Plant Circular RNA Database

Detail information of Os01g0534900_circ_g.35

			
						 General Information
					
						CircRNA Name
						Os01g0534900_circ_g.35
					
						ID in PlantcircBase
						osa_circ_002055
					
						Alias
						Os_ciR1708
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 19401701-19403270  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os01g0534900						
					
						Parent gene annotation
						
							Similar to Hv711N16.16 (Fragment). (Os01t0534900-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0534900_circ_g.2 Os01g0534900_circ_g.3 Os01g0534900_circ_g.4 Os01g0534900_circ_g.5 Os01g0534900_circ_g.6 Os01g0534900_circ_g.7 Os01g0534900_circ_g.8 Os01g0534900_circ_g.9 Os01g0534900_circ_g.10 Os01g0534900_circ_g.11 Os01g0534900_circ_g.12 Os01g0534900_circ_g.13 Os01g0534900_circ_g.14 Os01g0534900_circ_g.15 Os01g0534900_circ_g.16 Os01g0534900_circ_g.17 Os01g0534900_circ_g.18 Os01g0534900_circ_g.19 Os01g0534900_circ_g.20 Os01g0534900_circ_g.21 Os01g0534900_circ_g.22 Os01g0534900_circ_g.23 Os01g0534900_circ_g.24 Os01g0534900_circ_g.25 Os01g0534900_circ_g.26 Os01g0534900_circ_g.27 Os01g0534900_circ_g.28 Os01g0534900_circ_g.29 Os01g0534900_circ_g.30 Os01g0534900_circ_g.31 Os01g0534900_circ_g.32 Os01g0534900_circ_g.33 Os01g0534900_circ_g.34 Os01g0534900_circ_g.36 Os01g0534900_circ_g.37 						
					
						Support reads
						12/2
					
						Tissues
						root/shoot, root
					
						Exon boundary  
						
							Yes-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  
						
							CT-AC							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
						Os01t0534900-01:3

General Information
CircRNA Name	Os01g0534900_circ_g.35
ID in PlantcircBase	osa_circ_002055
Alias	Os_ciR1708
Organism	Oryza sativa
Position	chr1: 19401701-19403270 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ei-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os01g0534900
Parent gene annotation	Similar to Hv711N16.16 (Fragment). (Os01t0534900-01)
Parent gene strand	-
Alternative splicing	Os01g0534900_circ_g.2 Os01g0534900_circ_g.3 Os01g0534900_circ_g.4 Os01g0534900_circ_g.5 Os01g0534900_circ_g.6 Os01g0534900_circ_g.7 Os01g0534900_circ_g.8 Os01g0534900_circ_g.9 Os01g0534900_circ_g.10 Os01g0534900_circ_g.11 Os01g0534900_circ_g.12 Os01g0534900_circ_g.13 Os01g0534900_circ_g.14 Os01g0534900_circ_g.15 Os01g0534900_circ_g.16 Os01g0534900_circ_g.17 Os01g0534900_circ_g.18 Os01g0534900_circ_g.19 Os01g0534900_circ_g.20 Os01g0534900_circ_g.21 Os01g0534900_circ_g.22 Os01g0534900_circ_g.23 Os01g0534900_circ_g.24 Os01g0534900_circ_g.25 Os01g0534900_circ_g.26 Os01g0534900_circ_g.27 Os01g0534900_circ_g.28 Os01g0534900_circ_g.29 Os01g0534900_circ_g.30 Os01g0534900_circ_g.31 Os01g0534900_circ_g.32 Os01g0534900_circ_g.33 Os01g0534900_circ_g.34 Os01g0534900_circ_g.36 Os01g0534900_circ_g.37
Support reads	12/2
Tissues	root/shoot, root
Exon boundary	Yes-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	CT-AC 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	Os01t0534900-01:3

