Plant Circular RNA Database

Detail information of Os03g0784700_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os03g0784700_circ_g.4
					
						ID in PlantcircBase
						osa_circ_022144
					
						Alias
						Os_ciR1770
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 32567195-32568038  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os03g0784700						
					
						Parent gene annotation
						
							Ferredoxin--NADP reductase, root isozyme, chloroplast precursor 
(EC 1.18.1.2) (FNR). (Os03t0784700-01);Ferredoxin--NADP reductas
e, root isozyme, chloroplast precursor (EC 1.18.1.2) (FNR). (Os0
3t0784700-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0784700_circ_g.1 Os03g0784700_circ_g.2 Os03g0784700_circ_g.3 Os03g0784700_circ_g.5 Os03g0784700_circ_g.6 Os03g0784700_circ_g.7 Os03g0784700_circ_g.8 Os03g0784700_circ_g.9 Os03g0784700_circ_g.10 						
					
						Support reads
						8/1
					
						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
						Os03t0784700-01:2
Os03t0784700-02:2

General Information
CircRNA Name	Os03g0784700_circ_g.4
ID in PlantcircBase	osa_circ_022144
Alias	Os_ciR1770
Organism	Oryza sativa
Position	chr3: 32567195-32568038 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os03g0784700
Parent gene annotation	Ferredoxin--NADP reductase, root isozyme, chloroplast precursor (EC 1.18.1.2) (FNR). (Os03t0784700-01);Ferredoxin--NADP reductas e, root isozyme, chloroplast precursor (EC 1.18.1.2) (FNR). (Os0 3t0784700-02)
Parent gene strand	-
Alternative splicing	Os03g0784700_circ_g.1 Os03g0784700_circ_g.2 Os03g0784700_circ_g.3 Os03g0784700_circ_g.5 Os03g0784700_circ_g.6 Os03g0784700_circ_g.7 Os03g0784700_circ_g.8 Os03g0784700_circ_g.9 Os03g0784700_circ_g.10
Support reads	8/1
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	Os03t0784700-01:2 Os03t0784700-02:2

			
						 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  
						
							AACTAGTGGTCCTTCCATCGAATGAATCTCCATACCTTGTAGATGCAATTGAATAAAGACGGAC
ATTATGTGGTGCACCAGGCTTCTTCGGGTTCTCCCCctgaaattgtctggatactgcttaaggt
agcttgtgaactcttcatcatagagaaggctgtcagtgttagccacaccaaggaagagccaggc
caagccac

						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: 461
Transcript exons: 32567195-32567435,32567819-32568038
CTGAAATTGTCTGGATACTGCTTAAGGTAGCTTGTGAACTCTTCATCATAGAGAAGGCTGTCAG
TGTTAGCCACACCAAGGAAGAGCCAGGCCAAGCCACCAAATCTGTACTTTGGGACATCTTCCAT
GAACATACGGCGTAGGTAGCCACGGAATGGAGCAACACCAGTGCCAGTAGCTATCATGATGTGA
GTTGCATTTGGATCTTCCTCAGGCAGGAGCATTATTTTGCCTGACGGACCTGTCACTTTAACCT
TGTCCCCTGGTTTTGAATTACATAGGAAGTTACTGCAGACACCATTTTTTGAGGGGTCCTCCTT
GCCAGTTTCAGGATCATAATAAACGGCACGGCGCACACATAAACTAGTGGTCCTTCCATCGAAT
GAATCTCCATACCTTGTAGATGCAATTGAATAAAGACGGACATTATGTGGTGCACCAGGCTTCT
TCGGGTTCTCCCC
						
						Genomic sequence
						
							CTGAAATTGTCTGGATACTGCTTAAGGTAGCTTGTGAACTCTTCATCATAGAGAAGGCTGTCAG
TGTTAGCCACACCAAGGAAGAGCCAGGCCAAGCCACCAAATCTGTACTTTGGGACATCTTCCAT
GAACATACGGCGTAGGTAGCCACGGAATGGAGCAACACCAGTGCCAGTAGCTATCATGATGTGA
GTTGCATTTGGATCTTCCTCAGGCAGGAGCATTATTTTGCCTGACGGACCTGGTGTTCAGAAGG
AAATCACTGTGAGATACTTGGCATCCATCATGTGCCACAAAGGACATGATGACTAACAAAGAAA
AGGGTAAACTAAGATGCGATTGCAAACTTTAGTAAGAAAGGAAAAGAGCAAGATAAGATAATCA
TATTGTAGAAGGGGCATAATCATATTAGAGGAGAGGCTATTGGAACCTTTGTTGCAGAGAACCG
TTTATTTGTTGTTGGTATGTATGAACTCAGAAATAGGTTGTCTACCAAAGGTGGGTTTCAGGAA
AAACGCAACTAAAACAACTAATTTTGCTCCGCTTGGAATTAGAAGTTAAACAACCTCATAGGAA
ACTCACAAAGCCTTTGCATTCATCTGAAGCTGAAAGAAATCAACTAACCTGTCACTTTAACCTT
GTCCCCTGGTTTTGAATTACATAGGAAGTTACTGCAGACACCATTTTTTGAGGGGTCCTCCTTG
CCAGTTTCAGGATCATAATAAACGGCACGGCGCACACATAAACTAGTGGTCCTTCCATCGAATG
AATCTCCATACCTTGTAGATGCAATTGAATAAAGACGGACATTATGTGGTGCACCAGGCTTCTT
CGGGTTCTCCCC

