Plant Circular RNA Database

Detail information of Os02g0558600_circ_g.7

			
						 General Information
					
						CircRNA Name
						Os02g0558600_circ_g.7
					
						ID in PlantcircBase
						osa_circ_015060
					
						Alias
						Os_ciR3748
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr2: 21178040-21179203  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os02g0558600						
					
						Parent gene annotation
						
							Conserved hypothetical protein. (Os02t0558600-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os02g0558600_circ_g.2 Os02g0558600_circ_g.3 Os02g0558600_circ_g.4 Os02g0558600_circ_g.5 Os02g0558600_circ_g.6 						
					
						Support reads
						2/1
					
						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
						Os02t0558600-01:2

General Information
CircRNA Name	Os02g0558600_circ_g.7
ID in PlantcircBase	osa_circ_015060
Alias	Os_ciR3748
Organism	Oryza sativa
Position	chr2: 21178040-21179203 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os02g0558600
Parent gene annotation	Conserved hypothetical protein. (Os02t0558600-01)
Parent gene strand	-
Alternative splicing	Os02g0558600_circ_g.2 Os02g0558600_circ_g.3 Os02g0558600_circ_g.4 Os02g0558600_circ_g.5 Os02g0558600_circ_g.6
Support reads	2/1
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	Os02t0558600-01:2

			
						 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  
						
							TGCAGCCATTTCTTCCCTTCTTGTTTATCACCTGGCCAGCCTCAGCAGAAGAAGAATCCACTGA
TAAACTATACTCAACGCTGCTGCCTCTCCAATATATcttggaactctttgttggcatactactg
attagagcattcttccttggttcctgcctctcaagatcaattttcagatgttcccgttgcagac
ttgctatt

									
								

					

						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: 916
Transcript exons: 21178040-21178783,21179032-21179203
CTTGGAACTCTTTGTTGGCATACTACTGATTAGAGCATTCTTCCTTGGTTCCTGCCTCTCAAGA
TCAATTTTCAGATGTTCCCGTTGCAGACTTGCTATTGGCAAGGCAATCCTTGACACGGCAACAT
TTTCTCCATTATCATTTGACACAATATGCTTTGGTGCAAGAACCTTTCTCTCCAAAGGTTCATG
GTTGAGTACATCTCTGGTATTTGTGTGTGTGGCACATGGAAAATCTCCTTCAGCGTGATGCATT
TGATCAGAGACAGGACCCTCCAGCTGAATATTTTGCGATCCTGTTATCTGAGAAAACAAAGGAT
TAAATGTCAAGTACCCTAGCCCATGAGGGTCTTGGCATTTCTTTTCTCCTGATGAGCTCACTCC
AGTGGAAGGTTCAAAACTAGAGCTTGGAGCGCTAGCCACTGGATCTTCAGAACTAACTGCAGGT
AATTTATGTTCATGGATGTTATGGCCATTAGCATCATAGTGATCAGTCCCCTCTTCCGATGTGG
CTTCAGTCTGGTTGACCTCCTCCTGAGCCTTCAAAAGCCTGGCCCTCTTGTAATATTCTTCAAA
GAATGCCTTCTTTTGTGCAACCAAACCAGGCATTGTGAGATTGCTTAGCTCCTCTTGACGTCTG
TTATGGTCGAATACCGACCTTTTCTCCCATGACAAGGACTCTGCAGCAAACCTACCGAATGATA
CCGAGCCATGATCAAGTACCATTTGCTGAACTGAAGCATCTGTCTGTGCGTGGTGGTCGTTGTA
AGGCACATCCGAGTATGACCACCCACTGCAGAATCTCTGCCCAACCTCTGCAGCCATTTCTTCC
CTTCTTGTTTATCACCTGGCCAGCCTCAGCAGAAGAAGAATCCACTGATAAACTATACTCAACG
CTGCTGCCTCTCCAATATAT
						
					

