Plant Circular RNA Database

Detail information of Os01g0716800_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os01g0716800_circ_g.4
					
						ID in PlantcircBase
						osa_circ_003654
					
						Alias
						Os01circ22016
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 29833958-29835011  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl
					
						Parent gene
						
							Os01g0716800						
					
						Parent gene annotation
						
							Endonuclease/exonuclease/phosphatase domain containing protein. 
(Os01t0716800-01);Hypothetical conserved gene. (Os01t0716800-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						3/1
					
						Tissues
						leaf and panicle/shoot
					
						Exon boundary  
						
							No-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
						Os01t0716800-02:1
Os01t0716800-01:3

General Information
CircRNA Name	Os01g0716800_circ_g.4
ID in PlantcircBase	osa_circ_003654
Alias	Os01circ22016
Organism	Oryza sativa
Position	chr1: 29833958-29835011 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl
Parent gene	Os01g0716800
Parent gene annotation	Endonuclease/exonuclease/phosphatase domain containing protein. (Os01t0716800-01);Hypothetical conserved gene. (Os01t0716800-02)
Parent gene strand	+
Alternative splicing	NA
Support reads	3/1
Tissues	leaf and panicle/shoot
Exon boundary	No-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	Os01t0716800-02:1 Os01t0716800-01:3

			
						 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  
						
							CTGAAGGAGTTATCAGCTTTCCCCCGACATACAAGTACAAGGTTAACTCAGAGAAATACACGAG
TGATGAGCCAAAATCTGGAAGGAGAACACCTGCCTGggatcaatagcagtaagcatgtccattt
atcaaacactcttttgctttatatgttgccacctgacctctggagaaaaggatggagatgaact
gaaaagga

									
								

					

						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: 197
Transcript exons: 29833958-29834102,29834960-29835011
GGATCAATAGCAGTAAGCATGTCCATTTATCAAACACTCTTTTGCTTTATATGTTGCCACCTGA
CCTCTGGAGAAAAGGATGGAGATGAACTGAAAAGGAATGCTGATGTGCAAGAAATCCATCGAAG
GACAATATTTAATCCGGCAGAGAAATACACGAGTGATGAGCCAAAATCTGGAAGGAGAACACCT
GCCTG
Transcript length: 226
Transcript exons: 29833958-29834085,29834914-29835011
GGATCAATAGCAGTAAGCATGTCCATTTATCAAACACTCTTTTGCTTTATATGTTGCCACCTGA
CCTCTGGAGAAAAGGATGGAGATGAACTGAAAAGGAATGCTGATGTGCAAGAAATCCATCGAAG
GAAGGAGTTATCAGCTTTCCCCCGACATACAAGTACAAGGTTAACTCAGAGAAATACACGAGTG
ATGAGCCAAAATCTGGAAGGAGAACACCTGCCTG
Transcript length: 240
Transcript exons: 29833958-29834108,29834923-29835011
GGATCAATAGCAGTAAGCATGTCCATTTATCAAACACTCTTTTGCTTTATATGTTGCCACCTGA
CCTCTGGAGAAAAGGATGGAGATGAACTGAAAAGGAATGCTGATGTGCAAGAAATCCATCGAAG
GACAATATTTAATCCGGTTTCCAATCAGCTTTCCCCCGACATACAAGTACAAGGTTAACTCAGA
GAAATACACGAGTGATGAGCCAAAATCTGGAAGGAGAACACCTGCCTG
Transcript length: 241
Transcript exons: 29833958-29834109,29834923-29835011
GGATCAATAGCAGTAAGCATGTCCATTTATCAAACACTCTTTTGCTTTATATGTTGCCACCTGA
CCTCTGGAGAAAAGGATGGAGATGAACTGAAAAGGAATGCTGATGTGCAAGAAATCCATCGAAG
GACAATATTTAATCCGGTTTCCAGATCAGCTTTCCCCCGACATACAAGTACAAGGTTAACTCAG
AGAAATACACGAGTGATGAGCCAAAATCTGGAAGGAGAACACCTGCCTG
						
