Plant Circular RNA Database

Detail information of Os02g0287000_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os02g0287000_circ_g.4
					
						ID in PlantcircBase
						osa_circ_014305
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr2: 10823958-10824685  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os02g0287000						
					
						Parent gene annotation
						
							Similar to 40S ribosomal protein S3a (CYC07 protein). (Os02t0287
000-01);Ribosomal protein S3Ae domain containing protein. (Os02t
0287000-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os02g0287000_circ_g.1 Os02g0287000_circ_g.2 Os02g0287000_circ_g.3 Os02g0287000_circ_g.5 						
					
						Support reads
						4
					
						Tissues
						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
						Os02t0287000-02:3
Os02t0287000-01:3

General Information
CircRNA Name	Os02g0287000_circ_g.4
ID in PlantcircBase	osa_circ_014305
Alias	NA
Organism	Oryza sativa
Position	chr2: 10823958-10824685 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os02g0287000
Parent gene annotation	Similar to 40S ribosomal protein S3a (CYC07 protein). (Os02t0287 000-01);Ribosomal protein S3Ae domain containing protein. (Os02t 0287000-02)
Parent gene strand	-
Alternative splicing	Os02g0287000_circ_g.1 Os02g0287000_circ_g.2 Os02g0287000_circ_g.3 Os02g0287000_circ_g.5
Support reads	4
Tissues	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	Os02t0287000-02:3 Os02t0287000-01:3

			
						 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  
						
							CAGCACGAAGTCTAACCTTCCTGTAAGCCTGATCCTCGTCATTCTGAAGATCCGCCAAGGAGAC
TTCAAAGACACGATGCTTGAGACCCTCAGATGCAATctccatcaacttcccaagatcaaacttc
ggtgccttcaagatcttcaccttgcggatgaacacattttggagagggaatatacttgaagttg
acttctcg

						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: 525
Transcript exons: 10823958-10824158,10824267-10824452,10824548-10824685
CTCCATCAACTTCCCAAGATCAAACTTCGGTGCCTTCAAGATCTTCACCTTGCGGATGAACACA
TTTTGGAGAGGGAATATACTTGAAGTTGACTTCTCGATCTCCTTTCCAATGACTTCAGGGATGA
ATTTTGAAACCAGTTCTTTCAAGTCACATGTTGATGCCTGGTTGGCCATGATCTCAACCATCTT
CCGGCGGATCTGCCGGATCTGGCTAGCCTGAGCGTAACAGGTACGCTTCACCTGATTTGGGCGG
CGCTTGGTGAAACCAATGCAAAACAGGCGGAGCATGTAGTTATCTGTGGTCTTAACATCCACAT
GGGCTTCAATCAATGTTTGCCATTTCTTGACCAAGGACCTAAGTTTGTCCGTGGTAAAACTCAT
GCCCCAGAAATTCGTGAGGACATTCCTCCCCTGAACATCCTCAGCACGAAGTCTAACCTTCCTG
TAAGCCTGATCCTCGTCATTCTGAAGATCCGCCAAGGAGACTTCAAAGACACGATGCTTGAGAC
CCTCAGATGCAAT
						
						Genomic sequence
						
							CTCCATCAACTTCCCAAGATCAAACTTCGGTGCCTTCAAGATCTTCACCTTGCGGATGAACACA
TTTTGGAGAGGGAATATACTTGAAGTTGACTTCTCGATCTCCTTTCCAATGACTTCAGGGATGA
ATTTTGAAACCAGTTCTTTCAAGTCACATGTTGATGCCTGGTTGGCCATGATCTCAACCATCTT
CCGGCGGATCTTCAAACAGTGGACAAAAATAAAGTAAACAACAAGAACATACCTCATCTCAAAA
AACAAGAACTTACCTAGTACAGAACATGCAAAAAAGTATGACAAAACTTTTACCTGCCGGATCT
GGCTAGCCTGAGCGTAACAGGTACGCTTCACCTGATTTGGGCGGCGCTTGGTGAAACCAATGCA
AAACAGGCGGAGCATGTAGTTATCTGTGGTCTTAACATCCACATGGGCTTCAATCAATGTTTGC
CATTTCTTGACCAAGGACCTAAGTTTGTCCGTGGTAAAACTCATGCCCTAGAGAAAATATGTAT
TGGTTTAGACTACATAGGACAAAAGGGATCACAGATACAACACAAAAGGATTAATGAACAATCA
ATGCTCATTCTTACCCAGAAATTCGTGAGGACATTCCTCCCCTGAACATCCTCAGCACGAAGTC
TAACCTTCCTGTAAGCCTGATCCTCGTCATTCTGAAGATCCGCCAAGGAGACTTCAAAGACACG
ATGCTTGAGACCCTCAGATGCAAT