						Genomic sequence
						
							CTTGGAACTCTTTGTTGGCATACTACTGATTAGAGCATTCTTCCTTGGTTCCTGCCTCTCAAGA
TCAATTTTCAGATGTTCCCGTTGCAGACTTGCTATTGGCAAGGCAATCCTTGACACGGCAACAT
TTTCTCCATTATCATTTGACACAATATGCTTTGGTGCAAGAACCTTTCTCTCCAAAGGTTCATG
GTTGAGTACATCTCTGGTATTTGTGTGTGTGGCACATGGAAAATCTCCTTCAGCGTGATGCATT
TGATCAGAGACAGGACCCTCCAGCTGAATATTTTGCGATCCTGTTATCTGAGAAAACAAAGGAT
TAAATGTCAAGTACCCTAGCCCATGAGGGTCTTGGCATTTCTTTTCTCCTGATGAGCTCACTCC
AGTGGAAGGTTCAAAACTAGAGCTTGGAGCGCTAGCCACTGGATCTTCAGAACTAACTGCAGGT
AATTTATGTTCATGGATGTTATGGCCATTAGCATCATAGTGATCAGTCCCCTCTTCCGATGTGG
CTTCAGTCTGGTTGACCTCCTCCTGAGCCTTCAAAAGCCTGGCCCTCTTGTAATATTCTTCAAA
GAATGCCTTCTTTTGTGCAACCAAACCAGGCATTGTGAGATTGCTTAGCTCCTCTTGACGTCTG
TTATGGTCGAATACCGACCTTTTCTCCCATGACAAGGACTCTGCAGCAAACCTACCGAATGATA
CCGAGCCATGATCAAGTACCATTTGCTGAACTGAAGCATCCTGAACACCAACAAGATCACGCGT
AACGAAAAATCAGGATTTCGTAAACCTTTTTACCATAACAGCAGTACAGCACACAACAAGAAAC
CACTATCGAGCATTGTGAAAACAAGAAACCACAAAAAGTTATCAAACCATGTCATTAAGCTCTC
ATCTGAAATGTAAGACAGTAACTTATTCGGGAGCTATGCAAAATTGGTTTTTCATTTGGTAATT
CTAGTGAGCAATTGGAGGTGAGTAGAACATACTGTCTGTGCGTGGTGGTCGTTGTAAGGCACAT
CCGAGTATGACCACCCACTGCAGAATCTCTGCCCAACCTCTGCAGCCATTTCTTCCCTTCTTGT
TTATCACCTGGCCAGCCTCAGCAGAAGAAGAATCCACTGATAAACTATACTCAACGCTGCTGCC
TCTCCAATATAT
						
					

			
		

Sequences
Splice junction sequence	TGCAGCCATTTCTTCCCTTCTTGTTTATCACCTGGCCAGCCTCAGCAGAAGAAGAATCCACTGA TAAACTATACTCAACGCTGCTGCCTCTCCAATATATcttggaactctttgttggcatactactg attagagcattcttccttggttcctgcctctcaagatcaattttcagatgttcccgttgcagac ttgctatt
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: 916 Transcript exons: 21178040-21178783,21179032-21179203 CTTGGAACTCTTTGTTGGCATACTACTGATTAGAGCATTCTTCCTTGGTTCCTGCCTCTCAAGA TCAATTTTCAGATGTTCCCGTTGCAGACTTGCTATTGGCAAGGCAATCCTTGACACGGCAACAT TTTCTCCATTATCATTTGACACAATATGCTTTGGTGCAAGAACCTTTCTCTCCAAAGGTTCATG GTTGAGTACATCTCTGGTATTTGTGTGTGTGGCACATGGAAAATCTCCTTCAGCGTGATGCATT TGATCAGAGACAGGACCCTCCAGCTGAATATTTTGCGATCCTGTTATCTGAGAAAACAAAGGAT TAAATGTCAAGTACCCTAGCCCATGAGGGTCTTGGCATTTCTTTTCTCCTGATGAGCTCACTCC AGTGGAAGGTTCAAAACTAGAGCTTGGAGCGCTAGCCACTGGATCTTCAGAACTAACTGCAGGT AATTTATGTTCATGGATGTTATGGCCATTAGCATCATAGTGATCAGTCCCCTCTTCCGATGTGG CTTCAGTCTGGTTGACCTCCTCCTGAGCCTTCAAAAGCCTGGCCCTCTTGTAATATTCTTCAAA GAATGCCTTCTTTTGTGCAACCAAACCAGGCATTGTGAGATTGCTTAGCTCCTCTTGACGTCTG TTATGGTCGAATACCGACCTTTTCTCCCATGACAAGGACTCTGCAGCAAACCTACCGAATGATA CCGAGCCATGATCAAGTACCATTTGCTGAACTGAAGCATCTGTCTGTGCGTGGTGGTCGTTGTA AGGCACATCCGAGTATGACCACCCACTGCAGAATCTCTGCCCAACCTCTGCAGCCATTTCTTCC CTTCTTGTTTATCACCTGGCCAGCCTCAGCAGAAGAAGAATCCACTGATAAACTATACTCAACG CTGCTGCCTCTCCAATATAT
Genomic sequence	CTTGGAACTCTTTGTTGGCATACTACTGATTAGAGCATTCTTCCTTGGTTCCTGCCTCTCAAGA TCAATTTTCAGATGTTCCCGTTGCAGACTTGCTATTGGCAAGGCAATCCTTGACACGGCAACAT TTTCTCCATTATCATTTGACACAATATGCTTTGGTGCAAGAACCTTTCTCTCCAAAGGTTCATG GTTGAGTACATCTCTGGTATTTGTGTGTGTGGCACATGGAAAATCTCCTTCAGCGTGATGCATT TGATCAGAGACAGGACCCTCCAGCTGAATATTTTGCGATCCTGTTATCTGAGAAAACAAAGGAT TAAATGTCAAGTACCCTAGCCCATGAGGGTCTTGGCATTTCTTTTCTCCTGATGAGCTCACTCC AGTGGAAGGTTCAAAACTAGAGCTTGGAGCGCTAGCCACTGGATCTTCAGAACTAACTGCAGGT AATTTATGTTCATGGATGTTATGGCCATTAGCATCATAGTGATCAGTCCCCTCTTCCGATGTGG CTTCAGTCTGGTTGACCTCCTCCTGAGCCTTCAAAAGCCTGGCCCTCTTGTAATATTCTTCAAA GAATGCCTTCTTTTGTGCAACCAAACCAGGCATTGTGAGATTGCTTAGCTCCTCTTGACGTCTG TTATGGTCGAATACCGACCTTTTCTCCCATGACAAGGACTCTGCAGCAAACCTACCGAATGATA CCGAGCCATGATCAAGTACCATTTGCTGAACTGAAGCATCCTGAACACCAACAAGATCACGCGT AACGAAAAATCAGGATTTCGTAAACCTTTTTACCATAACAGCAGTACAGCACACAACAAGAAAC CACTATCGAGCATTGTGAAAACAAGAAACCACAAAAAGTTATCAAACCATGTCATTAAGCTCTC ATCTGAAATGTAAGACAGTAACTTATTCGGGAGCTATGCAAAATTGGTTTTTCATTTGGTAATT CTAGTGAGCAATTGGAGGTGAGTAGAACATACTGTCTGTGCGTGGTGGTCGTTGTAAGGCACAT CCGAGTATGACCACCCACTGCAGAATCTCTGCCCAACCTCTGCAGCCATTTCTTCCCTTCTTGT TTATCACCTGGCCAGCCTCAGCAGAAGAAGAATCCACTGATAAACTATACTCAACGCTGCTGCC TCTCCAATATAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.372035208