			
						 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  
						
							GATGGCACTCAGTATGTTGATAGCTGCAGAGACACCTATATCTTGAATAGTAGCCATATTTGTC
CTTCAAATAACTTGCGAGAATTACTACAGATGCTAGcgtgaactgatctgggcggcgcttctct
gatgcaagaaagcgcagacgcattgttgccactatttcatactcccgtaacagcacatagcatg
tccaaaat

									
								

					

						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
						
							CGTGAACTGATCTGGGCGGCGCTTCTCTGATGCAAGAAAGCGCAGACGCATTGTTGCCACTATT
TCATACTCCCGTAACAGCACATAGCATGTCCAAAATGTGAAAACATAAGCCATGGTCAGGTGAG
CTGCGAACCTGCATTAAAAAAAAGTCACAGGCATAGTGAACACTAAAACAATAGTTTCAGAGTT
GATGAACAGGGTATCCTGCAAGACTAATGTGCTGCCTGGAAGGCTAATATCAACTATAACCACT
CACCTACTTATCTATGGCAAGATCAAACCTTTGCGACTATTTGTCTAATTACTATTACAAAGTA
TCACACCAAACTGACACAACAAGCTAGGTTAAAATTAATGGCCTTCAGAATTGCACACCCCACA
CATGCAAGCTACTACCGTTTCTGACTCCCAGCTCATGTATTATCACAGAGGCTGGGTGGTTGTT
CATACTGCATGGTCATCTCTATACATCTTCGGATCTTCATGACTTTCCTAAGCCCAAATGGGGA
AAGAAAGTAAGAGCAATCATCATTCCACTTACCATTTGAACCAACCCCATACTCACTATCTTAA
ATTGTGTTTGAAGTAATCTATCAGGCATGCCCATATTTTAGCCAAAGATGGTACACAACATTAA
CAGTAATATGTAGGTATATTACTATATTTTAAGACAGAAAAATTATCTGGTACTAACCTCTTTG
ACCCTACAGGTATGTTGGATATTGAAAGTTTGTCAATATCACTGTGCTGCACCTTCGAGCTTTG
AAGGGTAATATTGGTCCAATTAACAGGCACAAGAATAATAAATGCTAGAACTGTGATTGGAGCA
AATATTTTAAGCCTGCAACAGTTAATAGTAAAGGAGATTAGTGTAAAAGTATTGGCAGAGAAAA
GTAACAGAGATGGGAGATACCCAGTGGATAAAACAGAAACATTCAACAAAACAACATTTTCGGT
ACTAGAAGTACACTTCTACATATGTAAGAAATGGAGAAATAGCAACGATTTAGAATCCATAAAA
ATATAAGACAATTAAAATGAATAGTATGTAAATATTAAAATATGGTCCAACACTAGAGCCCTTC
CCTTCTGTCAAGGAGAAAACCTGAAAGCTAAACCCCCCCCCCCCCCTCCCTTAAATATATGTCT
GACCTAAAGTATAATTGACGACTTAAAAAGTTAGCAGAATTTATGAATATAAATTGCATACCCT
ATTAAGTAGATCCGCAGATAGACAGCTGAATCAAGGCCTGCATGGCTAATTAACTCATCCTCTG
GCATTTTGAGAGCAGCAGGCATCCAACTTAAGACCTTCAAGTATGATCGCATGTCCAAATTGAC
AAACTTCCGCACAAATGCACCCCCATGACTTGGACTCTCTCTTGCACCTTTGAGATACCACTTT
GGGAAGTAAACCCTATCGTTGATGGGCTGTAGTCGCAGGAAAGCAAACGCTAGCAGGAAAGTGA
TGGCACTCAGTATGTTGATAGCTGCAGAGACACCTATATCTTGAATAGTAGCCATATTTGTCCT
TCAAATAACTTGCGAGAATTACTACAGATGCTAG
						
					

			
		