Sequences
Splice junction sequence	CAGCACGAAGTCTAACCTTCCTGTAAGCCTGATCCTCGTCATTCTGAAGATCCGCCAAGGAGAC TTCAAAGACACGATGCTTGAGACCCTCAGATGCAATctccatcaacttcccaagatcaaacttc ggtgccttcaagatcttcaccttgcggatgaacacattttggagagggaatatacttgaagttg acttctcg
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: 525 Transcript exons: 10823958-10824158,10824267-10824452,10824548-10824685 CTCCATCAACTTCCCAAGATCAAACTTCGGTGCCTTCAAGATCTTCACCTTGCGGATGAACACA TTTTGGAGAGGGAATATACTTGAAGTTGACTTCTCGATCTCCTTTCCAATGACTTCAGGGATGA ATTTTGAAACCAGTTCTTTCAAGTCACATGTTGATGCCTGGTTGGCCATGATCTCAACCATCTT CCGGCGGATCTGCCGGATCTGGCTAGCCTGAGCGTAACAGGTACGCTTCACCTGATTTGGGCGG CGCTTGGTGAAACCAATGCAAAACAGGCGGAGCATGTAGTTATCTGTGGTCTTAACATCCACAT GGGCTTCAATCAATGTTTGCCATTTCTTGACCAAGGACCTAAGTTTGTCCGTGGTAAAACTCAT GCCCCAGAAATTCGTGAGGACATTCCTCCCCTGAACATCCTCAGCACGAAGTCTAACCTTCCTG TAAGCCTGATCCTCGTCATTCTGAAGATCCGCCAAGGAGACTTCAAAGACACGATGCTTGAGAC CCTCAGATGCAAT
Genomic sequence	CTCCATCAACTTCCCAAGATCAAACTTCGGTGCCTTCAAGATCTTCACCTTGCGGATGAACACA TTTTGGAGAGGGAATATACTTGAAGTTGACTTCTCGATCTCCTTTCCAATGACTTCAGGGATGA ATTTTGAAACCAGTTCTTTCAAGTCACATGTTGATGCCTGGTTGGCCATGATCTCAACCATCTT CCGGCGGATCTTCAAACAGTGGACAAAAATAAAGTAAACAACAAGAACATACCTCATCTCAAAA AACAAGAACTTACCTAGTACAGAACATGCAAAAAAGTATGACAAAACTTTTACCTGCCGGATCT GGCTAGCCTGAGCGTAACAGGTACGCTTCACCTGATTTGGGCGGCGCTTGGTGAAACCAATGCA AAACAGGCGGAGCATGTAGTTATCTGTGGTCTTAACATCCACATGGGCTTCAATCAATGTTTGC CATTTCTTGACCAAGGACCTAAGTTTGTCCGTGGTAAAACTCATGCCCTAGAGAAAATATGTAT TGGTTTAGACTACATAGGACAAAAGGGATCACAGATACAACACAAAAGGATTAATGAACAATCA ATGCTCATTCTTACCCAGAAATTCGTGAGGACATTCCTCCCCTGAACATCCTCAGCACGAAGTC TAACCTTCCTGTAAGCCTGATCCTCGTCATTCTGAAGATCCGCCAAGGAGACTTCAAAGACACG ATGCTTGAGACCCTCAGATGCAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.387173329

Conservation Information
Conserved circRNAs	NA
PMCS	0.387173329

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							10824385-10824041(+)
10824680-10824013(+)
10824451-10823960(-)
						
