Plant Circular RNA Database

Detail information of Os04g0298200_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0298200_circ_g.2
					
						ID in PlantcircBase
						osa_circ_023340
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 13178198-13181748  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							Os04g0298200						
					
						Parent gene annotation
						
							Similar to metal tolerance protein. (Os04t0298200-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0298200_circ_g.1 						
					
						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  
						
							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
						Os04t0298200-01:9

General Information
CircRNA Name	Os04g0298200_circ_g.2
ID in PlantcircBase	osa_circ_023340
Alias	NA
Organism	Oryza sativa
Position	chr4: 13178198-13181748 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	PcircRNA_finder
Parent gene	Os04g0298200
Parent gene annotation	Similar to metal tolerance protein. (Os04t0298200-01)
Parent gene strand	-
Alternative splicing	Os04g0298200_circ_g.1
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	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	Os04t0298200-01:9

			
						 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  
						
							CTCAGCTAGCATAACATGACTAGATGTTGAAAGCCATACACCAAACTTCAACGAAAAGACAAGA
AAATTACACCACAGTGCTGTGTTAACCGCTCGATGGctgttttgcccattctccacgtccagtc
ctttccaaataattctgcaccaggactactccattgaaatctatgagaagattaggccagaaaa
ttgtcaag

									
								

					

