Plant Circular RNA Database

Detail information of Os04g0409600_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0409600_circ_g.3
					
						ID in PlantcircBase
						osa_circ_023756
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 20252767-20254636  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							Os04g0409600						
					
						Parent gene annotation
						
							Similar to Histone deacetylase. (Os04t0409600-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0409600_circ_g.4 Os04g0409600_circ_g.5 Os04g0409600_circ_g.6 						
					
						Support reads
						1
					
						Tissues
						seed
					
						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
						Os04t0409600-01:6

General Information
CircRNA Name	Os04g0409600_circ_g.3
ID in PlantcircBase	osa_circ_023756
Alias	NA
Organism	Oryza sativa
Position	chr4: 20252767-20254636 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	PcircRNA_finder
Parent gene	Os04g0409600
Parent gene annotation	Similar to Histone deacetylase. (Os04t0409600-01)
Parent gene strand	+
Alternative splicing	Os04g0409600_circ_g.4 Os04g0409600_circ_g.5 Os04g0409600_circ_g.6
Support reads	1
Tissues	seed
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	Os04t0409600-01:6

			
						 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  
						
							TATGAGTTTTGCATGACTTTCCTTTGCAGAAATTCCAGACAATGAATACATCAAATACTTTGCT
CCAGATTATACATTGAAAGTATCGAATGTGAACATGggtaatgactgtaagtttccacaagtat
ggtgattttttcttccctggcacaggtgatattaaggtaatgttccactaacaagctcctgaat
atttttta

									
								

					

						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
						
							GGTAATGACTGTAAGTTTCCACAAGTATGGTGATTTTTTCTTCCCTGGCACAGGTGATATTAAG
GTAATGTTCCACTAACAAGCTCCTGAATATTTTTTATGTACTTTTTGGTATGATGTGGTTGGTG
ATTGGCCCTTCTCTGCATTCTGTTTTATCCTTACCCTTTTCGCATGAAGTGTGTGTGACATGCG
TACTCTCATTTGTGTGAAAAAAGAAGAGACAGATTAACCAAAGATGGTCCCCAGTTGATTTTGT
AATGCACAAAATTGATAGCACCTGTAGGTAATTGTTTATGAGCAGTTAATCTTGTTTCTTTTTA
GTTCTACCCGCCAAGAGGCTGTAAATATGTAACATCATAGAGTTGAACTTTGGTTTTTTTTACT
GGAGATTCTTGGCATGTTATTCTATTTAAATATCAACCATTGTAATTGGGAATTCAGGTGGTTA
TGTATTTGAAAAACGTCATACTAGAATGCATCATAATTCGTATACGCATGCTTAATTGTCATCT
GGGCTGACAAAAAAAAAACATGTGCACATATACGCCCGTCATTTGAATCTTGTAGTATGTTAAT
TTGTTATGTATCCACTGTACTACTAGGCAACTTTATTAAATAAAAATATCCCAAATAACTGGAA
GGTAGAGCAAGTGTGCTACAAAAAGGGCAAGGTTGAAAATGAACATAAAACATGCCATGTTCTT
CTCAGTAACGATGATACTTTATATAGCTTCGTTTTAAATGATTGTGCTGCTTCATATTGATTTA
CCTGACTCTCATTTGAAGGATATAGGAGAAAGAGAAGGAAAATATTATGCCATTAACATTCCAC
TTAAAGATGGGATAGATGACTCCGGCTTTACTCGCCTTTTTAAAACAGTAAGCCCACTTTACAT
TACTTTCTCATCTTTCATGTCATTGTTTAGTCTTATCAAGTTATGCATGTCTATTATGTAGGTT
ATTGCCAAAGTTGTTGAGACATATCTGCCAGGTGCTATTGTTCTTCAATGCGGGGCTGATTCCT
TGGCACGGGACCGTCTGGGGTGCTTCAATCTGTCCATTGAAGGTTCTGTACTTCTTAAATCTGA
TGTGTACTTGTTGATTCAGCAGAACTGTGCTCTAGATGTAAAGTTAGTGAACTGTGCTGCATAT
TCTTGGATGAGCTATTAGGGTTCAGGCGGTATCTTCGAGATAATGTGAAACCTTCTCTCAAGTC
TCAATTATTTCTTACCATAGTTTTGAGATTGTTATTGCACTAATAGTTCTGACTTATTTTGAAA
TTTAAATTTTGTTTCTTTGAGCTATACTTAGTGAATGATCTTTTAATACTTGCATGTGTACTTG
CAAACAGGCCATGCTGAATGTGTGAAGTTTGTCAAGAAATTCAATATCCCTCTACTGGTAAGGA
GAAACCGTTACTGCGTGTGATTTCTCTTGTTCCTCCTTGGATATCAATGTATTTCCCATCATGC
AGGTGACTGGGGGTGGTGGATACACAAAAGAGAATGTAGCACGCTGTTGGGCTGTTGAAACTGG
TGTTCTTCTAGATACGGAGCTCCCAAATGGTATTCTTTTCTTTTGCAATTCTGTACTTCTCGGT
CCTTTTGGCCTGTTGTTTTAGAGGACACTACTAGTAATCCCTCAAATGCATGCAACAGTTCATG
TATTCTTTTCCTCACATTTGCTGGCATATCAAGTTGCAAACAGATCTATCAAGAACGGGATTGA
CTAGTAGAGTTCCTTAATAATTTCTAAAACAGCAGTCTGTGATATGAGTTTTGCATGACTTTCC
TTTGCAGAAATTCCAGACAATGAATACATCAAATACTTTGCTCCAGATTATACATTGAAAGTAT
CGAATGTGAACATG
						
