Plant Circular RNA Database

Detail information of Os12g0623900_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os12g0623900_circ_g.4
					
						ID in PlantcircBase
						osa_circ_012399
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 26649716-26650129  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os12g0623900						
					
						Parent gene annotation
						
							Similar to Ethylene-responsive methionine synthase (Fragment). (
Os12t0623900-01);Similar to Methionine synthase protein. (Os12t0
623900-02);Similar to Methionine synthase 2 enzyme. (Os12t062390
0-03)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os12g0623950_circ_ag.1 Os12g0623950_circ_g.1 Os12g0623950_circ_g.2 Os12g0623950_circ_ag.3 Os12g0623950_circ_g.4 Os12g0623950_circ_g.5 Os12g0623950_circ_g.6 Os12g0623950_circ_g.7 Os12g0623950_circ_ag.8 Os12g0623950_circ_ag.9 Os12g0623950_circ_ag.10 Os12g0623950_circ_g.11 Os12g0623950_circ_g.12 Os12g0623950_circ_ag.13 Os12g0623950_circ_ag.14 Os12g0623950_circ_ag.15 Os12g0623900_circ_g.1 Os12g0623900_circ_g.2 Os12g0623900_circ_g.3 Os12g0623900_circ_ag.1 Os12g0623900_circ_ag.2 Os12g0623900_circ_g.3 Os12g0623900_circ_ag.5 Os12g0623900_circ_ag.6 Os12g0623900_circ_g.7 Os12g0623900_circ_ag.8 Os12g0623900_circ_g.9 Os12g0623900_circ_ag.10 Os12g0623900_circ_ag.11 Os12g0623900_circ_ag.12 Os12g0624000_circ_g.1 Os12g0624000_circ_g.2 Os12g0624000_circ_g.3 						
					
						Support reads
						1
					
						Tissues
						root
					
						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  
						
							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
						Os12t0623900-01:2
Os12t0623900-03:2
Os12t0623900-02:2

General Information
CircRNA Name	Os12g0623900_circ_g.4
ID in PlantcircBase	osa_circ_012399
Alias	NA
Organism	Oryza sativa
Position	chr12: 26649716-26650129 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os12g0623900
Parent gene annotation	Similar to Ethylene-responsive methionine synthase (Fragment). ( Os12t0623900-01);Similar to Methionine synthase protein. (Os12t0 623900-02);Similar to Methionine synthase 2 enzyme. (Os12t062390 0-03)
Parent gene strand	+
Alternative splicing	Os12g0623950_circ_ag.1 Os12g0623950_circ_g.1 Os12g0623950_circ_g.2 Os12g0623950_circ_ag.3 Os12g0623950_circ_g.4 Os12g0623950_circ_g.5 Os12g0623950_circ_g.6 Os12g0623950_circ_g.7 Os12g0623950_circ_ag.8 Os12g0623950_circ_ag.9 Os12g0623950_circ_ag.10 Os12g0623950_circ_g.11 Os12g0623950_circ_g.12 Os12g0623950_circ_ag.13 Os12g0623950_circ_ag.14 Os12g0623950_circ_ag.15 Os12g0623900_circ_g.1 Os12g0623900_circ_g.2 Os12g0623900_circ_g.3 Os12g0623900_circ_ag.1 Os12g0623900_circ_ag.2 Os12g0623900_circ_g.3 Os12g0623900_circ_ag.5 Os12g0623900_circ_ag.6 Os12g0623900_circ_g.7 Os12g0623900_circ_ag.8 Os12g0623900_circ_g.9 Os12g0623900_circ_ag.10 Os12g0623900_circ_ag.11 Os12g0623900_circ_ag.12 Os12g0624000_circ_g.1 Os12g0624000_circ_g.2 Os12g0624000_circ_g.3
Support reads	1
Tissues	root
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	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	Os12t0623900-01:2 Os12t0623900-03:2 Os12t0623900-02:2

			
						 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  
						
							GAGTCTGACATTCATACGCTGGCTCAGGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAG
AAGGAGGTCGAGGACCTTGAGGCTGGTGGTATTCAGagaaacgatatggttgagtacttcggtg
agcagctttctggttttgcattcactgccaacggatgggtgcaatcttatggatcacggtgtgt
caagccac