					

						Genomic sequence
						
							GGATCAATAGCAGTAAGCATGTCCATTTATCAAACACTCTTTTGCTTTATATGTTGCCACCTGA
CCTCTGGAGAAAAGGATGGAGATGAACTGAAAAGGAATGCTGATGTGCAAGAAATCCATCGAAG
GACAATATTTAATCCGGTTTCCAGAGTTAGCATGCCTAAGACTATATATGACCATGAGTAAGTA
CGTAAACTTGCAACTCTAAAACACTAGAAGCTCAGTACGCAATTCCTAAAGCTCTAGCTAAACT
AAGCATGTTTTTTATCCATGCCATTTGATACTCTTTTGGAGATGATGGCTCAATTTCAGTTTAG
ATTGTGTTTGGCGTCACTGTTTACTTGTTTAAATATGATGGGATAACAAGGGATAAATGATTAA
AGTGAATCTGTGCATATTAGTGGCAAAAATCACATAATGAAGCAGATGATGGCTCAATTTCAGT
TTAGATTGTGTTTGGCGTCACTGTTTACTTGTTTAAATATGATGGTATAACAAGGGATAAATGG
TTGAAGTGAATCTGTGCATATTAGTGGCAAAAATCACATAATGAAGCATGTGTTCGAGGGTTGC
ACACATTTGAAATTTTTCTTATACTTCTTTTGTTCATTTTAGTTTTATTTGATCAAGAATTGCA
GGAAACATTGCTTATTAGTTTATATAAATCTTATCAGTTTGTCTAATATTTTTATTTTCTTGAA
TATTTCAGAAGGATAATATGGTTAGGAGATCTCAATTATAGGATCAACTTATCATATGAAAAAA
CACATGAATTCATATCCATGAAGGACTGGAATGGTTTGTTCCAGAATGACCAGGTAAAGTTTTG
GCAGCAGTGCAGCATCTTGTGACATACTCCTACTACTTTATAAATACATAGTACCTCACTGTTT
TCTACTCTATGATAGCTAAAACGAGAATTTAAGAAAGGGCATTTATTTGATGGGTGGACTGAAG
GAGTTATCAGCTTTCCCCCGACATACAAGTACAAGGTTAACTCAGAGAAATACACGAGTGATGA
GCCAAAATCTGGAAGGAGAACACCTGCCTG
						
					

			
		

