Plant Circular RNA Database

Detail information of Os09g0563800_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os09g0563800_circ_g.2
					
						ID in PlantcircBase
						osa_circ_040205
					
						Alias
						Os09circ11138/Os_ciR1024
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 22410735-22411666  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os09g0563800						
					
						Parent gene annotation
						
							ATPase, AAA-type, core domain containing protein. (Os09t0563800-
01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os09g0563800_circ_g.1 Os09g0563800_circ_g.3 						
					
						Support reads
						6/19/4
					
						Tissues
						leaf and panicle/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
						Os09t0563800-01:4

General Information
CircRNA Name	Os09g0563800_circ_g.2
ID in PlantcircBase	osa_circ_040205
Alias	Os09circ11138/Os_ciR1024
Organism	Oryza sativa
Position	chr9: 22410735-22411666 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, SMALT, Segemehl, find_circ
Parent gene	Os09g0563800
Parent gene annotation	ATPase, AAA-type, core domain containing protein. (Os09t0563800- 01)
Parent gene strand	-
Alternative splicing	Os09g0563800_circ_g.1 Os09g0563800_circ_g.3
Support reads	6/19/4
Tissues	leaf and panicle/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	Os09t0563800-01:4

			
						 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  
						
							AACCTGTAGTCATAGGCAGAGTTCCTAGAACCTTGAAGATCCCTATCTTTTCTTTGTTCACTAA
CAAAGGGAATGACATCCCTGGATACATCACACCGATctgggtggttgttatgtcagtcataact
gttgaaccacatctgttgtgagggaccaactcatcaaaccggtcaaggaagatcagaagtggac
catcacgt

									
								

					

						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: 588
Transcript exons: 22410735-22410863,22410961-22411155,22411311-22411477,22
411570-22411666
CTGGGTGGTTGTTATGTCAGTCATAACTGTTGAACCACATCTGTTGTGAGGGACCAACTCATCA
AACCGGTCAAGGAAGATCAGAAGTGGACCATCACGTGATTCAGGTCTCTGTATGCAGGTGTTGA
TCTGTGAGACAGAGTCAGAAGGGAAGTCCTTGATGAGTGACGAAGCATCCACGCTCGCAACAGG
AAGACCAAGGGTCCTTCCTATCCCTTCAACCACAGCTTTTTTATCACATGGACCATGTAAGAGA
AATGTCATTTTGCCCTTTGTGGCCTCATGTGGGAGGTGAGTATAGTAACTCATGAAATTACCAA
TCATCTTACTGGCTCTGCCAACCACATTAGAAAGAGCGGGGTCATCCACCATTTTCATTTGCAG
AGGAGTTGCAATGACTGGATGTAAGATTGGTGGGTACAGGGTCTCTCCAACAGTTTTCTCATCA
CTACCTTTCCAAATCATGATCTTGGTCCCTGAGGTAATTTGTCCTGTAGTCATAGGCAGAGTTC
CTAGAACCTTGAAGATCCCTATCTTTTCTTTGTTCACTAACAAAGGGAATGACATCCCTGGATA
CATCACACCGAT
						
					

						Genomic sequence
						
							CTGGGTGGTTGTTATGTCAGTCATAACTGTTGAACCACATCTGTTGTGAGGGACCAACTCATCA
AACCGGTCAAGGAAGATCAGAAGTGGACCATCACGTGATTCAGGTCTCTGTATGCAGGTGTTGA
TCTACAATTCATTCAATAGTTAATTATAATAGTATCAAATACAAACAAATAAAATGACAAAAAT
TAACTGTGAAAGTATACCTTAAGCCATATCTTACCTGTGAGACAGAGTCAGAAGGGAAGTCCTT
GATGAGTGACGAAGCATCCACGCTCGCAACAGGAAGACCAAGGGTCCTTCCTATCCCTTCAACC
ACAGCTTTTTTATCACATGGACCATGTAAGAGAAATGTCATTTTGCCCTTTGTGGCCTCATGTG
GGAGGTGAGTATAGTAACTCATGAAATTACCAATCATCTGCAAATTAACAAAGATACAACATGA
GAAACAAAAAAAGATCAAGATATATAGTCAAGTAAAGGCCTTAGACAAACTAGAACTATCTCAT
CCTTAGACAAACTAGAACTATCTCAATTCATACATACCACTAGAAGAACTAACTCAATCCATAC
CTTACTGGCTCTGCCAACCACATTAGAAAGAGCGGGGTCATCCACCATTTTCATTTGCAGAGGA
GTTGCAATGACTGGATGTAAGATTGGTGGGTACAGGGTCTCTCCAACAGTTTTCTCATCACTAC
CTTTCCAAATCATGATCTTGGTCCCTGAGGTAATTTGTCCTGGGAGTTTATGAAAAGAAAACAC
CGTTGGTTATAATAATTTCAGTATGCACTCAACAGATTTAAAATATATATGCTGGAATAAGTCC
AACCTGTAGTCATAGGCAGAGTTCCTAGAACCTTGAAGATCCCTATCTTTTCTTTGTTCACTAA
CAAAGGGAATGACATCCCTGGATACATCACACCGAT
						