						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
						
							CTGTTTTGCCCATTCTCCACGTCCAGTCCTTTCCAAATAATTCTGCACCAGGACTACTCCATTG
AAATCTATGAGAAGATTAGGCCAGAAAATTGTCAAGAAAAGAGCCGTAAGGGAGTATGCGAGGT
AAACAAAATAAGAAAGTAACAGGACTGATGTTATAGATGAGTTCAACAAATCAATAAGCAATGT
TAATGGGAATAGTCACTTGCAGACACATTACACCAGCTCACATGAGGAAAAATCCCTGTGGGCA
CTTGCTATCATGGGAATTTCAGATAGTTCTAGACTCAAGTAACACAACACTACAACAGTACATT
AATTTATCATCTGAATTGGAGCCAAGTCATGAGTTAGATTAACGAAGAAGTATACCATATTAGT
AGTAAGAAATACAGTAAATGGTTAATAGAAGGTACAACAGGTCTCTGCACATGAATAAAACCAT
CTTGATCATTTACAGATCACCAGTTCATCTCACAGAAACAAGATTGACTGTAATAAGTGCTCTA
GTATGACTCTTTTAAACAAAAGGTAGGCTTAAGAACAATGGATATAATCATAAATGAAGACGTC
TCAAACTAAAAATGACATGCATCACAAGTACTAACTGAAAATGACGACAAAAATAAAATAACTG
CCTTAAATTTGGAGAAAGCCAGATTATAAGAGCTGTACCAATTTCAGCTTTGAATCTAAAGAAT
CCTGGTCCAATCACCTCACTTTTGCAATCATAAAGAGCATCTACAACCTGCATGATGCAAGAAA
ATCAGCTCCATAACATAGATCCAGTGTGCGATATGGAATAAGGATATCCACAAATTTTCACCGG
ATCAGCCTTCAGAAACTCAAGAACACGCTGCATGTCATGATCATCAATAGCCCTTCCAATTAAA
GCATGCCTGTTTCTCTGGATTAGAAAAATAGCAACCTACAGAGAGCACAATAGTTTAATTTGGA
ACAAGGCATGGACAGGGATGAGAAAATTGGAGAAGCAAATCATCAGCAAACTCATATGAGTACA
CCTTTTGCACTGTGCACAATTTTGGTGATTCTTTGGCAATAGACTTTTAAAGTTCTTGTTCAAT
TTGGGTGGCATTTCATGAAAACAAGATTGGCTAAAGCTGGTTTTCAGTCATTAGTGTTTATGTT
TTGACTTTTCTGAAAATCAGGAAAAGGTGGTCTTACAGAAAAGAATGCAATTATATGCTTTTAG
AGATCTCCATGTTGCCCCAAACCAATGGAGACAAGATTTAAGGTGGTTCAAGCTAGAAACATGT
TTAACCAAATCTAGTATTATCAGAACTGTCTATCCAAAATCTCCTTTAAGACTACAGCTCTGTA
TGGTAAACCATAAATTGTTCCAGGCAAACAACAGCCACATGCATATCTGACCTGCTTACTTTTT
AGAGAGAACTTCCTTGGGAATTGGACACGTCATTTTTAAGTTTAGGAGGAGTTGGGTACTACTG
CAGATTATAAGCAGTAAGTGTTACCTAACAGTATCGACTGTATACGTGATACCTGAGTACCCGA
CAACCCATTTATGGTTCCAATTATGTAACAATATACAAATGAATTAGGCTTTTTTAGATTTTAG
AAACACACAAAAACATGGATAGCATCCACAATTTTAGTATGAGCAGAATACAGAATATCTGAAT
AAAATATACTTCAGAATAGATGTAGTCAACATACAAGAAATACACATCAATAAACAAATCTTTA
CTGGTAGCTATGAATCTTTTGGTCTTGGGGTTTCACAAACTGCTGATATCTGAACATAGTGCTC
ATCTGTTATGATAGCCAAAATACTGTTTTATCTTGCATAGAAATAAAAAATGAACAAAGCACCA
TTTGGCCCTTCCTAGCATAGTTGATGGGCATTCGATGAAGTGTAGACAGCAACAATAGAAATGC
AAGAAATAAGAAGTTTAACAAGATAAGTGGGATAAAAGATTTAGATTGTCATAGTTTATTTAAT
TATAAAGAAACGAGGACATGATATTTGTGTCAGACTAAGGGGTATACATGTATCCAATACCAAA
TGACCATTCAATAAGGCAGAAAACAATTGAACAAATATTCCGTTACATCAATTAGTCACACATA
GCAACAGAATATAAGCCAAGAAAGATAATAGAATAATATGAACCGACTATGTTAACATACCATT
CCCAGTAAGTTGCCAACAATGATGGAGCCAATTGGATCATACATAGCATTGCCTGTGGTTTGAA
CAGCCACCAAAGATGCTCCAGCAATTGCAAGACCTGTAACAGCAGCACCATCCTGTAGGACATT
ATCAGGGCATGAGAAGGAAATCAAGTAGAGGAATAGCAGGTGAGTGGTAAATGAACAAAACATT
TATTGATATGGCATCACCATATGATACTTATGAGCAACTGAAGCAGTCATCAACTGTTTTAGAA
ACAAAATTTCATTTCGACATGAAAAAAAAAAGTATTGAGGTAGTCTAGAACACATCACTCACTT
CAGTCATGACAGCAACTGAAGTTGGATCATGACCACGCCAGATGTAGTCCCTGATACTCATTCC
TTCTGCTGCTGCACCCTTCCTAACAGCCTTTATAGCAACCAGCAGTGAAGCACCTAAGAGGCAA
TAGGGTGACTCAATTATAACAAAGTAAAGACATGGTTAGAATGTCATGTAGCAAGCATGTAATA
CCTTCAATTAGGAAGGACCCACCAATCACTAATGCAGCATAGTGGATGTTCTCAGGGGGCTGTC
AAATAAATGTGTCACGATATAACAACTGTAGTTAGGTAACAAAGATTTTCTAATAAGATGGAGT
GCATGTGTAAAATCTTTTGGTGAATCAAATGATACATTTGCATCATACTTGCGAATTCCATAAG
TTTTGAACTCCATGCACAATGGTAGCACCTGAACCCAAACAAAATATTCCAACTGCAGATATCA
AGGACCATACAAATCTTTCTTTTGAATAACCATAGCTGCAGAAAGAGAAATTAAGACATGGGGC
AGGCAGCATGTCAGTTTATGGCATATCACAAATAGCCTTACCACTGATTCTATTGTGAGTAGCA
TTTAGTGGTATACTGGCATGACAATGAATAACAGGATTCCCTGTTTATCTTCAATTCAAGACAA
TTTTACTCTGGTGAAAATAACTGATTTTCCATGCAGAAATGGGACTAAATTTATGGTACAGAGA
AAATAACAGTAATGAAAGAAAGTGATATTTATATGTCAACAAAGCAGCATTTCCAAATTGACAA
TCGATACATACGGGTGTAGAGCATCTGGAGCACGTCTTGAGCTGCTCAAGCCATATGCAAGAAG
AGCCTGATGTTTAATCAACAATTAAGCCCTGGACATGAACCTTCAACAAAGCTTACAAAAAAAG
ATAGCAAAAGTAGAAGCATCAACTACCTGGTTAGCGAAGTCTGCAACTGAGTGCACTAGCTCAG
CTAGCATAACATGACTAGATGTTGAAAGCCATACACCAAACTTCAACGAAAAGACAAGAAAATT
ACACCACAGTGCTGTGTTAACCGCTCGATGG
						
					

			
		

