Plant Circular RNA Database

Detail information of Os05g0476200_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os05g0476200_circ_g.2
					
						ID in PlantcircBase
						osa_circ_028234
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 23421860-23422068  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os05g0476200						
					
						Parent gene annotation
						
							Similar to DNA replication licensing factor MCM3 homolog (Replic
ation origin activator) (ROA protein) (Fragment). (Os05t0476200-
01);Similar to DNA replication licensing factor MCM3 homolog (Re
plication origin activator) (ROA protein) (Fragment). (Os05t0476
200-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						1
					
						Tissues
						shoot, 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
						Os05t0476200-02:1
Os05t0476200-01:1

General Information
CircRNA Name	Os05g0476200_circ_g.2
ID in PlantcircBase	osa_circ_028234
Alias	NA
Organism	Oryza sativa
Position	chr5: 23421860-23422068 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os05g0476200
Parent gene annotation	Similar to DNA replication licensing factor MCM3 homolog (Replic ation origin activator) (ROA protein) (Fragment). (Os05t0476200- 01);Similar to DNA replication licensing factor MCM3 homolog (Re plication origin activator) (ROA protein) (Fragment). (Os05t0476 200-02)
Parent gene strand	+
Alternative splicing	NA
Support reads	1
Tissues	shoot, 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	Os05t0476200-02:1 Os05t0476200-01:1

			
						 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  
						
							TATGGAACAGCAAACTGTGACGATTGCAAAGGCAGGAATTCATGCGTCACTAAATGCGAGATGT
AGTGTGATTGCTGCAGCAAATCCAATATATGGAACTgtgagagaaggctggaggctggtgccat
ggttcttgctgatcgtggtgttgtctgcattgatgagtttgataagatgaatgatcaggaccga
gtggctat

						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: 209
Transcript exons: 23421860-23422068
GTGAGAGAAGGCTGGAGGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTTGTCTGCATTGATGA
GTTTGATAAGATGAATGATCAGGACCGAGTGGCTATTCATGAAGTTATGGAACAGCAAACTGTG
ACGATTGCAAAGGCAGGAATTCATGCGTCACTAAATGCGAGATGTAGTGTGATTGCTGCAGCAA
ATCCAATATATGGAACT
						
						Genomic sequence
						
							GTGAGAGAAGGCTGGAGGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTTGTCTGCATTGATGA
GTTTGATAAGATGAATGATCAGGACCGAGTGGCTATTCATGAAGTTATGGAACAGCAAACTGTG
ACGATTGCAAAGGCAGGAATTCATGCGTCACTAAATGCGAGATGTAGTGTGATTGCTGCAGCAA
ATCCAATATATGGAACT

Sequences
Splice junction sequence	TATGGAACAGCAAACTGTGACGATTGCAAAGGCAGGAATTCATGCGTCACTAAATGCGAGATGT AGTGTGATTGCTGCAGCAAATCCAATATATGGAACTgtgagagaaggctggaggctggtgccat ggttcttgctgatcgtggtgttgtctgcattgatgagtttgataagatgaatgatcaggaccga gtggctat
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: 209 Transcript exons: 23421860-23422068 GTGAGAGAAGGCTGGAGGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTTGTCTGCATTGATGA GTTTGATAAGATGAATGATCAGGACCGAGTGGCTATTCATGAAGTTATGGAACAGCAAACTGTG ACGATTGCAAAGGCAGGAATTCATGCGTCACTAAATGCGAGATGTAGTGTGATTGCTGCAGCAA ATCCAATATATGGAACT
Genomic sequence	GTGAGAGAAGGCTGGAGGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTTGTCTGCATTGATGA GTTTGATAAGATGAATGATCAGGACCGAGTGGCTATTCATGAAGTTATGGAACAGCAAACTGTG ACGATTGCAAAGGCAGGAATTCATGCGTCACTAAATGCGAGATGTAGTGTGATTGCTGCAGCAA ATCCAATATATGGAACT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.760719099

Conservation Information
Conserved circRNAs	NA
PMCS	0.760719099

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							23421887-23421934(+)
23422013-23422010(-)
23421919-23421970(-)
						
						Potential amino acid sequence
						
							MVLADRGVVCIDEFDKMNDQDRVAIHEVMEQQTVTIAKAGIHASLNARCSVIAAANPIYGTVRE
GWRLVPWFLLIVVLSALMSLIR*(+)
MNSCLCNRHSLLFHNFMNSHSVLIIHLIKLINADNTTISKNHGTSLQPSLTVPYIGFAAAITLH
LAFSDA*(-)
MQTTPRSARTMAPASSLLSQFHILDLLQQSHYISHLVTHEFLPLQSSQFAVP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	23421887-23421934(+) 23422013-23422010(-) 23421919-23421970(-)
Potential amino acid sequence	MVLADRGVVCIDEFDKMNDQDRVAIHEVMEQQTVTIAKAGIHASLNARCSVIAAANPIYGTVRE GWRLVPWFLLIVVLSALMSLIR(+) MNSCLCNRHSLLFHNFMNSHSVLIIHLIKLINADNTTISKNHGTSLQPSLTVPYIGFAAAITLH LAFSDA(-) MQTTPRSARTMAPASSLLSQFHILDLLQQSHYISHLVTHEFLPLQSSQFAVP*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os05g0476200_circ_g.2

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