Plant Circular RNA Database

Detail information of Os12g0573000_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os12g0573000_circ_g.1
					
						ID in PlantcircBase
						osa_circ_012080
					
						Alias
						Os_ciR2842
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 23618833-23619340  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os12g0573000						
					
						Parent gene annotation
						
							Domain of unknown function DUF304l domain containing protein. (O
s12t0573000-01);Hypothetical conserved gene. (Os12t0573000-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os12g0573000_circ_g.2 Os12g0573000_circ_g.3 						
					
						Support reads
						4/1
					
						Tissues
						root/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
						Os12t0573000-01:1
Os12t0573000-02:2

General Information
CircRNA Name	Os12g0573000_circ_g.1
ID in PlantcircBase	osa_circ_012080
Alias	Os_ciR2842
Organism	Oryza sativa
Position	chr12: 23618833-23619340 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os12g0573000
Parent gene annotation	Domain of unknown function DUF304l domain containing protein. (O s12t0573000-01);Hypothetical conserved gene. (Os12t0573000-02)
Parent gene strand	+
Alternative splicing	Os12g0573000_circ_g.2 Os12g0573000_circ_g.3
Support reads	4/1
Tissues	root/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	Os12t0573000-01:1 Os12t0573000-02:2

			
						 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  
						
							TGTTTTGCATGATATATATACAACACATTGAATTTTTCAGGTTCCTCCTCTTGGAGATTTGATA
CTTGAGAAGCTTGACGAAGTTGAAATCTCTGTGAAGgctgttcttgtccatcttttgaatacaa
gcaatctgaatctcagtagaaaagcttatgtacacgatgatcagcagagcacgagttctaaacc
tataacta

						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: 168
Transcript exons: 23618833-23618940,23619281-23619340
GCTGTTCTTGTCCATCTTTTGAATACAAGCAATCTGAATCTCAGTAGAAAAGCTTATGTACACG
ATGATCAGCAGAGCACGAGTTCTAAACCTATAACTATGTCTTCGGTTCCTCCTCTTGGAGATTT
GATACTTGAGAAGCTTGACGAAGTTGAAATCTCTGTGAAG
						
						Genomic sequence
						
							GCTGTTCTTGTCCATCTTTTGAATACAAGCAATCTGAATCTCAGTAGAAAAGCTTATGTACACG
ATGATCAGCAGAGCACGAGTTCTAAACCTATAACTATGTCTTCGGTATGTCTATTTCTTAATGG
TACCTTTTAATAGTTTAAACTGTAAAGATCCTTTGCATTTAGCAAGCCCTGGAGCTATGAGATC
CAACCTTTCTGAATGTGCGATAGTTATAAAACTAAGAACAAGCATATATTTTGTATATCGAGGT
TCTGTTTGTATAATACCTTAGGAAGTATTGTATTGTAGATATATAGCTTCTAACAACATACATG
GTTTTGCTAAGTCAAGATTGTATTTCCATATTACCCTATTAAACTTGGCTAATGTTTTCATTTT
ACAGACCATTTTCACTGATCCCCGTGTTTTGCATGATATATATACAACACATTGAATTTTTCAG
GTTCCTCCTCTTGGAGATTTGATACTTGAGAAGCTTGACGAAGTTGAAATCTCTGTGAAG

Sequences
Splice junction sequence	TGTTTTGCATGATATATATACAACACATTGAATTTTTCAGGTTCCTCCTCTTGGAGATTTGATA CTTGAGAAGCTTGACGAAGTTGAAATCTCTGTGAAGgctgttcttgtccatcttttgaatacaa gcaatctgaatctcagtagaaaagcttatgtacacgatgatcagcagagcacgagttctaaacc tataacta
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: 168 Transcript exons: 23618833-23618940,23619281-23619340 GCTGTTCTTGTCCATCTTTTGAATACAAGCAATCTGAATCTCAGTAGAAAAGCTTATGTACACG ATGATCAGCAGAGCACGAGTTCTAAACCTATAACTATGTCTTCGGTTCCTCCTCTTGGAGATTT GATACTTGAGAAGCTTGACGAAGTTGAAATCTCTGTGAAG
Genomic sequence	GCTGTTCTTGTCCATCTTTTGAATACAAGCAATCTGAATCTCAGTAGAAAAGCTTATGTACACG ATGATCAGCAGAGCACGAGTTCTAAACCTATAACTATGTCTTCGGTATGTCTATTTCTTAATGG TACCTTTTAATAGTTTAAACTGTAAAGATCCTTTGCATTTAGCAAGCCCTGGAGCTATGAGATC CAACCTTTCTGAATGTGCGATAGTTATAAAACTAAGAACAAGCATATATTTTGTATATCGAGGT TCTGTTTGTATAATACCTTAGGAAGTATTGTATTGTAGATATATAGCTTCTAACAACATACATG GTTTTGCTAAGTCAAGATTGTATTTCCATATTACCCTATTAAACTTGGCTAATGTTTTCATTTT ACAGACCATTTTCACTGATCCCCGTGTTTTGCATGATATATATACAACACATTGAATTTTTCAG GTTCCTCCTCTTGGAGATTTGATACTTGAGAAGCTTGACGAAGTTGAAATCTCTGTGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.211108924

Conservation Information
Conserved circRNAs	NA
PMCS	0.211108924

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							23618933-23619337(+)
23618849-23618835(-)
						
						Potential amino acid sequence
						
							MSSVPPLGDLILEKLDEVEISVKAVLVHLLNTSNLNLSRKAYVHDDQQSTSSKPITMSSVPPLG
DLILEKLDEVEISVKAVLVHLLNTSNLNLSRKAYVHDDQQSTSSKPITMSSVPPLGDLILEKLD
EVEISVKAVLVHLLNTSNLNLSRKAYVHDDQQSTSSKPITMSSVPPLGDLILEKLDEVEISVK(
+)
MDKNSLHRDFNFVKLLKYQISKRRNRRHSYRFRTRALLIIVYISFSTEIQIACIQKMDKNSLHR
DFNFVKLLKYQISKRRNRRHSYRFRTRALLIIVYISFSTEIQIACIQKMDKNSLHRDFNFVKLL
KYQISKRRNRRHSYRFRTRALLIIVYISFSTEIQIACIQKMDKNS(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	23618933-23619337(+) 23618849-23618835(-)
Potential amino acid sequence	MSSVPPLGDLILEKLDEVEISVKAVLVHLLNTSNLNLSRKAYVHDDQQSTSSKPITMSSVPPLG DLILEKLDEVEISVKAVLVHLLNTSNLNLSRKAYVHDDQQSTSSKPITMSSVPPLGDLILEKLD EVEISVKAVLVHLLNTSNLNLSRKAYVHDDQQSTSSKPITMSSVPPLGDLILEKLDEVEISVK( +) MDKNSLHRDFNFVKLLKYQISKRRNRRHSYRFRTRALLIIVYISFSTEIQIACIQKMDKNSLHR DFNFVKLLKYQISKRRNRRHSYRFRTRALLIIVYISFSTEIQIACIQKMDKNSLHRDFNFVKLL KYQISKRRNRRHSYRFRTRALLIIVYISFSTEIQIACIQKMDKNS(-)
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 Os12g0573000_circ_g.1

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