Plant Circular RNA Database

Detail information of Os10g0485000_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os10g0485000_circ_g.1
					
						ID in PlantcircBase
						osa_circ_007186
					
						Alias
						Os_ciR3608
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr10: 18322043-18322631  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, find_circ
					
						Parent gene
						
							Os10g0485000						
					
						Parent gene annotation
						
							FF domain containing protein. (Os10t0485000-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os10g0485000_circ_g.2 Os10g0485000_circ_g.3 						
					
						Support reads
						2/3
					
						Tissues
						root/shoot, root, seed
					
						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  
						
							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
						Os10t0485000-01:3

General Information
CircRNA Name	Os10g0485000_circ_g.1
ID in PlantcircBase	osa_circ_007186
Alias	Os_ciR3608
Organism	Oryza sativa
Position	chr10: 18322043-18322631 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, find_circ
Parent gene	Os10g0485000
Parent gene annotation	FF domain containing protein. (Os10t0485000-01)
Parent gene strand	-
Alternative splicing	Os10g0485000_circ_g.2 Os10g0485000_circ_g.3
Support reads	2/3
Tissues	root/shoot, root, seed
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	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	Os10t0485000-01:3

			
						 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  
						
							CAGCGGATTTTAGTTCTGCTATGTACTCATTAAAAGCAACCTCTCTTTCTTCGTGCTTCATGGC
TTTGTACCTTGCATCGCTCCGGAAATTTTCTTTCACctcatacaggtccttgacatggtcacga
aataacttttctgcatcacctttacctaaatcaggatttactgcacggccttgtggatcctttt
caagtctt

						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: 414
Transcript exons: 18322043-18322165,18322257-18322403,18322488-18322631
CTCATACAGGTCCTTGACATGGTCACGAAATAACTTTTCTGCATCACCTTTACCTAAATCAGGA
TTTACTGCACGGCCTTGTGGATCCTTTTCAAGTCTTGGTTTGGATTCTGTCCATGATGCCTTGG
GATCTTTTATGATTTCAACAAGTAAAGCTTGATATGAAGACACGGCCTCTTTTCTTCGGATCTT
CAATTTTACTCTCTCCATTTCCTGTTCTTCCCTTTCTTTCCTTTTCCGCATCTCGCGCTCCCTC
TCCTTTAACTTGGCTTGTTCATCCAGTTTGGCCTTGGCAGCTTGCTCTGCTTCCTTTTCAGCGG
ATTTTAGTTCTGCTATGTACTCATTAAAAGCAACCTCTCTTTCTTCGTGCTTCATGGCTTTGTA
CCTTGCATCGCTCCGGAAATTTTCTTTCAC
						
						Genomic sequence
						
							CTCATACAGGTCCTTGACATGGTCACGAAATAACTTTTCTGCATCACCTTTACCTAAATCAGGA
TTTACTGCACGGCCTTGTGGATCCTTTTCAAGTCTTGGTTTGGATTCTGTCCATGATGCCTATG
CAGAAAAAATAGCATAGTTAATATGAAGTTGTACAGTACATAGCAAAATAGCTTGTCAAATGGA
GTTCAACAAAGTGTCAAGTTACCTTGGGATCTTTTATGATTTCAACAAGTAAAGCTTGATATGA
AGACACGGCCTCTTTTCTTCGGATCTTCAATTTTACTCTCTCCATTTCCTGTTCTTCCCTTTCT
TTCCTTTTCCGCATCTCGCGCTCCCTCTCCTTTAACTTGGCCTGGGTTATTACATAGTATATGT
GAAGCTACAAAGCTACATTCAGTAAACAAAGCATCAGAGTACATCAGTTAAATTGACTGACTTG
TTCATCCAGTTTGGCCTTGGCAGCTTGCTCTGCTTCCTTTTCAGCGGATTTTAGTTCTGCTATG
TACTCATTAAAAGCAACCTCTCTTTCTTCGTGCTTCATGGCTTTGTACCTTGCATCGCTCCGGA
AATTTTCTTTCAC

