Plant Circular RNA Database

Detail information of Os10g0407000_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os10g0407000_circ_g.1
					
						ID in PlantcircBase
						osa_circ_006770
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr10: 13934004-13934299  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, circseq_cup
					
						Parent gene
						
							Os10g0407000						
					
						Parent gene annotation
						
							Pectin lyase fold/virulence factor domain containing protein. (O
s10t0407000-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						2/2
					
						Tissues
						root/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  
						
							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
						Os10t0407000-01:2

General Information
CircRNA Name	Os10g0407000_circ_g.1
ID in PlantcircBase	osa_circ_006770
Alias	NA
Organism	Oryza sativa
Position	chr10: 13934004-13934299 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, circseq_cup
Parent gene	Os10g0407000
Parent gene annotation	Pectin lyase fold/virulence factor domain containing protein. (O s10t0407000-01)
Parent gene strand	-
Alternative splicing	NA
Support reads	2/2
Tissues	root/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	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	Os10t0407000-01:2

			
						 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  
						
							GAGCTGAGTTCTCAAATGTGATATTCTCTGCGATGAAATCCTCCCCCTCCACAATAATTGTTCC
GCATCCAAACGTTCCTGTCCCAATAACCCTGGACGAttgccaaccaaggaacctgcaattgtag
aaggcacacctatctgctgttactcggagagcaactgcctgcccagacccctacaccacaacag
gcacatca

						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: 183
Transcript exons: 13934004-13934299
TTGCCAACCAAGGAACCTGCAATTGTAGAAGGCACACCTATCTGCTGTTACTCGGAGAGCAACT
GCCTGCCCAGACCCCTGAGGAGCTGAGTTCTCAAATGTGATATTCTCTGCGATGAAATCCTCCC
CCTCCACAATAATTGTTCCGCATCCAAACGTTCCTGTCCCAATAACCCTGGACGA
						
						Genomic sequence
						
							TTGCCAACCAAGGAACCTGCAATTGTAGAAGGCACACCTATCTGCTGTTACTCGGAGAGCAACT
GCCTGCCCAGACCCCTACACCACAACAGGCACATCAGCTTTCTGCACCCACTCATCACACATGC
ATCTCTCTATGCAAGAAGAACAAGTTTGGTCAAAAGAAAAAAGAACAAGGCAAAGACAAGCACC
TGAGGAGCTGAGTTCTCAAATGTGATATTCTCTGCGATGAAATCCTCCCCCTCCACAATAATTG
TTCCGCATCCAAACGTTCCTGTCCCAATAACCCTGGACGA

Sequences
Splice junction sequence	GAGCTGAGTTCTCAAATGTGATATTCTCTGCGATGAAATCCTCCCCCTCCACAATAATTGTTCC GCATCCAAACGTTCCTGTCCCAATAACCCTGGACGAttgccaaccaaggaacctgcaattgtag aaggcacacctatctgctgttactcggagagcaactgcctgcccagacccctacaccacaacag gcacatca
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: 183 Transcript exons: 13934004-13934299 TTGCCAACCAAGGAACCTGCAATTGTAGAAGGCACACCTATCTGCTGTTACTCGGAGAGCAACT GCCTGCCCAGACCCCTGAGGAGCTGAGTTCTCAAATGTGATATTCTCTGCGATGAAATCCTCCC CCTCCACAATAATTGTTCCGCATCCAAACGTTCCTGTCCCAATAACCCTGGACGA
Genomic sequence	TTGCCAACCAAGGAACCTGCAATTGTAGAAGGCACACCTATCTGCTGTTACTCGGAGAGCAACT GCCTGCCCAGACCCCTACACCACAACAGGCACATCAGCTTTCTGCACCCACTCATCACACATGC ATCTCTCTATGCAAGAAGAACAAGTTTGGTCAAAAGAAAAAAGAACAAGGCAAAGACAAGCACC TGAGGAGCTGAGTTCTCAAATGTGATATTCTCTGCGATGAAATCCTCCCCCTCCACAATAATTG TTCCGCATCCAAACGTTCCTGTCCCAATAACCCTGGACGA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.276473818

Conservation Information
Conserved circRNAs	NA
PMCS	0.276473818

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							13934233-13934028(+)
						
						Potential amino acid sequence
						
							MKSSPSTIIVPHPNVPVPITLDDCQPRNLQL*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	13934233-13934028(+)
Potential amino acid sequence	MKSSPSTIIVPHPNVPVPITLDDCQPRNLQL*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2016;Chu et al., 2017

circRNA

Detail information of Os10g0407000_circ_g.1

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