						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
						
							AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTCACTGCCAACGGAT
GGGTGCAATCTTATGGATCACGGTGTGTCAAGCCACCAATTATCTATGGTGATGTGAGCCGCCC
CAACCCCATGACTGTGTTCTGGTCCAAGTTGGCGCAGAGCATGACCTCTCGCCCCATGAAGGGA
ATGTTGACTGGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGGTCAG
TGCCTGTTGTTGATAATGTAATCTAATTTGTTCTGGTTGTGAATGAGCATTCTTTTCTGAGTCT
GACATTCATACGCTGGCTCAGGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAG
GTCGAGGACCTTGAGGCTGGTGGTATTCAG

Sequences
Splice junction sequence	GAGTCTGACATTCATACGCTGGCTCAGGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAG AAGGAGGTCGAGGACCTTGAGGCTGGTGGTATTCAGagaaacgatatggttgagtacttcggtg agcagctttctggttttgcattcactgccaacggatgggtgcaatcttatggatcacggtgtgt caagccac
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	AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTCACTGCCAACGGAT GGGTGCAATCTTATGGATCACGGTGTGTCAAGCCACCAATTATCTATGGTGATGTGAGCCGCCC CAACCCCATGACTGTGTTCTGGTCCAAGTTGGCGCAGAGCATGACCTCTCGCCCCATGAAGGGA ATGTTGACTGGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGGTCAG TGCCTGTTGTTGATAATGTAATCTAATTTGTTCTGGTTGTGAATGAGCATTCTTTTCTGAGTCT GACATTCATACGCTGGCTCAGGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAG GTCGAGGACCTTGAGGCTGGTGGTATTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.630728764

Conservation Information
Conserved circRNAs	NA
PMCS	0.630728764

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							26649726-26650126(+)
26649955-26649833(+)
26649766-26650091(-)
						
						Potential amino acid sequence
						
							MVEYFGEQLSGFAFTANGWVQSYGSRCVKPPIIYGDVSRPNPMTVFWSKLAQSMTSRPMKGMLT
GPVTILNWSFVRNDQPRFETCYQIALAIKKEVEDLEAGGIQRNDMVEYFGEQLSGFAFTANGWV
QSYGSRCVKPPIIYGDVSRPNPMTVFWSKLAQSMTSRPMKGMLTGPVTILNWSFVRNDQPRFET
CYQIALAIKKEVEDLEAGGIQRNDMVEYFGEQLSGFAFTANGWVQSYGSRCVKPPIIYGDVSRP
NPMTVFWSKLAQSMTSRPMKGMLTGPVTILNWSFVRNDQPRFETCYQIALAIKKEVEDLEAGGI
QRNDMVEYFGEQLSGFAFTANGWVQSYGSRCVKPPIIYGDVSRPNPMTVFWSKLAQSMTSRPMK
GMLTGPVTILNWSFVRNDQPRFETCYQIALAIKKEVEDLEAGGIQ(+)
MTSRGLRHATRLLLPSRRRSRTLRLVVFRETIWLSTSVSSFLVLHSLPTDGCNLMDHGVSSHQL
SMVM*(+)
MQNQKAAHRSTQPYRFSEYHQPQGPRPPS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	26649726-26650126(+) 26649955-26649833(+) 26649766-26650091(-)
Potential amino acid sequence	MVEYFGEQLSGFAFTANGWVQSYGSRCVKPPIIYGDVSRPNPMTVFWSKLAQSMTSRPMKGMLT GPVTILNWSFVRNDQPRFETCYQIALAIKKEVEDLEAGGIQRNDMVEYFGEQLSGFAFTANGWV QSYGSRCVKPPIIYGDVSRPNPMTVFWSKLAQSMTSRPMKGMLTGPVTILNWSFVRNDQPRFET CYQIALAIKKEVEDLEAGGIQRNDMVEYFGEQLSGFAFTANGWVQSYGSRCVKPPIIYGDVSRP NPMTVFWSKLAQSMTSRPMKGMLTGPVTILNWSFVRNDQPRFETCYQIALAIKKEVEDLEAGGI QRNDMVEYFGEQLSGFAFTANGWVQSYGSRCVKPPIIYGDVSRPNPMTVFWSKLAQSMTSRPMK GMLTGPVTILNWSFVRNDQPRFETCYQIALAIKKEVEDLEAGGIQ(+) MTSRGLRHATRLLLPSRRRSRTLRLVVFRETIWLSTSVSSFLVLHSLPTDGCNLMDHGVSSHQL SMVM(+) MQNQKAAHRSTQPYRFSEYHQPQGPRPPS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os12g0623900_circ_g.4

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