					

			
		

Sequences
Splice junction sequence	TATGAGTTTTGCATGACTTTCCTTTGCAGAAATTCCAGACAATGAATACATCAAATACTTTGCT CCAGATTATACATTGAAAGTATCGAATGTGAACATGggtaatgactgtaagtttccacaagtat ggtgattttttcttccctggcacaggtgatattaaggtaatgttccactaacaagctcctgaat atttttta
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	GGTAATGACTGTAAGTTTCCACAAGTATGGTGATTTTTTCTTCCCTGGCACAGGTGATATTAAG GTAATGTTCCACTAACAAGCTCCTGAATATTTTTTATGTACTTTTTGGTATGATGTGGTTGGTG ATTGGCCCTTCTCTGCATTCTGTTTTATCCTTACCCTTTTCGCATGAAGTGTGTGTGACATGCG TACTCTCATTTGTGTGAAAAAAGAAGAGACAGATTAACCAAAGATGGTCCCCAGTTGATTTTGT AATGCACAAAATTGATAGCACCTGTAGGTAATTGTTTATGAGCAGTTAATCTTGTTTCTTTTTA GTTCTACCCGCCAAGAGGCTGTAAATATGTAACATCATAGAGTTGAACTTTGGTTTTTTTTACT GGAGATTCTTGGCATGTTATTCTATTTAAATATCAACCATTGTAATTGGGAATTCAGGTGGTTA TGTATTTGAAAAACGTCATACTAGAATGCATCATAATTCGTATACGCATGCTTAATTGTCATCT GGGCTGACAAAAAAAAAACATGTGCACATATACGCCCGTCATTTGAATCTTGTAGTATGTTAAT TTGTTATGTATCCACTGTACTACTAGGCAACTTTATTAAATAAAAATATCCCAAATAACTGGAA GGTAGAGCAAGTGTGCTACAAAAAGGGCAAGGTTGAAAATGAACATAAAACATGCCATGTTCTT CTCAGTAACGATGATACTTTATATAGCTTCGTTTTAAATGATTGTGCTGCTTCATATTGATTTA CCTGACTCTCATTTGAAGGATATAGGAGAAAGAGAAGGAAAATATTATGCCATTAACATTCCAC TTAAAGATGGGATAGATGACTCCGGCTTTACTCGCCTTTTTAAAACAGTAAGCCCACTTTACAT TACTTTCTCATCTTTCATGTCATTGTTTAGTCTTATCAAGTTATGCATGTCTATTATGTAGGTT ATTGCCAAAGTTGTTGAGACATATCTGCCAGGTGCTATTGTTCTTCAATGCGGGGCTGATTCCT TGGCACGGGACCGTCTGGGGTGCTTCAATCTGTCCATTGAAGGTTCTGTACTTCTTAAATCTGA TGTGTACTTGTTGATTCAGCAGAACTGTGCTCTAGATGTAAAGTTAGTGAACTGTGCTGCATAT TCTTGGATGAGCTATTAGGGTTCAGGCGGTATCTTCGAGATAATGTGAAACCTTCTCTCAAGTC TCAATTATTTCTTACCATAGTTTTGAGATTGTTATTGCACTAATAGTTCTGACTTATTTTGAAA TTTAAATTTTGTTTCTTTGAGCTATACTTAGTGAATGATCTTTTAATACTTGCATGTGTACTTG