Plant Circular RNA Database

Detail information of Os01g0246100_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0246100_circ_g.3
					
						ID in PlantcircBase
						osa_circ_001028
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 8053452-8054801  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0246100						
					
						Parent gene annotation
						
							Zinc finger, RING/FYVE/PHD-type domain containing protein. (Os01
t0246100-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0246100_circ_g.4 						
					
						Support reads
						1
					
						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
						Os01t0246100-01:4

General Information
CircRNA Name	Os01g0246100_circ_g.3
ID in PlantcircBase	osa_circ_001028
Alias	NA
Organism	Oryza sativa
Position	chr1: 8053452-8054801 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0246100
Parent gene annotation	Zinc finger, RING/FYVE/PHD-type domain containing protein. (Os01 t0246100-01)
Parent gene strand	-
Alternative splicing	Os01g0246100_circ_g.4
Support reads	1
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	Os01t0246100-01:4

			
						 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  
						
							TGTCCAGCCACTTGTGGGGTATTGCTGGGTAGGAAATCCACTTGCTGCATATTGCTGTTGAGTC
CCTTGCAGGGTCTTTGCCATCATGCTTCTATCTCGCctgagaaatgttcttttatatggccaat
atgcagtacatcaatactagggctacatttcggtagagttgatgcacatgaggtaaaaatggtg
tttgctaa

									
								

					

						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: 692
Transcript exons: 8053452-8053634,8053718-8053937,8054205-8054313,8054622-
8054801
CTGAGAAATGTTCTTTTATATGGCCAATATGCAGTACATCAATACTAGGGCTACATTTCGGTAG
AGTTGATGCACATGAGGTAAAAATGGTGTTTGCTAATCTTTCAGGCATCTGCTTGGGTTTATCA
GCCAACGAATGAGCAAAGTTAGCAGCACCCATACAGTTTTCATATTGGTTATATCCCTGAGTGG
AGGATACATTATATGCACAGGAGGGCAGATTATTAGGTCCAGGAGTAACTCTATCATGGTAGAT
GGGCACCTCCATCACAGGCAGCTGTTGTGAGTTTAGTTTGGATGAAGCTGCTGAAGCACTCCAA
TGAAACATACTACCCCGAAATGATGCAGAATTGACGATAGCATTCAACCTGGTTCTTAAAGTTT
CAAGATCCATATACTTAATCTTTGAATCAGCTTTCTCAAAAAGATGTCGGTCAATACATTTTCC
AATTTCCATAAGAAAGGATAGGTCAAAGTTGCAGAATTCCTTCCGCTCATTTAGGTACTCTACA
ATTTTACGGTGAATAATATTGCGAACTACGGATGTATCTTGATCCATATTATCCAACTGAAGAA
TTTCAGCTGCAGATTGTGTCCAGCCACTTGTGGGGTATTGCTGGGTAGGAAATCCACTTGCTGC
ATATTGCTGTTGAGTCCCTTGCAGGGTCTTTGCCATCATGCTTCTATCTCGC
						
					

