Plant Circular RNA Database

Detail information of Os01g0688000_circ_ig.53

			
						 General Information
					
						CircRNA Name
						Os01g0688000_circ_ig.53
					
						ID in PlantcircBase
						osa_circ_003402
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 28382068-28382195  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						circseq_cup
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							Os01g0688000_circ_igg.1 Os01g0688000_circ_ig.1 Os01g0688000_circ_ig.2 Os01g0688000_circ_ig.3 Os01g0688000_circ_ig.4 Os01g0688000_circ_ig.5 Os01g0688000_circ_ig.6 Os01g0688000_circ_ig.7 Os01g0688000_circ_ig.8 Os01g0688000_circ_ig.9 Os01g0688000_circ_ig.10 Os01g0688000_circ_ig.11 Os01g0688000_circ_ig.12 Os01g0688000_circ_ig.13 Os01g0688000_circ_ig.14 Os01g0688000_circ_ig.15 Os01g0688000_circ_ig.16 Os01g0688000_circ_ig.17 Os01g0688000_circ_ig.18 Os01g0688000_circ_ig.19 Os01g0688000_circ_ig.20 Os01g0688000_circ_ig.21 Os01g0688000_circ_ig.22 Os01g0688000_circ_ig.23 Os01g0688000_circ_ig.24 Os01g0688000_circ_ig.25 Os01g0688000_circ_ig.26 Os01g0688000_circ_ig.27 Os01g0688000_circ_ig.28 Os01g0688000_circ_ig.29 Os01g0688000_circ_ig.30 Os01g0688000_circ_ig.31 Os01g0688000_circ_ig.32 Os01g0688000_circ_ig.33 Os01g0688000_circ_ig.34 Os01g0688000_circ_ig.35 Os01g0688000_circ_ig.36 Os01g0688000_circ_ig.37 Os01g0688000_circ_ig.38 Os01g0688000_circ_ig.39 Os01g0688000_circ_ig.40 Os01g0688000_circ_ig.41 Os01g0688000_circ_ig.42 Os01g0688000_circ_ig.43 Os01g0688000_circ_ig.44 Os01g0688000_circ_ig.45 Os01g0688000_circ_ig.46 Os01g0688000_circ_ig.47 Os01g0688000_circ_ig.48 Os01g0688000_circ_ig.49 Os01g0688000_circ_ig.50 Os01g0688000_circ_ig.51 Os01g0688000_circ_ig.52 Os01g0688000_circ_ig.54 Os01g0688000_circ_ig.55 Os01g0688000_circ_ig.56 Os01g0688000_circ_ig.57 Os01g0688000_circ_ig.58 						
					
						Support reads
						2
					
						Tissues
						root
					
						Exon boundary  
						
							No-No							"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  
						
							TT-CA							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
						NA

General Information
CircRNA Name	Os01g0688000_circ_ig.53
ID in PlantcircBase	osa_circ_003402
Alias	NA
Organism	Oryza sativa
Position	chr1: 28382068-28382195 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ig-circRNA
Identification method	circseq_cup
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	Os01g0688000_circ_igg.1 Os01g0688000_circ_ig.1 Os01g0688000_circ_ig.2 Os01g0688000_circ_ig.3 Os01g0688000_circ_ig.4 Os01g0688000_circ_ig.5 Os01g0688000_circ_ig.6 Os01g0688000_circ_ig.7 Os01g0688000_circ_ig.8 Os01g0688000_circ_ig.9 Os01g0688000_circ_ig.10 Os01g0688000_circ_ig.11 Os01g0688000_circ_ig.12 Os01g0688000_circ_ig.13 Os01g0688000_circ_ig.14 Os01g0688000_circ_ig.15 Os01g0688000_circ_ig.16 Os01g0688000_circ_ig.17 Os01g0688000_circ_ig.18 Os01g0688000_circ_ig.19 Os01g0688000_circ_ig.20 Os01g0688000_circ_ig.21 Os01g0688000_circ_ig.22 Os01g0688000_circ_ig.23 Os01g0688000_circ_ig.24 Os01g0688000_circ_ig.25 Os01g0688000_circ_ig.26 Os01g0688000_circ_ig.27 Os01g0688000_circ_ig.28 Os01g0688000_circ_ig.29 Os01g0688000_circ_ig.30 Os01g0688000_circ_ig.31 Os01g0688000_circ_ig.32 Os01g0688000_circ_ig.33 Os01g0688000_circ_ig.34 Os01g0688000_circ_ig.35 Os01g0688000_circ_ig.36 Os01g0688000_circ_ig.37 Os01g0688000_circ_ig.38 Os01g0688000_circ_ig.39 Os01g0688000_circ_ig.40 Os01g0688000_circ_ig.41 Os01g0688000_circ_ig.42 Os01g0688000_circ_ig.43 Os01g0688000_circ_ig.44 Os01g0688000_circ_ig.45 Os01g0688000_circ_ig.46 Os01g0688000_circ_ig.47 Os01g0688000_circ_ig.48 Os01g0688000_circ_ig.49 Os01g0688000_circ_ig.50 Os01g0688000_circ_ig.51 Os01g0688000_circ_ig.52 Os01g0688000_circ_ig.54 Os01g0688000_circ_ig.55 Os01g0688000_circ_ig.56 Os01g0688000_circ_ig.57 Os01g0688000_circ_ig.58
Support reads	2
Tissues	root
Exon boundary	No-No "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	TT-CA 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	NA

			
						 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  
						
							CGTCTTGCCGAACTCCTTCCTTTCTCATTTCAGTCCTCGCCTTTTTCATCTTCCGTAGGGGCCT
tgccggctccggctccgcgcacctgctgacacctttcgaagcactttcacgtgtgaaccgaagt

						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: 128
Transcript exons: 28382068-28382195
TGCCGGCTCCGGCTCCGCGCACCTGCTGACACCTTTCGAAGCACTTTCACGTGTGAACCGAAGT
CGTCTTGCCGAACTCCTTCCTTTCTCATTTCAGTCCTCGCCTTTTTCATCTTCCGTAGGGGCCT
						
						Genomic sequence
						
							TGCCGGCTCCGGCTCCGCGCACCTGCTGACACCTTTCGAAGCACTTTCACGTGTGAACCGAAGT
CGTCTTGCCGAACTCCTTCCTTTCTCATTTCAGTCCTCGCCTTTTTCATCTTCCGTAGGGGCCT

Sequences
Splice junction sequence	CGTCTTGCCGAACTCCTTCCTTTCTCATTTCAGTCCTCGCCTTTTTCATCTTCCGTAGGGGCCT tgccggctccggctccgcgcacctgctgacacctttcgaagcactttcacgtgtgaaccgaagt
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: 128 Transcript exons: 28382068-28382195 TGCCGGCTCCGGCTCCGCGCACCTGCTGACACCTTTCGAAGCACTTTCACGTGTGAACCGAAGT CGTCTTGCCGAACTCCTTCCTTTCTCATTTCAGTCCTCGCCTTTTTCATCTTCCGTAGGGGCCT
Genomic sequence	TGCCGGCTCCGGCTCCGCGCACCTGCTGACACCTTTCGAAGCACTTTCACGTGTGAACCGAAGT CGTCTTGCCGAACTCCTTCCTTTCTCATTTCAGTCCTCGCCTTTTTCATCTTCCGTAGGGGCCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.468801953

Conservation Information
Conserved circRNAs	NA
PMCS	0.468801953

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2016

circRNA

Detail information of Os01g0688000_circ_ig.53

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