Plant Circular RNA Database

Detail information of Os01g0229250_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os01g0229250_circ_g.1
					
						ID in PlantcircBase
						osa_circ_000929
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 7130944-7132102  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0229200						
					
						Parent gene annotation
						
							VHS domain containing protein. (Os01t0229200-01);Hypothetical co
nserved gene. (Os01t0229200-02);Hypothetical conserved gene. (Os
01t0229200-03);Hypothetical conserved gene. (Os01t0229200-04)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						1
					
						Tissues
						shoot, 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  
						
							GT-AG							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
						Os01t0229250-00:4
Os01t0229250-00:4
Os01t0229200-02:2
Os01t0229200-01:4

General Information
CircRNA Name	Os01g0229250_circ_g.1
ID in PlantcircBase	osa_circ_000929
Alias	NA
Organism	Oryza sativa
Position	chr1: 7130944-7132102 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0229200
Parent gene annotation	VHS domain containing protein. (Os01t0229200-01);Hypothetical co nserved gene. (Os01t0229200-02);Hypothetical conserved gene. (Os 01t0229200-03);Hypothetical conserved gene. (Os01t0229200-04)
Parent gene strand	+
Alternative splicing	NA
Support reads	1
Tissues	shoot, 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	GT-AG 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	Os01t0229250-00:4 Os01t0229250-00:4 Os01t0229200-02:2 Os01t0229200-01:4

			
						 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  
						
							CATTGTTTAATGGCCAGTCTCCAGCAGGCAGAAATATGCGTAGTCCTGATCAGCAGGATGAAGC
TGAATCGTCTGCTGGAAATGATTTTCCTGCTTTGAGgcaatcaaaagatgttgttaaggcactc
aagaaaaggattgggcacaaaaatccaaaagtccaaattcttgcgctgactgtgagtttatcat
aactttac

									
								

					

						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: 435
Transcript exons: 7130944-7131022,7131470-7131568,7131654-7131767,7131960-
7132102
GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAA
ATTCTTGCGCTGACTCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATG
TTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAGTCTGATCAGAATGT
CAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGA
TATCCACAGTACTATGCAGCGTACCATGACTTGGTGCGTGCTGGAGCTGCATTTCCAAAGAGAT
CTGATCGACCTGCACCATTGTTTAATGGCCAGTCTCCAGCAGGCAGAAATATGCGTAGTCCTGA
TCAGCAGGATGAAGCTGAATCGTCTGCTGGAAATGATTTTCCTGCTTTGAG
						
					

						Genomic sequence
						
							GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAA
ATTCTTGCGCTGACTGTGAGTTTATCATAACTTTACATCCTTTTTAAGAGTGGTGCTAATGGTA
CAAGCAATGGGAAGAATCTCTTCTCTGTGTGTTTTAACATCAAGCATATATGTCTATTGCTCAG
CTATATTTGTGTGTTTATTTTGTTCACTAAGCACTACTGTTCCAGTCTGTATTAATATTATTGT
CCAATATTTCATGAACATGTGTTAATGTAATGATCAGTTGCAACCATGCAACCTGAAGCATCAT
TAGCACAAAGGAACATCATTTCATAATAAACATGTGTGTATTAATTCCTTGTCCAGTCCACGAA
GGTGGGAGGGAGATTTGATGAGGATACAACTTATTTTACTTATGCTTCATTATTATTTTGGAGA
TGTATCTTGTTTAGGACAACTTGCACAGGATCTAAAATGAATAATATCCTGATTTTTTTTGGGG
GAGCTCTGTTTCAGCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGT
TGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAGGTTTGATATGCTCCA
TAGTTTTGATCTCAAGCTGTTTTGTTTTAATGTCCTGAATATGATGGCATATGTTCTTGTCCTA
TTACAGTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCAT
TCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGTACCATGACTTGGTGGTATGGTT
TTGAATCCCAGATTGGTTTATCAAGCTCTGAAGTTTTTTCCCACACTGAATTTTCCATATTCAG
AAGTCGTTGCATTGTTTGATCATGTGATTAATTGGTTACTGATCTATCTATATTTGTTAGAATT
AAGGGGGAATTCACCTTGCTGTTTGACATAGCTATCCTCCTATTTCACTATTGCAGCGTGCTGG
AGCTGCATTTCCAAAGAGATCTGATCGACCTGCACCATTGTTTAATGGCCAGTCTCCAGCAGGC
AGAAATATGCGTAGTCCTGATCAGCAGGATGAAGCTGAATCGTCTGCTGGAAATGATTTTCCTG
CTTTGAG
						
					

			
		