						Genomic sequence
						
							CTGAGAAATGTTCTTTTATATGGCCAATATGCAGTACATCAATACTAGGGCTACATTTCGGTAG
AGTTGATGCACATGAGGTAAAAATGGTGTTTGCTAATCTTTCAGGCATCTGCTTGGGTTTATCA
GCCAACGAATGAGCAAAGTTAGCAGCACCCATACAGTTTTCATATTGGTTATATCCTGCCAAAA
TCAAGCCAATAAAGAATTAAAAAAATTAAGGTGTATTGTGAGGTTAAAATAGGTAACTCATCAT
CTCAACTCACCCTGAGTGGAGGATACATTATATGCACAGGAGGGCAGATTATTAGGTCCAGGAG
TAACTCTATCATGGTAGATGGGCACCTCCATCACAGGCAGCTGTTGTGAGTTTAGTTTGGATGA
AGCTGCTGAAGCACTCCAATGAAACATACTACCCCGAAATGATGCAGAATTGACGATAGCATTC
AACCTGGTTCTTAAAGTTTCAAGATCCATATACTTAATCTGAGAGAGAATCAGATGTTAGCAAG
TGACTGAGAACTATTTAGATAAATGAATCCAAATAATCAACTTCTAAGTACACCAAACTGTTCA
GCAGTAACAATTCTGTTTAAGGATTACAAGAATATGCTGAATTTTGTATTTATTCAATAAAGCA
TGTAGATAAGTTCAATATTGTCCAATATTAGAGTAGAAACCACACCAAATTAAAGCACCATAGG
TGATCATATATCCTATAATAGTTCTAATGCAGCAAGAGACAACACAAACCTTTGAATCAGCTTT
CTCAAAAAGATGTCGGTCAATACATTTTCCAATTTCCATAAGAAAGGATAGGTCAAAGTTGCAG
AATTCCTTCCGCTCATTTAGGTACTCTACACTGGATAAGAAAAAAGAATCAGGATATAGTTGAA
CAAGAGATAATAACTGCAATAAGTTATCGGTTTGCTACAACTTAAGTTGCAACAAGCCACCAAA
AGCACGTGATGTTATCAGACAGACTGGTCACTAGCAGTCACAGATTTTAGATAAAATCGTGCCA
GTAGCATTGCAGTTTTTGAAATGTTCAACTAAAGTTGCAGAAAACATATGTACAGTGTATACTT
TGTTGGTACGGCATGCTAGTATAAAGCAACTAGTAATCTGCGAGTCAAAGCTAATCCCAATATT
GGTGGTTTAAGAACTTACATTTTACGGTGAATAATATTGCGAACTACGGATGTATCTTGATCCA
TATTATCCAACTGAAGAATTTCAGCTGCAGATTGTGTCCAGCCACTTGTGGGGTATTGCTGGGT
AGGAAATCCACTTGCTGCATATTGCTGTTGAGTCCCTTGCAGGGTCTTTGCCATCATGCTTCTA
TCTCGC
						
					

			
		