Sequences
Splice junction sequence	CAGCGGATTTTAGTTCTGCTATGTACTCATTAAAAGCAACCTCTCTTTCTTCGTGCTTCATGGC TTTGTACCTTGCATCGCTCCGGAAATTTTCTTTCACctcatacaggtccttgacatggtcacga aataacttttctgcatcacctttacctaaatcaggatttactgcacggccttgtggatcctttt caagtctt
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: 414 Transcript exons: 18322043-18322165,18322257-18322403,18322488-18322631 CTCATACAGGTCCTTGACATGGTCACGAAATAACTTTTCTGCATCACCTTTACCTAAATCAGGA TTTACTGCACGGCCTTGTGGATCCTTTTCAAGTCTTGGTTTGGATTCTGTCCATGATGCCTTGG GATCTTTTATGATTTCAACAAGTAAAGCTTGATATGAAGACACGGCCTCTTTTCTTCGGATCTT CAATTTTACTCTCTCCATTTCCTGTTCTTCCCTTTCTTTCCTTTTCCGCATCTCGCGCTCCCTC TCCTTTAACTTGGCTTGTTCATCCAGTTTGGCCTTGGCAGCTTGCTCTGCTTCCTTTTCAGCGG ATTTTAGTTCTGCTATGTACTCATTAAAAGCAACCTCTCTTTCTTCGTGCTTCATGGCTTTGTA CCTTGCATCGCTCCGGAAATTTTCTTTCAC
Genomic sequence	CTCATACAGGTCCTTGACATGGTCACGAAATAACTTTTCTGCATCACCTTTACCTAAATCAGGA TTTACTGCACGGCCTTGTGGATCCTTTTCAAGTCTTGGTTTGGATTCTGTCCATGATGCCTATG CAGAAAAAATAGCATAGTTAATATGAAGTTGTACAGTACATAGCAAAATAGCTTGTCAAATGGA GTTCAACAAAGTGTCAAGTTACCTTGGGATCTTTTATGATTTCAACAAGTAAAGCTTGATATGA AGACACGGCCTCTTTTCTTCGGATCTTCAATTTTACTCTCTCCATTTCCTGTTCTTCCCTTTCT TTCCTTTTCCGCATCTCGCGCTCCCTCTCCTTTAACTTGGCCTGGGTTATTACATAGTATATGT GAAGCTACAAAGCTACATTCAGTAAACAAAGCATCAGAGTACATCAGTTAAATTGACTGACTTG TTCATCCAGTTTGGCCTTGGCAGCTTGCTCTGCTTCCTTTTCAGCGGATTTTAGTTCTGCTATG TACTCATTAAAAGCAACCTCTCTTTCTTCGTGCTTCATGGCTTTGTACCTTGCATCGCTCCGGA AATTTTCTTTCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002866* osi_circ_008534 						
					
						PMCS
						0.344958008

Conservation Information
Conserved circRNAs	osi_circ_002866* osi_circ_008534
PMCS	0.344958008

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							18322553-18322290(+)
18322594-18322045(-)
						
						Potential amino acid sequence
						
							MYSLKATSLSSCFMALYLASLRKFSFTSYRSLTWSRNNFSASPLPKSGFTARPCGSFSSLGLDS
VHDALGSFMISTSKA*(+)
MKHEEREVAFNEYIAELKSAEKEAEQAAKAKLDEQAKLKEREREMRKRKEREEQEMERVKLKIR
RKEAVSSYQALLVEIIKDPKASWTESKPRLEKDPQGRAVNPDLGKGDAEKLFRDHVKDLYEVKE
NFRSDARYKAMKHEEREVAFNEYIAELKSAEKEAEQAAKAKLDEQAKLKEREREMRKRKEREEQ
EMERVKLKIRRKEAVSSYQALLVEIIKDPKASWTESKPRLEKDPQGRAVNPDLGKGDAEKLFRD
HVKDLYEVKENFRSDARYKAMKHEEREVAFNEYIAELKSAEKEAEQAAKAKLDEQAKLKERERE
MRKRKEREEQEMERVKLKIRRKEAVSSYQALLVEIIKDPKASWTESKPRLEKDPQGRAVNPDLG
KGDAEKLFRDHVKDLYEVKENFRSDARYKAMKHEEREVAFNEYIAELKSAEKEAEQAAKAKLDE
QAKLKEREREMRKRKEREEQEMERVKLKIRRKEAVSSYQALLVEIIKDPKASWTESKPRLEKDP
QGRAVNPDLGKGDAEKLFRDHVKDLYE(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	18322553-18322290(+) 18322594-18322045(-)
Potential amino acid sequence	MYSLKATSLSSCFMALYLASLRKFSFTSYRSLTWSRNNFSASPLPKSGFTARPCGSFSSLGLDS VHDALGSFMISTSKA*(+) MKHEEREVAFNEYIAELKSAEKEAEQAAKAKLDEQAKLKEREREMRKRKEREEQEMERVKLKIR RKEAVSSYQALLVEIIKDPKASWTESKPRLEKDPQGRAVNPDLGKGDAEKLFRDHVKDLYEVKE NFRSDARYKAMKHEEREVAFNEYIAELKSAEKEAEQAAKAKLDEQAKLKEREREMRKRKEREEQ EMERVKLKIRRKEAVSSYQALLVEIIKDPKASWTESKPRLEKDPQGRAVNPDLGKGDAEKLFRD HVKDLYEVKENFRSDARYKAMKHEEREVAFNEYIAELKSAEKEAEQAAKAKLDEQAKLKERERE MRKRKEREEQEMERVKLKIRRKEAVSSYQALLVEIIKDPKASWTESKPRLEKDPQGRAVNPDLG KGDAEKLFRDHVKDLYEVKENFRSDARYKAMKHEEREVAFNEYIAELKSAEKEAEQAAKAKLDE QAKLKEREREMRKRKEREEQEMERVKLKIRRKEAVSSYQALLVEIIKDPKASWTESKPRLEKDP QGRAVNPDLGKGDAEKLFRDHVKDLYE(-)
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 Os10g0485000_circ_g.1

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