					

			
		

Sequences
Splice junction sequence	AACCTGTAGTCATAGGCAGAGTTCCTAGAACCTTGAAGATCCCTATCTTTTCTTTGTTCACTAA CAAAGGGAATGACATCCCTGGATACATCACACCGATctgggtggttgttatgtcagtcataact gttgaaccacatctgttgtgagggaccaactcatcaaaccggtcaaggaagatcagaagtggac catcacgt
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: 588 Transcript exons: 22410735-22410863,22410961-22411155,22411311-22411477,22 411570-22411666 CTGGGTGGTTGTTATGTCAGTCATAACTGTTGAACCACATCTGTTGTGAGGGACCAACTCATCA AACCGGTCAAGGAAGATCAGAAGTGGACCATCACGTGATTCAGGTCTCTGTATGCAGGTGTTGA TCTGTGAGACAGAGTCAGAAGGGAAGTCCTTGATGAGTGACGAAGCATCCACGCTCGCAACAGG AAGACCAAGGGTCCTTCCTATCCCTTCAACCACAGCTTTTTTATCACATGGACCATGTAAGAGA AATGTCATTTTGCCCTTTGTGGCCTCATGTGGGAGGTGAGTATAGTAACTCATGAAATTACCAA TCATCTTACTGGCTCTGCCAACCACATTAGAAAGAGCGGGGTCATCCACCATTTTCATTTGCAG AGGAGTTGCAATGACTGGATGTAAGATTGGTGGGTACAGGGTCTCTCCAACAGTTTTCTCATCA CTACCTTTCCAAATCATGATCTTGGTCCCTGAGGTAATTTGTCCTGTAGTCATAGGCAGAGTTC CTAGAACCTTGAAGATCCCTATCTTTTCTTTGTTCACTAACAAAGGGAATGACATCCCTGGATA CATCACACCGAT
Genomic sequence	CTGGGTGGTTGTTATGTCAGTCATAACTGTTGAACCACATCTGTTGTGAGGGACCAACTCATCA AACCGGTCAAGGAAGATCAGAAGTGGACCATCACGTGATTCAGGTCTCTGTATGCAGGTGTTGA TCTACAATTCATTCAATAGTTAATTATAATAGTATCAAATACAAACAAATAAAATGACAAAAAT TAACTGTGAAAGTATACCTTAAGCCATATCTTACCTGTGAGACAGAGTCAGAAGGGAAGTCCTT GATGAGTGACGAAGCATCCACGCTCGCAACAGGAAGACCAAGGGTCCTTCCTATCCCTTCAACC ACAGCTTTTTTATCACATGGACCATGTAAGAGAAATGTCATTTTGCCCTTTGTGGCCTCATGTG GGAGGTGAGTATAGTAACTCATGAAATTACCAATCATCTGCAAATTAACAAAGATACAACATGA GAAACAAAAAAAGATCAAGATATATAGTCAAGTAAAGGCCTTAGACAAACTAGAACTATCTCAT CCTTAGACAAACTAGAACTATCTCAATTCATACATACCACTAGAAGAACTAACTCAATCCATAC CTTACTGGCTCTGCCAACCACATTAGAAAGAGCGGGGTCATCCACCATTTTCATTTGCAGAGGA GTTGCAATGACTGGATGTAAGATTGGTGGGTACAGGGTCTCTCCAACAGTTTTCTCATCACTAC CTTTCCAAATCATGATCTTGGTCCCTGAGGTAATTTGTCCTGGGAGTTTATGAAAAGAAAACAC CGTTGGTTATAATAATTTCAGTATGCACTCAACAGATTTAAAATATATATGCTGGAATAAGTCC AACCTGTAGTCATAGGCAGAGTTCCTAGAACCTTGAAGATCCCTATCTTTTCTTTGTTCACTAA CAAAGGGAATGACATCCCTGGATACATCACACCGAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_008236* osi_circ_018775 						
					
