Plant Circular RNA Database

Detail information of Os09g0477900_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os09g0477900_circ_g.2
					
						ID in PlantcircBase
						osa_circ_039579
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 18310205-18311073  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ie-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os09g0477900						
					
						Parent gene annotation
						
							NusB/RsmB/TIM44 domain containing protein. (Os09t0477900-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os09g0477900_circ_ag.1 Os09g0478100_circ_ag.1 Os09g0478100_circ_ag.3 Os09g0477900_circ_g.4 Os09g0478100_circ_ag.5 Os09g0478300_circ_g.1 Os09g0478300_circ_g.2 						
					
						Support reads
						1
					
						Tissues
						shoot
					
						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
						Os09t0478100-01:3
Os09t0478100-02:3
Os09t0477900-01:2
Os09t0478100-01:3
Os09t0478100-02:3

General Information
CircRNA Name	Os09g0477900_circ_g.2
ID in PlantcircBase	osa_circ_039579
Alias	NA
Organism	Oryza sativa
Position	chr9: 18310205-18311073 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ie-circRNA
Identification method	CIRCexplorer
Parent gene	Os09g0477900
Parent gene annotation	NusB/RsmB/TIM44 domain containing protein. (Os09t0477900-01)
Parent gene strand	+
Alternative splicing	Os09g0477900_circ_ag.1 Os09g0478100_circ_ag.1 Os09g0478100_circ_ag.3 Os09g0477900_circ_g.4 Os09g0478100_circ_ag.5 Os09g0478300_circ_g.1 Os09g0478300_circ_g.2
Support reads	1
Tissues	shoot
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	Os09t0478100-01:3 Os09t0478100-02:3 Os09t0477900-01:2 Os09t0478100-01:3 Os09t0478100-02:3

			
						 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  
						
							CATAACTGATAGGATGGTAGAGATGACAAGGCTTGGTGGCTCTGATTGTGGATCCGCAGTGCAT
ACAAAGATATCCACACCAGGTAGATTTTGTTCATATcaaagcgttcaatgccccagctttgaag
ttatggtggtactgaggcctcttctcgcgcgccacgtataccattgttggtagcacatttctat
catcatca

						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: 592
Transcript exons: 18310205-18310336,18310455-18310595,18310755-18311073
CAAAGCGTTCAATGCCCCAGCTTTGAAGTTATGGTGGTACTGAGGCCTCTTCTCGCGCGCCACG
TATACCATTGTTGGTAGCACATTTCTATCATCATCAATTGCATTTCGGTTTTTCCCATCTATCA
GAATCTGAACAATTGGCTGGTGATTTTTCAAAGTAAAATCTGAGTTCCATTCATCAAATCCTTT
ATGCTTTAGCTTCATTTCTTCAGGAATTTTTCCTGACATGGTAGCTGTATCAATTCTCTCTCTC
ATTTCTTCATACAGGTTCTTGATCAGTGCCCATTCTTTTGGGATGCACAGATTGTGATGCACTT
TTGACTCTGAGAAGTAAGCAGCTGGTGACCTTGGCTCAATGTTATATCTTTTGCAGAATGGTAG
CCATTTCTTTGCAAATATGGAGGCCTCCCATAAAGCATAGAAAGTAAGAATTGAACCTCCATCA
TCGGAAAGGTACACACTTATTTTTTCTGATGGGTAATTGTATGCCATAACTGATAGGATGGTAG
AGATGACAAGGCTTGGTGGCTCTGATTGTGGATCCGCAGTGCATACAAAGATATCCACACCAGG
TAGATTTTGTTCATAT
						
						Genomic sequence
						
							CAAAGCGTTCAATGCCCCAGCTTTGAAGTTATGGTGGTACTGAGGCCTCTTCTCGCGCGCCACG
TATACCATTGTTGGTAGCACATTTCTATCATCATCAATTGCATTTCGGTTTTTCCCATCTATCA
GAATCTACCAAAGAAGCAATATTTAGAACCTCAAATTATCAAAACTGAAGTGTTATGAACTTCT
TTACTTTAATTTGTATAGTGAAAAACTTTGTGCTGTTTTCTGGGACAGTGAAGCCTACCTGAAC
AATTGGCTGGTGATTTTTCAAAGTAAAATCTGAGTTCCATTCATCAAATCCTTTATGCTTTAGC
TTCATTTCTTCAGGAATTTTTCCTGACATGGTAGCTGTATCAATTCTCTCTCTCATTTCTTCAT
ACAGGTTCTGCCAAAAAAAAAATCGGTTGCCATGCCAAATATTGAGCACTATGAAGTTATGACT
AGGACATATATAGTTCTAGTCATATGTGAGAGCTGATTTAATTGTGGCCTACCTGTTGATTATA
AAAATCTCGAAGAATTATGCTTATAAAAATGCACATACCTTGATCAGTGCCCATTCTTTTGGGA
TGCACAGATTGTGATGCACTTTTGACTCTGAGAAGTAAGCAGCTGGTGACCTTGGCTCAATGTT
ATATCTTTTGCAGAATGGTAGCCATTTCTTTGCAAATATGGAGGCCTCCCATAAAGCATAGAAA
GTAAGAATTGAACCTCCATCATCGGAAAGGTACACACTTATTTTTTCTGATGGGTAATTGTATG
CCATAACTGATAGGATGGTAGAGATGACAAGGCTTGGTGGCTCTGATTGTGGATCCGCAGTGCA
TACAAAGATATCCACACCAGGTAGATTTTGTTCATAT

