGCGGAGGAAGTGGAGGAGGAAGAGGGCGGAGCAAGGGGTCTACGTGGAGCTGAGCGAGGCGA TGGACTGCCTGAGCCACATCTGCACGGAGGGGTGCACGGAGGTCGGGCCGGTGGGGCGTGCGCC GGCGGCGGCGCCGTGCCCGGCGTACGCGACGGCGTGCCGGGGACTGCAGCTGCTGATCCGCCAC TTCTCCCGGTGCCACCGCACCAGCTGCCCGCGCTGCCAGCGCATGTGGCAGCTGCTCCGCCTCC ACGCCGCCCTCTGCGACCTCCCCGACGGCCACTGCAACACCCCTCTCTGCAT
Genomic sequence	CGGCGGAGGAAGTGGAGGAGGAAGAGGGCGGAGCAAGGGGTCTACGTGGAGCTGAGCGAGGCGA TGGACTGCCTGAGCCACATCTGCACGGAGGGGTGCACGGAGGTCGGGCCGGTGGGGCGTGCGCC GGCGGCGGCGCCGTGCCCGGCGTACGCGACGGCGTGCCGGGGACTGCAGCTGCTGATCCGCCAC TTCTCCCGGTGCCACCGCACCAGCTGCCCGCGCTGCCAGCGCATGTGGCAGCTGCTCCGCCTCC ACGCCGCCCTCTGCGACCTCCCCGACGGCCACTGCAACACCCCTCTCTGCAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.420652408

Conservation Information
Conserved circRNAs	NA
PMCS	0.420652408

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							39547719-39547706(+)
						
						Potential amino acid sequence
						
							MDCLSHICTEGCTEVGPVGRAPAAAPCPAYATACRGLQLLIRHFSRCHRTSCPRCQRMWQLLRL
HAALCDLPDGHCNTPLCIGGGSGGGRGRSKGSTWS*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	39547719-39547706(+)
Potential amino acid sequence	MDCLSHICTEGCTEVGPVGRAPAAAPCPAYATACRGLQLLIRHFSRCHRTSCPRCQRMWQLLRL HAALCDLPDGHCNTPLCIGGGSGGGRGRSKGSTWS*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2016;Chu et al., 2017

circRNA

Detail information of Os01g0908200_circ_g.7

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