						PMCS
						0.608199246

Conservation Information
Conserved circRNAs	osi_circ_008236* osi_circ_018775
PMCS	0.608199246

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							22411140-22410780(+)
22411659-22410737(-)
						
						Potential amino acid sequence
						
							MKLPIILLALPTTLERAGSSTIFICRGVAMTGCKIGGYRVSPTVFSSLPFQIMILVPEVICPVV
IGRVPRTLKIPIFSLFTNKGNDIPGYITPIWVVVMSVITVEPHLL*(+)
MYPGMSFPLLVNKEKIGIFKVLGTLPMTTGQITSGTKIMIWKGSDEKTVGETLYPPILHPVIAT
PLQMKMVDDPALSNVVGRASKMIGNFMSYYTHLPHEATKGKMTFLLHGPCDKKAVVEGIGRTLG
LPVASVDASSLIKDFPSDSVSQINTCIQRPESRDGPLLIFLDRFDELVPHNRCGSTVMTDITTT
QIGVMYPGMSFPLLVNKEKIGIFKVLGTLPMTTGQITSGTKIMIWKGSDEKTVGETLYPPILHP
VIATPLQMKMVDDPALSNVVGRASKMIGNFMSYYTHLPHEATKGKMTFLLHGPCDKKAVVEGIG
RTLGLPVASVDASSLIKDFPSDSVSQINTCIQRPESRDGPLLIFLDRFDELVPHNRCGSTVMTD
ITTTQIGVMYPGMSFPLLVNKEKIGIFKVLGTLPMTTGQITSGTKIMIWKGSDEKTVGETLYPP
ILHPVIATPLQMKMVDDPALSNVVGRASKMIGNFMSYYTHLPHEATKGKMTFLLHGPCDKKAVV
EGIGRTLGLPVASVDASSLIKDFPSDSVSQINTCIQRPESRDGPLLIFLDRFDELVPHNRCGST
VMTDITTTQIGVMYPGMSFPLLVNKEKIGIFKVLGTLPMTTGQITSGTKIMIWKGSDEKTVGET
LYPPILHPVIATPLQMKMVDDPALSNVVGRASKMIGNFMSYYTHLPHEATKGKMTFLLHGPCDK
KAVVEGIGRTLGLPVASVDASSLIKDFPSDSVSQINTCIQRPESRDGPLLIFLDRFDELVPHNR
CGSTVMTDITTTQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	22411140-22410780(+) 22411659-22410737(-)
Potential amino acid sequence	MKLPIILLALPTTLERAGSSTIFICRGVAMTGCKIGGYRVSPTVFSSLPFQIMILVPEVICPVV IGRVPRTLKIPIFSLFTNKGNDIPGYITPIWVVVMSVITVEPHLL*(+) MYPGMSFPLLVNKEKIGIFKVLGTLPMTTGQITSGTKIMIWKGSDEKTVGETLYPPILHPVIAT PLQMKMVDDPALSNVVGRASKMIGNFMSYYTHLPHEATKGKMTFLLHGPCDKKAVVEGIGRTLG LPVASVDASSLIKDFPSDSVSQINTCIQRPESRDGPLLIFLDRFDELVPHNRCGSTVMTDITTT QIGVMYPGMSFPLLVNKEKIGIFKVLGTLPMTTGQITSGTKIMIWKGSDEKTVGETLYPPILHP VIATPLQMKMVDDPALSNVVGRASKMIGNFMSYYTHLPHEATKGKMTFLLHGPCDKKAVVEGIG RTLGLPVASVDASSLIKDFPSDSVSQINTCIQRPESRDGPLLIFLDRFDELVPHNRCGSTVMTD ITTTQIGVMYPGMSFPLLVNKEKIGIFKVLGTLPMTTGQITSGTKIMIWKGSDEKTVGETLYPP ILHPVIATPLQMKMVDDPALSNVVGRASKMIGNFMSYYTHLPHEATKGKMTFLLHGPCDKKAVV EGIGRTLGLPVASVDASSLIKDFPSDSVSQINTCIQRPESRDGPLLIFLDRFDELVPHNRCGST VMTDITTTQIGVMYPGMSFPLLVNKEKIGIFKVLGTLPMTTGQITSGTKIMIWKGSDEKTVGET LYPPILHPVIATPLQMKMVDDPALSNVVGRASKMIGNFMSYYTHLPHEATKGKMTFLLHGPCDK KAVVEGIGRTLGLPVASVDASSLIKDFPSDSVSQINTCIQRPESRDGPLLIFLDRFDELVPHNR CGSTVMTDITTTQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os09g0563800_circ_g.2

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