Sequences
Splice junction sequence	CATTGTTTAATGGCCAGTCTCCAGCAGGCAGAAATATGCGTAGTCCTGATCAGCAGGATGAAGC TGAATCGTCTGCTGGAAATGATTTTCCTGCTTTGAGgcaatcaaaagatgttgttaaggcactc aagaaaaggattgggcacaaaaatccaaaagtccaaattcttgcgctgactgtgagtttatcat aactttac
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: 435 Transcript exons: 7130944-7131022,7131470-7131568,7131654-7131767,7131960- 7132102 GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAA ATTCTTGCGCTGACTCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATG TTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAGTCTGATCAGAATGT CAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGA TATCCACAGTACTATGCAGCGTACCATGACTTGGTGCGTGCTGGAGCTGCATTTCCAAAGAGAT CTGATCGACCTGCACCATTGTTTAATGGCCAGTCTCCAGCAGGCAGAAATATGCGTAGTCCTGA TCAGCAGGATGAAGCTGAATCGTCTGCTGGAAATGATTTTCCTGCTTTGAG
Genomic sequence	GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAA ATTCTTGCGCTGACTGTGAGTTTATCATAACTTTACATCCTTTTTAAGAGTGGTGCTAATGGTA CAAGCAATGGGAAGAATCTCTTCTCTGTGTGTTTTAACATCAAGCATATATGTCTATTGCTCAG CTATATTTGTGTGTTTATTTTGTTCACTAAGCACTACTGTTCCAGTCTGTATTAATATTATTGT CCAATATTTCATGAACATGTGTTAATGTAATGATCAGTTGCAACCATGCAACCTGAAGCATCAT TAGCACAAAGGAACATCATTTCATAATAAACATGTGTGTATTAATTCCTTGTCCAGTCCACGAA GGTGGGAGGGAGATTTGATGAGGATACAACTTATTTTACTTATGCTTCATTATTATTTTGGAGA TGTATCTTGTTTAGGACAACTTGCACAGGATCTAAAATGAATAATATCCTGATTTTTTTTGGGG GAGCTCTGTTTCAGCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGT TGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAGGTTTGATATGCTCCA TAGTTTTGATCTCAAGCTGTTTTGTTTTAATGTCCTGAATATGATGGCATATGTTCTTGTCCTA TTACAGTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCAT TCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGTACCATGACTTGGTGGTATGGTT TTGAATCCCAGATTGGTTTATCAAGCTCTGAAGTTTTTTCCCACACTGAATTTTCCATATTCAG AAGTCGTTGCATTGTTTGATCATGTGATTAATTGGTTACTGATCTATCTATATTTGTTAGAATT AAGGGGGAATTCACCTTGCTGTTTGACATAGCTATCCTCCTATTTCACTATTGCAGCGTGCTGG AGCTGCATTTCCAAAGAGATCTGATCGACCTGCACCATTGTTTAATGGCCAGTCTCCAGCAGGC AGAAATATGCGTAGTCCTGATCAGCAGGATGAAGCTGAATCGTCTGCTGGAAATGATTTTCCTG CTTTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_011418 						
					
						PMCS
						0.241221995

Conservation Information
Conserved circRNAs	osi_circ_011418
PMCS	0.241221995

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7131513-7132099(+)
7131515-7132054(-)
						
						Potential amino acid sequence
						
							MHVAERDVLHEMVKIVKKKSDQNVKEKVLTMIDTWQEAFGGPRARYPQYYAAYHDLVRAGAAFP
KRSDRPAPLFNGQSPAGRNMRSPDQQDEAESSAGNDFPALRQSKDVVKALKKRIGHKNPKVQIL
ALTLLETAIKNCGDIFHMHVAERDVLHEMVKIVKKKSDQNVKEKVLTMIDTWQEAFGGPRARYP
QYYAAYHDLVRAGAAFPKRSDRPAPLFNGQSPAGRNMRSPDQQDEAESSAGNDFPALRQSKDVV
KALKKRIGHKNPKVQILALTLLETAIKNCGDIFHMHVAERDVLHEMVKIVKKKSDQNVKEKVLT
MIDTWQEAFGGPRARYPQYYAAYHDLVRAGAAFPKRSDRPAPLFNGQSPAGRNMRSPDQQDEAE
SSAGNDFPALRQSKDVVKALKKRIGHKNPKVQILALTLLETAIKNCGDIFHMHVAERDVLHEMV
KIVKKKSDQNVKEKVLTMIDTWQEAFGGPRARYPQYYAAYHDLVRAGAAFPKRSDRPAPLFNGQ
SPAGRNMRSPDQQDEAESSAGNDFPAL(+)
MWNISPQFLIAVSKRVSARIWTFGFLCPILFLSALTTSFDCLKAGKSFPADDSASSC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7131513-7132099(+) 7131515-7132054(-)
Potential amino acid sequence	MHVAERDVLHEMVKIVKKKSDQNVKEKVLTMIDTWQEAFGGPRARYPQYYAAYHDLVRAGAAFP KRSDRPAPLFNGQSPAGRNMRSPDQQDEAESSAGNDFPALRQSKDVVKALKKRIGHKNPKVQIL ALTLLETAIKNCGDIFHMHVAERDVLHEMVKIVKKKSDQNVKEKVLTMIDTWQEAFGGPRARYP QYYAAYHDLVRAGAAFPKRSDRPAPLFNGQSPAGRNMRSPDQQDEAESSAGNDFPALRQSKDVV KALKKRIGHKNPKVQILALTLLETAIKNCGDIFHMHVAERDVLHEMVKIVKKKSDQNVKEKVLT MIDTWQEAFGGPRARYPQYYAAYHDLVRAGAAFPKRSDRPAPLFNGQSPAGRNMRSPDQQDEAE SSAGNDFPALRQSKDVVKALKKRIGHKNPKVQILALTLLETAIKNCGDIFHMHVAERDVLHEMV KIVKKKSDQNVKEKVLTMIDTWQEAFGGPRARYPQYYAAYHDLVRAGAAFPKRSDRPAPLFNGQ SPAGRNMRSPDQQDEAESSAGNDFPAL(+) MWNISPQFLIAVSKRVSARIWTFGFLCPILFLSALTTSFDCLKAGKSFPADDSASSC*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0229250_circ_g.1

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