Plant Circular RNA Database

Detail information of Os01g0588900_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os01g0588900_circ_g.4
					
						ID in PlantcircBase
						osa_circ_002388
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 22956507-22958330  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							Os01g0588900						
					
						Parent gene annotation
						
							Cytokinin-activating enzyme, Bioactive cytokinin synthesis (Os01
t0588900-01);Similar to carboxy-lyase. (Os01t0588900-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0588900_circ_g.5 Os01g0588900_circ_g.6 Os01g0588900_circ_g.7 Os01g0588900_circ_g.8 Os01g0588900_circ_g.9 Os01g0588900_circ_g.10 Os01g0588900_circ_g.11 Os01g0588900_circ_g.12 						
					
						Support reads
						2
					
						Tissues
						shoot, 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
						Os01t0588900-01:4
Os01t0588900-02:1

General Information
CircRNA Name	Os01g0588900_circ_g.4
ID in PlantcircBase	osa_circ_002388
Alias	NA
Organism	Oryza sativa
Position	chr1: 22956507-22958330 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	Os01g0588900
Parent gene annotation	Cytokinin-activating enzyme, Bioactive cytokinin synthesis (Os01 t0588900-01);Similar to carboxy-lyase. (Os01t0588900-02)
Parent gene strand	-
Alternative splicing	Os01g0588900_circ_g.5 Os01g0588900_circ_g.6 Os01g0588900_circ_g.7 Os01g0588900_circ_g.8 Os01g0588900_circ_g.9 Os01g0588900_circ_g.10 Os01g0588900_circ_g.11 Os01g0588900_circ_g.12
Support reads	2
Tissues	shoot, 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	Os01t0588900-01:4 Os01t0588900-02:1

			
						 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  
						
							ACCCAATGACATGGCGACCACCGTCGTGAACAGCGTGGGAGACGAGGCCCATGAGGCCGATGGA
GCCACCGCCGTAGACCAGGTCTATGCCCCTCTCGACcggcttcttgtggattcctagttgggcc
caggtgatgacctcaagcaactcctcaagagtcccgtagccgcctgtcgcgcaaattaagagtg
tcaaattt

									
								

					

						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: 300
Transcript exons: 22956507-22956577,22956679-22956778,22957573-22957603,22
958233-22958330
CGGCTTCTTGTGGATTCCTAGTTGGGCCCAGGTGATGACCTCAAGCAACTCCTCAAGAGTCCCG
TAGCCGCCAGGCAGTGCAATGAACGCATCAGCAAACCGGGCCATTTCAGCCTTCCTCTCGTGCA
TGCCAGAGACCGCTCTAACTTCACCAACAGGCTCACCAGTGACCTCTCTGGGCATCAAGGATTT
CGGGATGACCCCAATGACATGGCGACCACCGTCGTGAACAGCGTGGGAGACGAGGCCCATGAGG
CCGATGGAGCCACCGCCGTAGACCAGGTCTATGCCCCTCTCGAC
						
					

