Plant Circular RNA Database

Detail information of Os04g0306800_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0306800_circ_g.3
					
						ID in PlantcircBase
						osa_circ_023367
					
						Alias
						Os_ciR3900
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 13827214-13828254  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os04g0306800						
					
						Parent gene annotation
						
							RNA recognition motif, RNP-1 domain containing protein. (Os04t03
06800-01);Similar to OSIGBa0096F13.9 protein. (Os04t0306800-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0306800_circ_g.1 Os04g0306800_circ_g.2 Os04g0306800_circ_g.4 Os04g0306800_circ_g.5 						
					
						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
						Os04t0306800-02:2
Os04t0306800-01:4

General Information
CircRNA Name	Os04g0306800_circ_g.3
ID in PlantcircBase	osa_circ_023367
Alias	Os_ciR3900
Organism	Oryza sativa
Position	chr4: 13827214-13828254 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os04g0306800
Parent gene annotation	RNA recognition motif, RNP-1 domain containing protein. (Os04t03 06800-01);Similar to OSIGBa0096F13.9 protein. (Os04t0306800-02)
Parent gene strand	-
Alternative splicing	Os04g0306800_circ_g.1 Os04g0306800_circ_g.2 Os04g0306800_circ_g.4 Os04g0306800_circ_g.5
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	Os04t0306800-02:2 Os04t0306800-01:4

			
						 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  
						
							ATGAAACAAATTTTGCACTATCATCACCAAGGAAGGCCTCCAAGTCATCACGTGCTTGGTACTG
GTGTTTCCCATTACAGACTAGAATGACAATGTATTCcttgtggcaatgcttgtgctgtccttac
agctacaccagacttcagtgtggagaaatttctgccacttgatgatctctgatctttctgctct
aagacaga

									
								

					

						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: 490
Transcript exons: 13827214-13827298,13827383-13827544,13827923-13828064,13
828154-13828254
CTTGTGGCAATGCTTGTGCTGTCCTTACAGCTACACCAGACTTCAGTGTGGAGAAATTTCTGCC
ACTTGATGATCTCTGATCTTTCTTCTGATGTTGGCCCTCCCAATAACATTGATCGTCAACCAAC
TTTTCAGGAGTAACAGTAACCGTCGAGCTAATGTGGCGTCGGGCCACATTTTGTCCTTCAGTTG
AGTCATGCTTCTGAAGAGTATGATGCTCTTGAGGTGATGAGATATCTGAATTGACAATGAAAGT
ATCCTCGGATAGCGCATTTGCAACCTGAAGATTTTTCTTGGTACTACGGTTCCGGATCTCATTT
GTCAGACCATGCTGGATGCTAGAATTGTCAGCCAATGTTAAAGCCTTTTTACTGAGGTAACCCC
AAAGCCATGAAACAAATTTTGCACTATCATCACCAAGGAAGGCCTCCAAGTCATCACGTGCTTG
GTACTGGTGTTTCCCATTACAGACTAGAATGACAATGTATTC
						
					

						Genomic sequence
						
							CTTGTGGCAATGCTTGTGCTGTCCTTACAGCTACACCAGACTTCAGTGTGGAGAAATTTCTGCC
ACTTGATGATCTCTGATCTTTCTGCTCTAAGACAGAGAATCATAAAATTAAATGCCTCATGTCA
TAATAAAGGAGGAGTTTAGGATAAAGGTATAACATATTGACCTTCTGATGTTGGCCCTCCCAAT
AACATTGATCGTCAACCAACTTTTCAGGAGTAACAGTAACCGTCGAGCTAATGTGGCGTCGGGC
CACATTTTGTCCTTCAGTTGAGTCATGCTTCTGAAGAGTATGATGCTCTTGAGGTGATGAGATA
TCTGAATTGACCTGATCAATATTGGATGAGTTCGTTGAGTCCAAAAATATGAGCAATTTTTACT
TGAAGTCCTTCAGTGTTCATGTTAGTTTAGAACTTCAGATATATGATGAAAAAGTTGAACGCTG
TATGGACACAAACATTCAAAAAGTTGGTATTAATTGGTCGGTTACGGGTACCAGAACAAAACTG
GACAGAATACTTCAAATACAATCTAAATTCAGTTTGTTAATTTCTTAGCGCTATTATTTTCAGT
CCTTACCAGCCGGTAACCATTATTTGTATTTGAAATGATTTCCGGTAAATTCTGGTAACTGGCA
GCAACCGATCCGGCCCAGGAAACCTTGATGGACACTGATGATCATAAGACAATGCGATAAGATT
CTTACAATGAAAGTATCCTCGGATAGCGCATTTGCAACCTGAAGATTTTTCTTGGTACTACGGT
TCCGGATCTCATTTGTCAGACCATGCTGGATGCTAGAATTGTCAGCCAATGTTAAAGCCTTTTT
ACTGAGGTAACCCCAAAGCCTGTTTAGCCATATTAAAGCAACATAACTTCATAGAGGTAGACAA
AATAAACAAAAACAGTTAACTGATCAAAAGAACAGATAAATTACCATGAAACAAATTTTGCACT
ATCATCACCAAGGAAGGCCTCCAAGTCATCACGTGCTTGGTACTGGTGTTTCCCATTACAGACT
AGAATGACAATGTATTC
						