						Potential amino acid sequence
						
							MGFNQCLPFLDQGPKFVRGKTHAPEIREDIPPLNILSTKSNLPVSLILVILKIRQGDFKDTMLE
TLRCNLHQLPKIKLRCLQDLHLADEHILEREYT*(+)
MQSPSTSQDQTSVPSRSSPCG*(+)
MSFTTDKLRSLVKKWQTLIEAHVDVKTTDNYMLRLFCIGFTKRRPNQVKRTCYAQASQIRQIRR
KMVEIMANQASTCDLKELVSKFIPEVIGKEIEKSTSSIFPLQNVFIRKVKILKAPKFDLGKLME
IASEGLKHRVFEVSLADLQNDEDQAYRKVRLRAEDVQGRNVLTNFWGMSFTTDKLRSLVKKWQT
LIEAHVDVKTTDNYMLRLFCIGFTKRRPNQVKRTCYAQASQIRQIRRKMVEIMANQASTCDLKE
LVSKFIPEVIGKEIEKSTSSIFPLQNVFIRKVKILKAPKFDLGKLMEIASEGLKHRVFEVSLAD
LQNDEDQAYRKVRLRAEDVQGRNVLTNFWGMSFTTDKLRSLVKKWQTLIEAHVDVKTTDNYMLR
LFCIGFTKRRPNQVKRTCYAQASQIRQIRRKMVEIMANQASTCDLKELVSKFIPEVIGKEIEKS
TSSIFPLQNVFIRKVKILKAPKFDLGKLMEIASEGLKHRVFEVSLADLQNDEDQAYRKVRLRAE
DVQGRNVLTNFWGMSFTTDKLRSLVKKWQTLIEAHVDVKTTDNYMLRLFCIGFTKRRPNQVKRT
CYAQASQIRQIRRKMVEIMANQASTCDLKELVSKFIPEVIGKEIEKSTSSIFPLQNVFIRKVKI
LKAPKFDLGKLME(-)
						
						Sponge-miRNAs
						
							osa-miR2923 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	10824385-10824041(+) 10824680-10824013(+) 10824451-10823960(-)
Potential amino acid sequence	MGFNQCLPFLDQGPKFVRGKTHAPEIREDIPPLNILSTKSNLPVSLILVILKIRQGDFKDTMLE TLRCNLHQLPKIKLRCLQDLHLADEHILEREYT(+) MQSPSTSQDQTSVPSRSSPCG(+) MSFTTDKLRSLVKKWQTLIEAHVDVKTTDNYMLRLFCIGFTKRRPNQVKRTCYAQASQIRQIRR KMVEIMANQASTCDLKELVSKFIPEVIGKEIEKSTSSIFPLQNVFIRKVKILKAPKFDLGKLME IASEGLKHRVFEVSLADLQNDEDQAYRKVRLRAEDVQGRNVLTNFWGMSFTTDKLRSLVKKWQT LIEAHVDVKTTDNYMLRLFCIGFTKRRPNQVKRTCYAQASQIRQIRRKMVEIMANQASTCDLKE LVSKFIPEVIGKEIEKSTSSIFPLQNVFIRKVKILKAPKFDLGKLMEIASEGLKHRVFEVSLAD LQNDEDQAYRKVRLRAEDVQGRNVLTNFWGMSFTTDKLRSLVKKWQTLIEAHVDVKTTDNYMLR LFCIGFTKRRPNQVKRTCYAQASQIRQIRRKMVEIMANQASTCDLKELVSKFIPEVIGKEIEKS TSSIFPLQNVFIRKVKILKAPKFDLGKLMEIASEGLKHRVFEVSLADLQNDEDQAYRKVRLRAE DVQGRNVLTNFWGMSFTTDKLRSLVKKWQTLIEAHVDVKTTDNYMLRLFCIGFTKRRPNQVKRT CYAQASQIRQIRRKMVEIMANQASTCDLKELVSKFIPEVIGKEIEKSTSSIFPLQNVFIRKVKI LKAPKFDLGKLME(-)
Sponge-miRNAs	osa-miR2923
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os02g0287000_circ_g.4

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