Sequences
Splice junction sequence	CTCAGCTAGCATAACATGACTAGATGTTGAAAGCCATACACCAAACTTCAACGAAAAGACAAGA AAATTACACCACAGTGCTGTGTTAACCGCTCGATGGctgttttgcccattctccacgtccagtc ctttccaaataattctgcaccaggactactccattgaaatctatgagaagattaggccagaaaa ttgtcaag
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	CTGTTTTGCCCATTCTCCACGTCCAGTCCTTTCCAAATAATTCTGCACCAGGACTACTCCATTG AAATCTATGAGAAGATTAGGCCAGAAAATTGTCAAGAAAAGAGCCGTAAGGGAGTATGCGAGGT AAACAAAATAAGAAAGTAACAGGACTGATGTTATAGATGAGTTCAACAAATCAATAAGCAATGT TAATGGGAATAGTCACTTGCAGACACATTACACCAGCTCACATGAGGAAAAATCCCTGTGGGCA CTTGCTATCATGGGAATTTCAGATAGTTCTAGACTCAAGTAACACAACACTACAACAGTACATT AATTTATCATCTGAATTGGAGCCAAGTCATGAGTTAGATTAACGAAGAAGTATACCATATTAGT AGTAAGAAATACAGTAAATGGTTAATAGAAGGTACAACAGGTCTCTGCACATGAATAAAACCAT CTTGATCATTTACAGATCACCAGTTCATCTCACAGAAACAAGATTGACTGTAATAAGTGCTCTA GTATGACTCTTTTAAACAAAAGGTAGGCTTAAGAACAATGGATATAATCATAAATGAAGACGTC TCAAACTAAAAATGACATGCATCACAAGTACTAACTGAAAATGACGACAAAAATAAAATAACTG CCTTAAATTTGGAGAAAGCCAGATTATAAGAGCTGTACCAATTTCAGCTTTGAATCTAAAGAAT CCTGGTCCAATCACCTCACTTTTGCAATCATAAAGAGCATCTACAACCTGCATGATGCAAGAAA ATCAGCTCCATAACATAGATCCAGTGTGCGATATGGAATAAGGATATCCACAAATTTTCACCGG ATCAGCCTTCAGAAACTCAAGAACACGCTGCATGTCATGATCATCAATAGCCCTTCCAATTAAA GCATGCCTGTTTCTCTGGATTAGAAAAATAGCAACCTACAGAGAGCACAATAGTTTAATTTGGA ACAAGGCATGGACAGGGATGAGAAAATTGGAGAAGCAAATCATCAGCAAACTCATATGAGTACA CCTTTTGCACTGTGCACAATTTTGGTGATTCTTTGGCAATAGACTTTTAAAGTTCTTGTTCAAT TTGGGTGGCATTTCATGAAAACAAGATTGGCTAAAGCTGGTTTTCAGTCATTAGTGTTTATGTT TTGACTTTTCTGAAAATCAGGAAAAGGTGGTCTTACAGAAAAGAATGCAATTATATGCTTTTAG AGATCTCCATGTTGCCCCAAACCAATGGAGACAAGATTTAAGGTGGTTCAAGCTAGAAACATGT TTAACCAAATCTAGTATTATCAGAACTGTCTATCCAAAATCTCCTTTAAGACTACAGCTCTGTA TGGTAAACCATAAATTGTTCCAGGCAAACAACAGCCACATGCATATCTGACCTGCTTACTTTTT AGAGAGAACTTCCTTGGGAATTGGACACGTCATTTTTAAGTTTAGGAGGAGTTGGGTACTACTG CAGATTATAAGCAGTAAGTGTTACCTAACAGTATCGACTGTATACGTGATACCTGAGTACCCGA CAACCCATTTATGGTTCCAATTATGTAACAATATACAAATGAATTAGGCTTTTTTAGATTTTAG AAACACACAAAAACATGGATAGCATCCACAATTTTAGTATGAGCAGAATACAGAATATCTGAAT AAAATATACTTCAGAATAGATGTAGTCAACATACAAGAAATACACATCAATAAACAAATCTTTA CTGGTAGCTATGAATCTTTTGGTCTTGGGGTTTCACAAACTGCTGATATCTGAACATAGTGCTC ATCTGTTATGATAGCCAAAATACTGTTTTATCTTGCATAGAAATAAAAAATGAACAAAGCACCA TTTGGCCCTTCCTAGCATAGTTGATGGGCATTCGATGAAGTGTAGACAGCAACAATAGAAATGC AAGAAATAAGAAGTTTAACAAGATAAGTGGGATAAAAGATTTAGATTGTCATAGTTTATTTAAT TATAAAGAAACGAGGACATGATATTTGTGTCAGACTAAGGGGTATACATGTATCCAATACCAAA TGACCATTCAATAAGGCAGAAAACAATTGAACAAATATTCCGTTACATCAATTAGTCACACATA GCAACAGAATATAAGCCAAGAAAGATAATAGAATAATATGAACCGACTATGTTAACATACCATT CCCAGTAAGTTGCCAACAATGATGGAGCCAATTGGATCATACATAGCATTGCCTGTGGTTTGAA CAGCCACCAAAGATGCTCCAGCAATTGCAAGACCTGTAACAGCAGCACCATCCTGTAGGACATT ATCAGGGCATGAGAAGGAAATCAAGTAGAGGAATAGCAGGTGAGTGGTAAATGAACAAAACATT TATTGATATGGCATCACCATATGATACTTATGAGCAACTGAAGCAGTCATCAACTGTTTTAGAA ACAAAATTTCATTTCGACATGAAAAAAAAAAGTATTGAGGTAGTCTAGAACACATCACTCACTT CAGTCATGACAGCAACTGAAGTTGGATCATGACCACGCCAGATGTAGTCCCTGATACTCATTCC TTCTGCTGCTGCACCCTTCCTAACAGCCTTTATAGCAACCAGCAGTGAAGCACCTAAGAGGCAA TAGGGTGACTCAATTATAACAAAGTAAAGACATGGTTAGAATGTCATGTAGCAAGCATGTAATA CCTTCAATTAGGAAGGACCCACCAATCACTAATGCAGCATAGTGGATGTTCTCAGGGGGCTGTC AAATAAATGTGTCACGATATAACAACTGTAGTTAGGTAACAAAGATTTTCTAATAAGATGGAGT GCATGTGTAAAATCTTTTGGTGAATCAAATGATACATTTGCATCATACTTGCGAATTCCATAAG TTTTGAACTCCATGCACAATGGTAGCACCTGAACCCAAACAAAATATTCCAACTGCAGATATCA AGGACCATACAAATCTTTCTTTTGAATAACCATAGCTGCAGAAAGAGAAATTAAGACATGGGGC AGGCAGCATGTCAGTTTATGGCATATCACAAATAGCCTTACCACTGATTCTATTGTGAGTAGCA TTTAGTGGTATACTGGCATGACAATGAATAACAGGATTCCCTGTTTATCTTCAATTCAAGACAA TTTTACTCTGGTGAAAATAACTGATTTTCCATGCAGAAATGGGACTAAATTTATGGTACAGAGA AAATAACAGTAATGAAAGAAAGTGATATTTATATGTCAACAAAGCAGCATTTCCAAATTGACAA TCGATACATACGGGTGTAGAGCATCTGGAGCACGTCTTGAGCTGCTCAAGCCATATGCAAGAAG AGCCTGATGTTTAATCAACAATTAAGCCCTGGACATGAACCTTCAACAAAGCTTACAAAAAAAG ATAGCAAAAGTAGAAGCATCAACTACCTGGTTAGCGAAGTCTGCAACTGAGTGCACTAGCTCAG CTAGCATAACATGACTAGATGTTGAAAGCCATACACCAAACTTCAACGAAAAGACAAGAAAATT ACACCACAGTGCTGTGTTAACCGCTCGATGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.121668246