					

			
		

Sequences
Splice junction sequence	ATGAAACAAATTTTGCACTATCATCACCAAGGAAGGCCTCCAAGTCATCACGTGCTTGGTACTG GTGTTTCCCATTACAGACTAGAATGACAATGTATTCcttgtggcaatgcttgtgctgtccttac agctacaccagacttcagtgtggagaaatttctgccacttgatgatctctgatctttctgctct aagacaga
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: 490 Transcript exons: 13827214-13827298,13827383-13827544,13827923-13828064,13 828154-13828254 CTTGTGGCAATGCTTGTGCTGTCCTTACAGCTACACCAGACTTCAGTGTGGAGAAATTTCTGCC ACTTGATGATCTCTGATCTTTCTTCTGATGTTGGCCCTCCCAATAACATTGATCGTCAACCAAC TTTTCAGGAGTAACAGTAACCGTCGAGCTAATGTGGCGTCGGGCCACATTTTGTCCTTCAGTTG AGTCATGCTTCTGAAGAGTATGATGCTCTTGAGGTGATGAGATATCTGAATTGACAATGAAAGT ATCCTCGGATAGCGCATTTGCAACCTGAAGATTTTTCTTGGTACTACGGTTCCGGATCTCATTT GTCAGACCATGCTGGATGCTAGAATTGTCAGCCAATGTTAAAGCCTTTTTACTGAGGTAACCCC AAAGCCATGAAACAAATTTTGCACTATCATCACCAAGGAAGGCCTCCAAGTCATCACGTGCTTG GTACTGGTGTTTCCCATTACAGACTAGAATGACAATGTATTC
Genomic sequence	CTTGTGGCAATGCTTGTGCTGTCCTTACAGCTACACCAGACTTCAGTGTGGAGAAATTTCTGCC ACTTGATGATCTCTGATCTTTCTGCTCTAAGACAGAGAATCATAAAATTAAATGCCTCATGTCA TAATAAAGGAGGAGTTTAGGATAAAGGTATAACATATTGACCTTCTGATGTTGGCCCTCCCAAT AACATTGATCGTCAACCAACTTTTCAGGAGTAACAGTAACCGTCGAGCTAATGTGGCGTCGGGC CACATTTTGTCCTTCAGTTGAGTCATGCTTCTGAAGAGTATGATGCTCTTGAGGTGATGAGATA TCTGAATTGACCTGATCAATATTGGATGAGTTCGTTGAGTCCAAAAATATGAGCAATTTTTACT TGAAGTCCTTCAGTGTTCATGTTAGTTTAGAACTTCAGATATATGATGAAAAAGTTGAACGCTG TATGGACACAAACATTCAAAAAGTTGGTATTAATTGGTCGGTTACGGGTACCAGAACAAAACTG GACAGAATACTTCAAATACAATCTAAATTCAGTTTGTTAATTTCTTAGCGCTATTATTTTCAGT CCTTACCAGCCGGTAACCATTATTTGTATTTGAAATGATTTCCGGTAAATTCTGGTAACTGGCA GCAACCGATCCGGCCCAGGAAACCTTGATGGACACTGATGATCATAAGACAATGCGATAAGATT CTTACAATGAAAGTATCCTCGGATAGCGCATTTGCAACCTGAAGATTTTTCTTGGTACTACGGT TCCGGATCTCATTTGTCAGACCATGCTGGATGCTAGAATTGTCAGCCAATGTTAAAGCCTTTTT ACTGAGGTAACCCCAAAGCCTGTTTAGCCATATTAAAGCAACATAACTTCATAGAGGTAGACAA AATAAACAAAAACAGTTAACTGATCAAAAGAACAGATAAATTACCATGAAACAAATTTTGCACT ATCATCACCAAGGAAGGCCTCCAAGTCATCACGTGCTTGGTACTGGTGTTTCCCATTACAGACT AGAATGACAATGTATTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.223534902

Conservation Information
Conserved circRNAs	NA
PMCS	0.223534902

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							13828242-13827280(+)
13827412-13828238(-)
						
						Potential amino acid sequence
						
							MTMYSLWQCLCCPYSYTRLQCGEISAT*(+)
MLLGGPTSEERSEIIKWQKFLHTEVWCSCKDSTSIATRNTLSF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	13828242-13827280(+) 13827412-13828238(-)
Potential amino acid sequence	MTMYSLWQCLCCPYSYTRLQCGEISAT(+) MLLGGPTSEERSEIIKWQKFLHTEVWCSCKDSTSIATRNTLSF(-)
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 Os04g0306800_circ_g.3

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