Sequences
Splice junction sequence	CTGAAGGAGTTATCAGCTTTCCCCCGACATACAAGTACAAGGTTAACTCAGAGAAATACACGAG TGATGAGCCAAAATCTGGAAGGAGAACACCTGCCTGggatcaatagcagtaagcatgtccattt atcaaacactcttttgctttatatgttgccacctgacctctggagaaaaggatggagatgaact gaaaagga
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: 197 Transcript exons: 29833958-29834102,29834960-29835011 GGATCAATAGCAGTAAGCATGTCCATTTATCAAACACTCTTTTGCTTTATATGTTGCCACCTGA CCTCTGGAGAAAAGGATGGAGATGAACTGAAAAGGAATGCTGATGTGCAAGAAATCCATCGAAG GACAATATTTAATCCGGCAGAGAAATACACGAGTGATGAGCCAAAATCTGGAAGGAGAACACCT GCCTG Transcript length: 226 Transcript exons: 29833958-29834085,29834914-29835011 GGATCAATAGCAGTAAGCATGTCCATTTATCAAACACTCTTTTGCTTTATATGTTGCCACCTGA CCTCTGGAGAAAAGGATGGAGATGAACTGAAAAGGAATGCTGATGTGCAAGAAATCCATCGAAG GAAGGAGTTATCAGCTTTCCCCCGACATACAAGTACAAGGTTAACTCAGAGAAATACACGAGTG ATGAGCCAAAATCTGGAAGGAGAACACCTGCCTG Transcript length: 240 Transcript exons: 29833958-29834108,29834923-29835011 GGATCAATAGCAGTAAGCATGTCCATTTATCAAACACTCTTTTGCTTTATATGTTGCCACCTGA CCTCTGGAGAAAAGGATGGAGATGAACTGAAAAGGAATGCTGATGTGCAAGAAATCCATCGAAG GACAATATTTAATCCGGTTTCCAATCAGCTTTCCCCCGACATACAAGTACAAGGTTAACTCAGA GAAATACACGAGTGATGAGCCAAAATCTGGAAGGAGAACACCTGCCTG Transcript length: 241 Transcript exons: 29833958-29834109,29834923-29835011 GGATCAATAGCAGTAAGCATGTCCATTTATCAAACACTCTTTTGCTTTATATGTTGCCACCTGA CCTCTGGAGAAAAGGATGGAGATGAACTGAAAAGGAATGCTGATGTGCAAGAAATCCATCGAAG GACAATATTTAATCCGGTTTCCAGATCAGCTTTCCCCCGACATACAAGTACAAGGTTAACTCAG AGAAATACACGAGTGATGAGCCAAAATCTGGAAGGAGAACACCTGCCTG
Genomic sequence	GGATCAATAGCAGTAAGCATGTCCATTTATCAAACACTCTTTTGCTTTATATGTTGCCACCTGA CCTCTGGAGAAAAGGATGGAGATGAACTGAAAAGGAATGCTGATGTGCAAGAAATCCATCGAAG GACAATATTTAATCCGGTTTCCAGAGTTAGCATGCCTAAGACTATATATGACCATGAGTAAGTA CGTAAACTTGCAACTCTAAAACACTAGAAGCTCAGTACGCAATTCCTAAAGCTCTAGCTAAACT AAGCATGTTTTTTATCCATGCCATTTGATACTCTTTTGGAGATGATGGCTCAATTTCAGTTTAG ATTGTGTTTGGCGTCACTGTTTACTTGTTTAAATATGATGGGATAACAAGGGATAAATGATTAA AGTGAATCTGTGCATATTAGTGGCAAAAATCACATAATGAAGCAGATGATGGCTCAATTTCAGT TTAGATTGTGTTTGGCGTCACTGTTTACTTGTTTAAATATGATGGTATAACAAGGGATAAATGG TTGAAGTGAATCTGTGCATATTAGTGGCAAAAATCACATAATGAAGCATGTGTTCGAGGGTTGC ACACATTTGAAATTTTTCTTATACTTCTTTTGTTCATTTTAGTTTTATTTGATCAAGAATTGCA GGAAACATTGCTTATTAGTTTATATAAATCTTATCAGTTTGTCTAATATTTTTATTTTCTTGAA TATTTCAGAAGGATAATATGGTTAGGAGATCTCAATTATAGGATCAACTTATCATATGAAAAAA CACATGAATTCATATCCATGAAGGACTGGAATGGTTTGTTCCAGAATGACCAGGTAAAGTTTTG GCAGCAGTGCAGCATCTTGTGACATACTCCTACTACTTTATAAATACATAGTACCTCACTGTTT TCTACTCTATGATAGCTAAAACGAGAATTTAAGAAAGGGCATTTATTTGATGGGTGGACTGAAG GAGTTATCAGCTTTCCCCCGACATACAAGTACAAGGTTAACTCAGAGAAATACACGAGTGATGA GCCAAAATCTGGAAGGAGAACACCTGCCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002357* osi_circ_010644 						
					
						PMCS
						0.265529499

Conservation Information
Conserved circRNAs	osi_circ_002357* osi_circ_010644
PMCS	0.265529499

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

			
						 Other Information
					
						References
						Lu et al., 2015;Chu et al., 2017

circRNA

Detail information of Os01g0716800_circ_g.4

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