Sequences
Splice junction sequence	CATAACTGATAGGATGGTAGAGATGACAAGGCTTGGTGGCTCTGATTGTGGATCCGCAGTGCAT ACAAAGATATCCACACCAGGTAGATTTTGTTCATATcaaagcgttcaatgccccagctttgaag ttatggtggtactgaggcctcttctcgcgcgccacgtataccattgttggtagcacatttctat catcatca
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: 592 Transcript exons: 18310205-18310336,18310455-18310595,18310755-18311073 CAAAGCGTTCAATGCCCCAGCTTTGAAGTTATGGTGGTACTGAGGCCTCTTCTCGCGCGCCACG TATACCATTGTTGGTAGCACATTTCTATCATCATCAATTGCATTTCGGTTTTTCCCATCTATCA GAATCTGAACAATTGGCTGGTGATTTTTCAAAGTAAAATCTGAGTTCCATTCATCAAATCCTTT ATGCTTTAGCTTCATTTCTTCAGGAATTTTTCCTGACATGGTAGCTGTATCAATTCTCTCTCTC ATTTCTTCATACAGGTTCTTGATCAGTGCCCATTCTTTTGGGATGCACAGATTGTGATGCACTT TTGACTCTGAGAAGTAAGCAGCTGGTGACCTTGGCTCAATGTTATATCTTTTGCAGAATGGTAG CCATTTCTTTGCAAATATGGAGGCCTCCCATAAAGCATAGAAAGTAAGAATTGAACCTCCATCA TCGGAAAGGTACACACTTATTTTTTCTGATGGGTAATTGTATGCCATAACTGATAGGATGGTAG AGATGACAAGGCTTGGTGGCTCTGATTGTGGATCCGCAGTGCATACAAAGATATCCACACCAGG TAGATTTTGTTCATAT
Genomic sequence	CAAAGCGTTCAATGCCCCAGCTTTGAAGTTATGGTGGTACTGAGGCCTCTTCTCGCGCGCCACG TATACCATTGTTGGTAGCACATTTCTATCATCATCAATTGCATTTCGGTTTTTCCCATCTATCA GAATCTACCAAAGAAGCAATATTTAGAACCTCAAATTATCAAAACTGAAGTGTTATGAACTTCT TTACTTTAATTTGTATAGTGAAAAACTTTGTGCTGTTTTCTGGGACAGTGAAGCCTACCTGAAC AATTGGCTGGTGATTTTTCAAAGTAAAATCTGAGTTCCATTCATCAAATCCTTTATGCTTTAGC TTCATTTCTTCAGGAATTTTTCCTGACATGGTAGCTGTATCAATTCTCTCTCTCATTTCTTCAT ACAGGTTCTGCCAAAAAAAAAATCGGTTGCCATGCCAAATATTGAGCACTATGAAGTTATGACT AGGACATATATAGTTCTAGTCATATGTGAGAGCTGATTTAATTGTGGCCTACCTGTTGATTATA AAAATCTCGAAGAATTATGCTTATAAAAATGCACATACCTTGATCAGTGCCCATTCTTTTGGGA TGCACAGATTGTGATGCACTTTTGACTCTGAGAAGTAAGCAGCTGGTGACCTTGGCTCAATGTT ATATCTTTTGCAGAATGGTAGCCATTTCTTTGCAAATATGGAGGCCTCCCATAAAGCATAGAAA GTAAGAATTGAACCTCCATCATCGGAAAGGTACACACTTATTTTTTCTGATGGGTAATTGTATG CCATAACTGATAGGATGGTAGAGATGACAAGGCTTGGTGGCTCTGATTGTGGATCCGCAGTGCA TACAAAGATATCCACACCAGGTAGATTTTGTTCATAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.616344517

Conservation Information
Conserved circRNAs	NA
PMCS	0.616344517

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							18310988-18310282(+)
18310978-18311070(-)
						
						Potential amino acid sequence
						
							MVEMTRLGGSDCGSAVHTKISTPGRFCSYQSVQCPSFEVMVVLRPLLARHVYHCW*(+)
MAYNYPSEKISVYLSDDGGSILTFYALWEASIFAKKWLPFCKRYNIEPRSPAAYFSESKVHHNL
CIPKEWALIKNLYEEMRERIDTATMSGKIPEEMKLKHKGFDEWNSDFTLKNHQPIVQILIDGKN
RNAIDDDRNVLPTMVYVAREKRPQYHHNFKAGALNALI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	18310988-18310282(+) 18310978-18311070(-)
Potential amino acid sequence	MVEMTRLGGSDCGSAVHTKISTPGRFCSYQSVQCPSFEVMVVLRPLLARHVYHCW(+) MAYNYPSEKISVYLSDDGGSILTFYALWEASIFAKKWLPFCKRYNIEPRSPAAYFSESKVHHNL CIPKEWALIKNLYEEMRERIDTATMSGKIPEEMKLKHKGFDEWNSDFTLKNHQPIVQILIDGKN RNAIDDDRNVLPTMVYVAREKRPQYHHNFKAGALNALI(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os09g0477900_circ_g.2

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