CAAACAGGCCATGCTGAATGTGTGAAGTTTGTCAAGAAATTCAATATCCCTCTACTGGTAAGGA GAAACCGTTACTGCGTGTGATTTCTCTTGTTCCTCCTTGGATATCAATGTATTTCCCATCATGC AGGTGACTGGGGGTGGTGGATACACAAAAGAGAATGTAGCACGCTGTTGGGCTGTTGAAACTGG TGTTCTTCTAGATACGGAGCTCCCAAATGGTATTCTTTTCTTTTGCAATTCTGTACTTCTCGGT CCTTTTGGCCTGTTGTTTTAGAGGACACTACTAGTAATCCCTCAAATGCATGCAACAGTTCATG TATTCTTTTCCTCACATTTGCTGGCATATCAAGTTGCAAACAGATCTATCAAGAACGGGATTGA CTAGTAGAGTTCCTTAATAATTTCTAAAACAGCAGTCTGTGATATGAGTTTTGCATGACTTTCC TTTGCAGAAATTCCAGACAATGAATACATCAAATACTTTGCTCCAGATTATACATTGAAAGTAT CGAATGTGAACATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.145228173

Conservation Information
Conserved circRNAs	NA
PMCS	0.145228173

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20252772-20252796(+)
20254124-20254589(-)
						
						Potential amino acid sequence
						
							MTVSFHKYGDFFFPGTGDIKDIGEREGKYYAINIPLKDGIDDSGFTRLFKTVIAKVVETYLPGA
IVLQCGADSLARDRLGCFNLSIEGHAECVKFVKKFNIPLLVTGGGGYTKENVARCWAVETGVLL
DTELPNEIPDNEYIKYFAPDYTLKVSNVNMGNDCKFPQVW*(+)
MAFNGQIEAPQTVPCQGISPALKNNSTWQICLNNFGNNCFKKASKAGVIYPIFKWNVNGIIFSF
SFSYILNITCAREEKITILVETYSHYPCSHSILSMYNLEQSI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	20252772-20252796(+) 20254124-20254589(-)
Potential amino acid sequence	MTVSFHKYGDFFFPGTGDIKDIGEREGKYYAINIPLKDGIDDSGFTRLFKTVIAKVVETYLPGA IVLQCGADSLARDRLGCFNLSIEGHAECVKFVKKFNIPLLVTGGGGYTKENVARCWAVETGVLL DTELPNEIPDNEYIKYFAPDYTLKVSNVNMGNDCKFPQVW(+) MAFNGQIEAPQTVPCQGISPALKNNSTWQICLNNFGNNCFKKASKAGVIYPIFKWNVNGIIFSF SFSYILNITCAREEKITILVETYSHYPCSHSILSMYNLEQSI(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0409600_circ_g.3

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