Sequences
Splice junction sequence	GATGGCACTCAGTATGTTGATAGCTGCAGAGACACCTATATCTTGAATAGTAGCCATATTTGTC CTTCAAATAACTTGCGAGAATTACTACAGATGCTAGcgtgaactgatctgggcggcgcttctct gatgcaagaaagcgcagacgcattgttgccactatttcatactcccgtaacagcacatagcatg tccaaaat
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	CGTGAACTGATCTGGGCGGCGCTTCTCTGATGCAAGAAAGCGCAGACGCATTGTTGCCACTATT TCATACTCCCGTAACAGCACATAGCATGTCCAAAATGTGAAAACATAAGCCATGGTCAGGTGAG CTGCGAACCTGCATTAAAAAAAAGTCACAGGCATAGTGAACACTAAAACAATAGTTTCAGAGTT GATGAACAGGGTATCCTGCAAGACTAATGTGCTGCCTGGAAGGCTAATATCAACTATAACCACT CACCTACTTATCTATGGCAAGATCAAACCTTTGCGACTATTTGTCTAATTACTATTACAAAGTA TCACACCAAACTGACACAACAAGCTAGGTTAAAATTAATGGCCTTCAGAATTGCACACCCCACA CATGCAAGCTACTACCGTTTCTGACTCCCAGCTCATGTATTATCACAGAGGCTGGGTGGTTGTT CATACTGCATGGTCATCTCTATACATCTTCGGATCTTCATGACTTTCCTAAGCCCAAATGGGGA AAGAAAGTAAGAGCAATCATCATTCCACTTACCATTTGAACCAACCCCATACTCACTATCTTAA ATTGTGTTTGAAGTAATCTATCAGGCATGCCCATATTTTAGCCAAAGATGGTACACAACATTAA CAGTAATATGTAGGTATATTACTATATTTTAAGACAGAAAAATTATCTGGTACTAACCTCTTTG ACCCTACAGGTATGTTGGATATTGAAAGTTTGTCAATATCACTGTGCTGCACCTTCGAGCTTTG AAGGGTAATATTGGTCCAATTAACAGGCACAAGAATAATAAATGCTAGAACTGTGATTGGAGCA AATATTTTAAGCCTGCAACAGTTAATAGTAAAGGAGATTAGTGTAAAAGTATTGGCAGAGAAAA GTAACAGAGATGGGAGATACCCAGTGGATAAAACAGAAACATTCAACAAAACAACATTTTCGGT ACTAGAAGTACACTTCTACATATGTAAGAAATGGAGAAATAGCAACGATTTAGAATCCATAAAA ATATAAGACAATTAAAATGAATAGTATGTAAATATTAAAATATGGTCCAACACTAGAGCCCTTC CCTTCTGTCAAGGAGAAAACCTGAAAGCTAAACCCCCCCCCCCCCCTCCCTTAAATATATGTCT GACCTAAAGTATAATTGACGACTTAAAAAGTTAGCAGAATTTATGAATATAAATTGCATACCCT ATTAAGTAGATCCGCAGATAGACAGCTGAATCAAGGCCTGCATGGCTAATTAACTCATCCTCTG GCATTTTGAGAGCAGCAGGCATCCAACTTAAGACCTTCAAGTATGATCGCATGTCCAAATTGAC AAACTTCCGCACAAATGCACCCCCATGACTTGGACTCTCTCTTGCACCTTTGAGATACCACTTT GGGAAGTAAACCCTATCGTTGATGGGCTGTAGTCGCAGGAAAGCAAACGCTAGCAGGAAAGTGA TGGCACTCAGTATGTTGATAGCTGCAGAGACACCTATATCTTGAATAGTAGCCATATTTGTCCT TCAAATAACTTGCGAGAATTACTACAGATGCTAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002120* osi_circ_009881 						
					
						PMCS
						0.376035658

Conservation Information
Conserved circRNAs	osi_circ_002120* osi_circ_009881
PMCS	0.376035658

			
						 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
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os01g0534900_circ_g.35

Address

Any questions?

Supported by