						Genomic sequence
						
							CGGCTTCTTGTGGATTCCTAGTTGGGCCCAGGTGATGACCTCAAGCAACTCCTCAAGAGTCCCG
TAGCCGCCTGTCGCGCAAATTAAGAGTGTCAAATTTTGCATCCTTAGGATGCAGCATCAAAAAA
AATTCACTGCAAACGACGTCGTAGTAGCAACTAAATTATCATACCAGGCAGTGCAATGAACGCA
TCAGCAAACCGGGCCATTTCAGCCTTCCTCTCGTGCATGCCAGAGACCGCTCTAACTTCACCAA
CAGGCTCACCAGTGACCTGCAAACGAAAAACCAGTATATATTGAGGATCCGGCACACATCACAC
TTGTTTCTCTTTCAGAATCATGTTAATAAGCTCATCATCCTAGTAGAAAAATATTTAAAAACCT
TTTTTAGTGAAACTAGCAATGCAAAAGTCCATAGAAATACATGGCTGACAACATTCGGATGCAA
ACTACGGCACACAGAGTTGTTCAGCGTGAGATCATCATCGACATTAGAATACACAGGAAATACA
AGTTCTACGTACGTAATGCAGTGGTCAAAGACCACGACAATCAAGAAAGTCCCATTTTTAAGAC
ATTGTACTACCGAATGAGTACTAGTACAAGTAGAGATACGTACAAGAAGAGTAAATAATCCCAG
TTACTGCACTTACTACTACGTGCAAGCCCCAGTAAATTATCCGAAGGCAAGGCAAATGCGATGG
CACATCCTAGACAGCTACTATAGCTCAAAATCCATTTAAGAGCAGCACGCAATGCTGTTGGATA
GGCGCATTAGATTCATGTGATGAGCATAAATGCATCATGTCCCCCCAATAAGCACTAGCAGCAT
GCCAACTTGGTTCTTTATTGCAACTCCTATTTTTCAGCTGCGCACAGCAGCAGCAGCAGCAGCA
GAAGCCAGCAGGGAGAGGAATTGAAAGCATTCATCAATTTCGCCCCGAACAAAATGGAGCAGCA
CGGCCACATTAAAAACAGCAATCAAGATTATATCTATCTCTATCGATCGAGCTTGTGTAATAGC
AGTAGTACTACTCCTACTAGCTTCCAGGAGTAGACAGCTCACCTCTCTGGGCATCAAGGATTTC
GGGATGACCCTGCCAAGAACACAAAGAGAGAGGAAACAGAAAAGCACATCAGTTTTTAGCACAA
AAGCGGTCAAACAGGTGTAGTAAGAACAAGCAGGCTTGCTTTCTCTCCCTTGGTAAAGAGACTG
GCAAAGCCAAGGCCCAGGCTATTGCACAGGCAGCACAGCTACACCACACTAGCAATACAGATAG
ATAGAGAGAGAGAGGGAGCTGGACCAAATAAACACTGCACAATAATGAGAGCAAAGAAGAGAAG
AGCACTAGTACTAGCAAGCTAGCAGCAGCAGCAGCAGCAGCAGATTGCAGGAGCTGAGCTATGC
AGGAGCAGGCCAAGTGAAGTTGGAGTGTGCTGCTGCACAAACAACAATTCAAGCATGCAGGCGA
GTAGCCTTTCGGAAACGGAGGCGAAAAGGCCCCAGATGCATTCAAAATGCCCCCCCCCCCCCCA
CACTGAGACCCAAGAAAGAGAGACGAAAATGGGCAGGGACTCAGCACCTACTACTCCTCCTACC
CCCAATCTGGCGATCAAAAGCTGCCGTTTTTATCATCCCAGCGACGCATGCATTCTCACACATC
TCACCTGGCAAGCAACCAGAGAAAGATAGAGAGAGAGAGAGATGGACAAATGGATCACTCACCC
AATGACATGGCGACCACCGTCGTGAACAGCGTGGGAGACGAGGCCCATGAGGCCGATGGAGCCA
CCGCCGTAGACCAGGTCTATGCCCCTCTCGAC
						
					

			
		

Sequences
Splice junction sequence	ACCCAATGACATGGCGACCACCGTCGTGAACAGCGTGGGAGACGAGGCCCATGAGGCCGATGGA GCCACCGCCGTAGACCAGGTCTATGCCCCTCTCGACcggcttcttgtggattcctagttgggcc caggtgatgacctcaagcaactcctcaagagtcccgtagccgcctgtcgcgcaaattaagagtg tcaaattt
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: 300 Transcript exons: 22956507-22956577,22956679-22956778,22957573-22957603,22 958233-22958330 CGGCTTCTTGTGGATTCCTAGTTGGGCCCAGGTGATGACCTCAAGCAACTCCTCAAGAGTCCCG TAGCCGCCAGGCAGTGCAATGAACGCATCAGCAAACCGGGCCATTTCAGCCTTCCTCTCGTGCA TGCCAGAGACCGCTCTAACTTCACCAACAGGCTCACCAGTGACCTCTCTGGGCATCAAGGATTT CGGGATGACCCCAATGACATGGCGACCACCGTCGTGAACAGCGTGGGAGACGAGGCCCATGAGG CCGATGGAGCCACCGCCGTAGACCAGGTCTATGCCCCTCTCGAC
Genomic sequence	CGGCTTCTTGTGGATTCCTAGTTGGGCCCAGGTGATGACCTCAAGCAACTCCTCAAGAGTCCCG TAGCCGCCTGTCGCGCAAATTAAGAGTGTCAAATTTTGCATCCTTAGGATGCAGCATCAAAAAA AATTCACTGCAAACGACGTCGTAGTAGCAACTAAATTATCATACCAGGCAGTGCAATGAACGCA TCAGCAAACCGGGCCATTTCAGCCTTCCTCTCGTGCATGCCAGAGACCGCTCTAACTTCACCAA CAGGCTCACCAGTGACCTGCAAACGAAAAACCAGTATATATTGAGGATCCGGCACACATCACAC TTGTTTCTCTTTCAGAATCATGTTAATAAGCTCATCATCCTAGTAGAAAAATATTTAAAAACCT TTTTTAGTGAAACTAGCAATGCAAAAGTCCATAGAAATACATGGCTGACAACATTCGGATGCAA ACTACGGCACACAGAGTTGTTCAGCGTGAGATCATCATCGACATTAGAATACACAGGAAATACA AGTTCTACGTACGTAATGCAGTGGTCAAAGACCACGACAATCAAGAAAGTCCCATTTTTAAGAC ATTGTACTACCGAATGAGTACTAGTACAAGTAGAGATACGTACAAGAAGAGTAAATAATCCCAG TTACTGCACTTACTACTACGTGCAAGCCCCAGTAAATTATCCGAAGGCAAGGCAAATGCGATGG CACATCCTAGACAGCTACTATAGCTCAAAATCCATTTAAGAGCAGCACGCAATGCTGTTGGATA GGCGCATTAGATTCATGTGATGAGCATAAATGCATCATGTCCCCCCAATAAGCACTAGCAGCAT GCCAACTTGGTTCTTTATTGCAACTCCTATTTTTCAGCTGCGCACAGCAGCAGCAGCAGCAGCA GAAGCCAGCAGGGAGAGGAATTGAAAGCATTCATCAATTTCGCCCCGAACAAAATGGAGCAGCA CGGCCACATTAAAAACAGCAATCAAGATTATATCTATCTCTATCGATCGAGCTTGTGTAATAGC AGTAGTACTACTCCTACTAGCTTCCAGGAGTAGACAGCTCACCTCTCTGGGCATCAAGGATTTC GGGATGACCCTGCCAAGAACACAAAGAGAGAGGAAACAGAAAAGCACATCAGTTTTTAGCACAA AAGCGGTCAAACAGGTGTAGTAAGAACAAGCAGGCTTGCTTTCTCTCCCTTGGTAAAGAGACTG GCAAAGCCAAGGCCCAGGCTATTGCACAGGCAGCACAGCTACACCACACTAGCAATACAGATAG ATAGAGAGAGAGAGGGAGCTGGACCAAATAAACACTGCACAATAATGAGAGCAAAGAAGAGAAG AGCACTAGTACTAGCAAGCTAGCAGCAGCAGCAGCAGCAGCAGATTGCAGGAGCTGAGCTATGC AGGAGCAGGCCAAGTGAAGTTGGAGTGTGCTGCTGCACAAACAACAATTCAAGCATGCAGGCGA GTAGCCTTTCGGAAACGGAGGCGAAAAGGCCCCAGATGCATTCAAAATGCCCCCCCCCCCCCCA CACTGAGACCCAAGAAAGAGAGACGAAAATGGGCAGGGACTCAGCACCTACTACTCCTCCTACC CCCAATCTGGCGATCAAAAGCTGCCGTTTTTATCATCCCAGCGACGCATGCATTCTCACACATC TCACCTGGCAAGCAACCAGAGAAAGATAGAGAGAGAGAGAGATGGACAAATGGATCACTCACCC AATGACATGGCGACCACCGTCGTGAACAGCGTGGGAGACGAGGCCCATGAGGCCGATGGAGCCA CCGCCGTAGACCAGGTCTATGCCCCTCTCGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_010229 						
					
