Plant Circular RNA Database

Detail information of Os05g0139100_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os05g0139100_circ_g.1
					
						ID in PlantcircBase
						osa_circ_026508
					
						Alias
						Os05circ02399
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 2247916-2248170  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl
					
						Parent gene
						
							Os05g0139100						
					
						Parent gene annotation
						
							Helix-loop-helix DNA-binding domain containing protein. (Os05t01
39100-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						2/1
					
						Tissues
						leaf and panicle/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
						Os05t0139100-01:2

General Information
CircRNA Name	Os05g0139100_circ_g.1
ID in PlantcircBase	osa_circ_026508
Alias	Os05circ02399
Organism	Oryza sativa
Position	chr5: 2247916-2248170 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl
Parent gene	Os05g0139100
Parent gene annotation	Helix-loop-helix DNA-binding domain containing protein. (Os05t01 39100-01)
Parent gene strand	+
Alternative splicing	NA
Support reads	2/1
Tissues	leaf and panicle/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	Os05t0139100-01:2

			
						 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  
						
							TCATCTCGCCATTGAATTGCTTTCGAGCTCGCAGAGGAGAAGAGACCGGATCAACGAGAAGATG
CGGGCGCTGCAAGAGCTCATCCCAAACTGCAACAAGctggacctcgacgacgagctcgcaggcg
tccaccggaggtcggcggcgaggagctccaagcgcagccgcaccgccgaagtccacaacctgtc
agagcggg

						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
						
							CTGGACCTCGACGACGAGCTCGCAGGCGTCCACCGGAGGTCGGCGGCGAGGAGCTCCAAGCGCA
GCCGCACCGCCGAAGTCCACAACCTGTCAGAGCGGGTAAGCACACACACCATGCACCATCCACA
ACACCCGCGTCGTGTCATGACGTCATCTCATCTCGCCATTGAATTGCTTTCGAGCTCGCAGAGG
AGAAGAGACCGGATCAACGAGAAGATGCGGGCGCTGCAAGAGCTCATCCCAAACTGCAACAAG

Sequences
Splice junction sequence	TCATCTCGCCATTGAATTGCTTTCGAGCTCGCAGAGGAGAAGAGACCGGATCAACGAGAAGATG CGGGCGCTGCAAGAGCTCATCCCAAACTGCAACAAGctggacctcgacgacgagctcgcaggcg tccaccggaggtcggcggcgaggagctccaagcgcagccgcaccgccgaagtccacaacctgtc agagcggg
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	CTGGACCTCGACGACGAGCTCGCAGGCGTCCACCGGAGGTCGGCGGCGAGGAGCTCCAAGCGCA GCCGCACCGCCGAAGTCCACAACCTGTCAGAGCGGGTAAGCACACACACCATGCACCATCCACA ACACCCGCGTCGTGTCATGACGTCATCTCATCTCGCCATTGAATTGCTTTCGAGCTCGCAGAGG AGAAGAGACCGGATCAACGAGAAGATGCGGGCGCTGCAAGAGCTCATCCCAAACTGCAACAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.138888954

Conservation Information
Conserved circRNAs	NA
PMCS	0.138888954

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2248133-2248167(+)
2248156-2247918(-)
						
						Potential amino acid sequence
						
							MRALQELIPNCNKLDLDDELAGVHRRSAARSSKRSRTAEVHNLSERRRRDRINEKMRALQELIP
NCNKLDLDDELAGVHRRSAARSSKRSRTAEVHNLSERRRRDRINEKMRALQELIPNCNKLDLDD
ELAGVHRRSAARSSKRSRTAEVHNLSERRRRDRINEKMRALQELIPNCNK(+)
MSSCSARIFSLIRSLLLRSDRLWTSAVRLRLELLAADLRWTPASSSSRSSLLQFGMSSCSARIF
SLIRSLLLRSDRLWTSAVRLRLELLAADLRWTPASSSSRSSLLQFGMSSCSARIFSLIRSLLLR
SDRLWTSAVRLRLELLAADLRWTPASSSSRSSLLQFGMSSCSARIFSLIRSLLLRSDRLWTSAV
RLRLELLAADLRWTPASSSSRS(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2248133-2248167(+) 2248156-2247918(-)
Potential amino acid sequence	MRALQELIPNCNKLDLDDELAGVHRRSAARSSKRSRTAEVHNLSERRRRDRINEKMRALQELIP NCNKLDLDDELAGVHRRSAARSSKRSRTAEVHNLSERRRRDRINEKMRALQELIPNCNKLDLDD ELAGVHRRSAARSSKRSRTAEVHNLSERRRRDRINEKMRALQELIPNCNK(+) MSSCSARIFSLIRSLLLRSDRLWTSAVRLRLELLAADLRWTPASSSSRSSLLQFGMSSCSARIF SLIRSLLLRSDRLWTSAVRLRLELLAADLRWTPASSSSRSSLLQFGMSSCSARIFSLIRSLLLR SDRLWTSAVRLRLELLAADLRWTPASSSSRSSLLQFGMSSCSARIFSLIRSLLLRSDRLWTSAV RLRLELLAADLRWTPASSSSRS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os05g0139100_circ_g.1

Address

Any questions?

Supported by