Conservation Information
Conserved circRNAs	NA
PMCS	0.372035208

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21178709-21178286(+)
21179114-21178757(-)
						
						Potential amino acid sequence
						
							MTRTLQQTYRMIPSHDQVPFAELKHLSVRGGRCKAHPSMTTHCRISAQPLQPFLPFLFITWPAS
AEEESTDKLYSTLLPLQYILELFVGILLIRAFFLGSCLSRSIFRCSRCRLAIGKAILDTATFSP
LSFDTICFGARTFLSKGSWLSTSLVFVCVAHGKSPSA*(+)
MAAEVGQRFCSGWSYSDVPYNDHHAQTDASVQQMVLDHGSVSFGRFAAESLSWEKRSVFDHNRR
QEELSNLTMPGLVAQKKAFFEEYYKRARLLKAQEEVNQTEATSEEGTDHYDANGHNIHEHKLPA
VSSEDPVASAPSSSFEPSTGVSSSGEKKCQDPHGLGYLTFNPLFSQITGSQNIQLEGPVSDQMH
HAEGDFPCATHTNTRDVLNHEPLERKVLAPKHIVSNDNGENVAVSRIALPIASLQREHLKIDLE
RQEPRKNALISSMPTKSSKIYWRGSSVEYSLSVDSSSAEAGQVINKKGRNGCRGWAEILQWVVI
LGCALQRPPRTDRCFSSANGT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21178709-21178286(+) 21179114-21178757(-)
Potential amino acid sequence	MTRTLQQTYRMIPSHDQVPFAELKHLSVRGGRCKAHPSMTTHCRISAQPLQPFLPFLFITWPAS AEEESTDKLYSTLLPLQYILELFVGILLIRAFFLGSCLSRSIFRCSRCRLAIGKAILDTATFSP LSFDTICFGARTFLSKGSWLSTSLVFVCVAHGKSPSA(+) MAAEVGQRFCSGWSYSDVPYNDHHAQTDASVQQMVLDHGSVSFGRFAAESLSWEKRSVFDHNRR QEELSNLTMPGLVAQKKAFFEEYYKRARLLKAQEEVNQTEATSEEGTDHYDANGHNIHEHKLPA VSSEDPVASAPSSSFEPSTGVSSSGEKKCQDPHGLGYLTFNPLFSQITGSQNIQLEGPVSDQMH HAEGDFPCATHTNTRDVLNHEPLERKVLAPKHIVSNDNGENVAVSRIALPIASLQREHLKIDLE RQEPRKNALISSMPTKSSKIYWRGSSVEYSLSVDSSSAEAGQVINKKGRNGCRGWAEILQWVVI LGCALQRPPRTDRCFSSANGT(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os02g0558600_circ_g.7

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