						PMCS
						0.218742992

Conservation Information
Conserved circRNAs	osi_circ_010229
PMCS	0.218742992

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							22958242-22956524(+)
22958318-22956570(+)
22958284-22956509(-)
						
						Potential amino acid sequence
						
							MATTVVNSVGDEAHEADGATAVDQVYAPLDRLLVDS*(+)
MPLSTGFLWIPSWAQVMTSSNSSRVP*(+)
MGLVSHAVHDGGRHVIGVIPKSLMPREVTGEPVGEVRAVSGMHERKAEMARFADAFIALPGGYG
TLEELLEVITWAQLGIHKKPVERGIDLVYGGGSIGLMGLVSHAVHDGGRHVIGVIPKSLMPREV
TGEPVGEVRAVSGMHERKAEMARFADAFIALPGGYGTLEELLEVITWAQLGIHKKPVERGIDLV
YGGGSIGLMGLVSHAVHDGGRHVIGVIPKSLMPREVTGEPVGEVRAVSGMHERKAEMARFADAF
IALPGGYGTLEELLEVITWAQLGIHKKPVERGIDLVYGGGSIGLMGLVSHAVHDGGRHVIGVIP
KSLMPREVTGEPVGEVRAVSGMHERKAEMARFADAFIALPGGYGTLEELLEVITWAQLGIHKKP
(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	22958242-22956524(+) 22958318-22956570(+) 22958284-22956509(-)
Potential amino acid sequence	MATTVVNSVGDEAHEADGATAVDQVYAPLDRLLVDS(+) MPLSTGFLWIPSWAQVMTSSNSSRVP(+) MGLVSHAVHDGGRHVIGVIPKSLMPREVTGEPVGEVRAVSGMHERKAEMARFADAFIALPGGYG TLEELLEVITWAQLGIHKKPVERGIDLVYGGGSIGLMGLVSHAVHDGGRHVIGVIPKSLMPREV TGEPVGEVRAVSGMHERKAEMARFADAFIALPGGYGTLEELLEVITWAQLGIHKKPVERGIDLV YGGGSIGLMGLVSHAVHDGGRHVIGVIPKSLMPREVTGEPVGEVRAVSGMHERKAEMARFADAF IALPGGYGTLEELLEVITWAQLGIHKKPVERGIDLVYGGGSIGLMGLVSHAVHDGGRHVIGVIP KSLMPREVTGEPVGEVRAVSGMHERKAEMARFADAFIALPGGYGTLEELLEVITWAQLGIHKKP (-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0588900_circ_g.4

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