Sequences
Splice junction sequence	TGTCCAGCCACTTGTGGGGTATTGCTGGGTAGGAAATCCACTTGCTGCATATTGCTGTTGAGTC CCTTGCAGGGTCTTTGCCATCATGCTTCTATCTCGCctgagaaatgttcttttatatggccaat atgcagtacatcaatactagggctacatttcggtagagttgatgcacatgaggtaaaaatggtg tttgctaa
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: 692 Transcript exons: 8053452-8053634,8053718-8053937,8054205-8054313,8054622- 8054801 CTGAGAAATGTTCTTTTATATGGCCAATATGCAGTACATCAATACTAGGGCTACATTTCGGTAG AGTTGATGCACATGAGGTAAAAATGGTGTTTGCTAATCTTTCAGGCATCTGCTTGGGTTTATCA GCCAACGAATGAGCAAAGTTAGCAGCACCCATACAGTTTTCATATTGGTTATATCCCTGAGTGG AGGATACATTATATGCACAGGAGGGCAGATTATTAGGTCCAGGAGTAACTCTATCATGGTAGAT GGGCACCTCCATCACAGGCAGCTGTTGTGAGTTTAGTTTGGATGAAGCTGCTGAAGCACTCCAA TGAAACATACTACCCCGAAATGATGCAGAATTGACGATAGCATTCAACCTGGTTCTTAAAGTTT CAAGATCCATATACTTAATCTTTGAATCAGCTTTCTCAAAAAGATGTCGGTCAATACATTTTCC AATTTCCATAAGAAAGGATAGGTCAAAGTTGCAGAATTCCTTCCGCTCATTTAGGTACTCTACA ATTTTACGGTGAATAATATTGCGAACTACGGATGTATCTTGATCCATATTATCCAACTGAAGAA TTTCAGCTGCAGATTGTGTCCAGCCACTTGTGGGGTATTGCTGGGTAGGAAATCCACTTGCTGC ATATTGCTGTTGAGTCCCTTGCAGGGTCTTTGCCATCATGCTTCTATCTCGC
Genomic sequence	CTGAGAAATGTTCTTTTATATGGCCAATATGCAGTACATCAATACTAGGGCTACATTTCGGTAG AGTTGATGCACATGAGGTAAAAATGGTGTTTGCTAATCTTTCAGGCATCTGCTTGGGTTTATCA GCCAACGAATGAGCAAAGTTAGCAGCACCCATACAGTTTTCATATTGGTTATATCCTGCCAAAA TCAAGCCAATAAAGAATTAAAAAAATTAAGGTGTATTGTGAGGTTAAAATAGGTAACTCATCAT CTCAACTCACCCTGAGTGGAGGATACATTATATGCACAGGAGGGCAGATTATTAGGTCCAGGAG TAACTCTATCATGGTAGATGGGCACCTCCATCACAGGCAGCTGTTGTGAGTTTAGTTTGGATGA AGCTGCTGAAGCACTCCAATGAAACATACTACCCCGAAATGATGCAGAATTGACGATAGCATTC AACCTGGTTCTTAAAGTTTCAAGATCCATATACTTAATCTGAGAGAGAATCAGATGTTAGCAAG TGACTGAGAACTATTTAGATAAATGAATCCAAATAATCAACTTCTAAGTACACCAAACTGTTCA GCAGTAACAATTCTGTTTAAGGATTACAAGAATATGCTGAATTTTGTATTTATTCAATAAAGCA TGTAGATAAGTTCAATATTGTCCAATATTAGAGTAGAAACCACACCAAATTAAAGCACCATAGG TGATCATATATCCTATAATAGTTCTAATGCAGCAAGAGACAACACAAACCTTTGAATCAGCTTT CTCAAAAAGATGTCGGTCAATACATTTTCCAATTTCCATAAGAAAGGATAGGTCAAAGTTGCAG AATTCCTTCCGCTCATTTAGGTACTCTACACTGGATAAGAAAAAAGAATCAGGATATAGTTGAA CAAGAGATAATAACTGCAATAAGTTATCGGTTTGCTACAACTTAAGTTGCAACAAGCCACCAAA AGCACGTGATGTTATCAGACAGACTGGTCACTAGCAGTCACAGATTTTAGATAAAATCGTGCCA GTAGCATTGCAGTTTTTGAAATGTTCAACTAAAGTTGCAGAAAACATATGTACAGTGTATACTT TGTTGGTACGGCATGCTAGTATAAAGCAACTAGTAATCTGCGAGTCAAAGCTAATCCCAATATT GGTGGTTTAAGAACTTACATTTTACGGTGAATAATATTGCGAACTACGGATGTATCTTGATCCA TATTATCCAACTGAAGAATTTCAGCTGCAGATTGTGTCCAGCCACTTGTGGGGTATTGCTGGGT AGGAAATCCACTTGCTGCATATTGCTGTTGAGTCCCTTGCAGGGTCTTTGCCATCATGCTTCTA TCTCGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.202354981

Conservation Information
Conserved circRNAs	NA
PMCS	0.202354981

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8054788-8053496(+)
8054790-8054787(-)
						
						Potential amino acid sequence
						
							MLLSRLRNVLLYGQYAVHQY*(+)
MMAKTLQGTQQQYAASGFPTQQYPTSGWTQSAAEILQLDNMDQDTSVVRNIIHRKIVEYLNERK
EFCNFDLSFLMEIGKCIDRHLFEKADSKIKYMDLETLRTRLNAIVNSASFRGSMFHWSASAASS
KLNSQQLPVMEVPIYHDRVTPGPNNLPSCAYNVSSTQGYNQYENCMGAANFAHSLADKPKQMPE
RLANTIFTSCASTLPKCSPSIDVLHIGHIKEHFSGEIEA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	8054788-8053496(+) 8054790-8054787(-)
Potential amino acid sequence	MLLSRLRNVLLYGQYAVHQY(+) MMAKTLQGTQQQYAASGFPTQQYPTSGWTQSAAEILQLDNMDQDTSVVRNIIHRKIVEYLNERK EFCNFDLSFLMEIGKCIDRHLFEKADSKIKYMDLETLRTRLNAIVNSASFRGSMFHWSASAASS KLNSQQLPVMEVPIYHDRVTPGPNNLPSCAYNVSSTQGYNQYENCMGAANFAHSLADKPKQMPE RLANTIFTSCASTLPKCSPSIDVLHIGHIKEHFSGEIEA(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0246100_circ_g.3

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