Conservation Information
Conserved circRNAs	NA
PMCS	0.121668246

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							13181746-13178259(+)
13178212-13181698(-)
13181662-13181736(-)
						
						Potential amino acid sequence
						
							MAVLPILHVQSFPNNSAPGLLH*(+)
MGKTAIERLTQHCGVIFLSFR*(-)
MLAELVHSVADFANQALLAYGLSSSRRAPDALHPYGYSKERFVWSLISAVGIFCLGSGATIVHG
VQNLWNSQPPENIHYAALVIGGSFLIEGASLLVAIKAVRKGAAAEGMSIRDYIWRGHDPTSVAV
MTEDGAAVTGLAIAGASLVAVQTTGNAMYDPIGSIIVGNLLGMVAIFLIQRNRHALIGRAIDDH
DMQRVLEFLKADPVVDALYDCKSEVIGPGFFRFKAEIDFNGVVLVQNYLERTGRGEWAKQPSSG
*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	13181746-13178259(+) 13178212-13181698(-) 13181662-13181736(-)
Potential amino acid sequence	MAVLPILHVQSFPNNSAPGLLH(+) MGKTAIERLTQHCGVIFLSFR(-) MLAELVHSVADFANQALLAYGLSSSRRAPDALHPYGYSKERFVWSLISAVGIFCLGSGATIVHG VQNLWNSQPPENIHYAALVIGGSFLIEGASLLVAIKAVRKGAAAEGMSIRDYIWRGHDPTSVAV MTEDGAAVTGLAIAGASLVAVQTTGNAMYDPIGSIIVGNLLGMVAIFLIQRNRHALIGRAIDDH DMQRVLEFLKADPVVDALYDCKSEVIGPGFFRFKAEIDFNGVVLVQNYLERTGRGEWAKQPSSG *(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0298200_circ_g.2

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