Sequences
Splice junction sequence	AACTAGTGGTCCTTCCATCGAATGAATCTCCATACCTTGTAGATGCAATTGAATAAAGACGGAC ATTATGTGGTGCACCAGGCTTCTTCGGGTTCTCCCCctgaaattgtctggatactgcttaaggt agcttgtgaactcttcatcatagagaaggctgtcagtgttagccacaccaaggaagagccaggc caagccac
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: 461 Transcript exons: 32567195-32567435,32567819-32568038 CTGAAATTGTCTGGATACTGCTTAAGGTAGCTTGTGAACTCTTCATCATAGAGAAGGCTGTCAG TGTTAGCCACACCAAGGAAGAGCCAGGCCAAGCCACCAAATCTGTACTTTGGGACATCTTCCAT GAACATACGGCGTAGGTAGCCACGGAATGGAGCAACACCAGTGCCAGTAGCTATCATGATGTGA GTTGCATTTGGATCTTCCTCAGGCAGGAGCATTATTTTGCCTGACGGACCTGTCACTTTAACCT TGTCCCCTGGTTTTGAATTACATAGGAAGTTACTGCAGACACCATTTTTTGAGGGGTCCTCCTT GCCAGTTTCAGGATCATAATAAACGGCACGGCGCACACATAAACTAGTGGTCCTTCCATCGAAT GAATCTCCATACCTTGTAGATGCAATTGAATAAAGACGGACATTATGTGGTGCACCAGGCTTCT TCGGGTTCTCCCC
Genomic sequence	CTGAAATTGTCTGGATACTGCTTAAGGTAGCTTGTGAACTCTTCATCATAGAGAAGGCTGTCAG TGTTAGCCACACCAAGGAAGAGCCAGGCCAAGCCACCAAATCTGTACTTTGGGACATCTTCCAT GAACATACGGCGTAGGTAGCCACGGAATGGAGCAACACCAGTGCCAGTAGCTATCATGATGTGA GTTGCATTTGGATCTTCCTCAGGCAGGAGCATTATTTTGCCTGACGGACCTGGTGTTCAGAAGG AAATCACTGTGAGATACTTGGCATCCATCATGTGCCACAAAGGACATGATGACTAACAAAGAAA AGGGTAAACTAAGATGCGATTGCAAACTTTAGTAAGAAAGGAAAAGAGCAAGATAAGATAATCA TATTGTAGAAGGGGCATAATCATATTAGAGGAGAGGCTATTGGAACCTTTGTTGCAGAGAACCG TTTATTTGTTGTTGGTATGTATGAACTCAGAAATAGGTTGTCTACCAAAGGTGGGTTTCAGGAA AAACGCAACTAAAACAACTAATTTTGCTCCGCTTGGAATTAGAAGTTAAACAACCTCATAGGAA ACTCACAAAGCCTTTGCATTCATCTGAAGCTGAAAGAAATCAACTAACCTGTCACTTTAACCTT GTCCCCTGGTTTTGAATTACATAGGAAGTTACTGCAGACACCATTTTTTGAGGGGTCCTCCTTG CCAGTTTCAGGATCATAATAAACGGCACGGCGCACACATAAACTAGTGGTCCTTCCATCGAATG AATCTCCATACCTTGTAGATGCAATTGAATAAAGACGGACATTATGTGGTGCACCAGGCTTCTT CGGGTTCTCCCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_013728 						
					
						PMCS
						0.309903752

Conservation Information
Conserved circRNAs	osi_circ_013728
PMCS	0.309903752

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							32567982-32567334(+)
32568007-32567221(+)
32567420-32567824(-)
32567317-32568006(-)
						
						Potential amino acid sequence
						
							MQLNKDGHYVVHQASSGSPPEIVWILLKVACELFIIEKAVSVSHTKEEPGQATKSVLWDIFHEH
TA*(+)
MWCTRLLRVLPLKLSGYCLR*(+)
MLLPEEDPNATHIMIATGTGVAPFRGYLRRMFMEDVPKYRFGGLAWLFLGVANTDSLLYDEEFT
SYLKQYPDNFRGRTRRSLVHHIMSVFIQLHLQGMEIHSMEGPLVYVCAVPFIMILKLARRTPQK
MVSAVTSYVIQNQGTRLK*(-)
MSQSTDLVAWPGSSLVWLTLTAFSMMKSSQATLSSIQTISGGEPEEAWCTT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	32567982-32567334(+) 32568007-32567221(+) 32567420-32567824(-) 32567317-32568006(-)
Potential amino acid sequence	MQLNKDGHYVVHQASSGSPPEIVWILLKVACELFIIEKAVSVSHTKEEPGQATKSVLWDIFHEH TA(+) MWCTRLLRVLPLKLSGYCLR(+) MLLPEEDPNATHIMIATGTGVAPFRGYLRRMFMEDVPKYRFGGLAWLFLGVANTDSLLYDEEFT SYLKQYPDNFRGRTRRSLVHHIMSVFIQLHLQGMEIHSMEGPLVYVCAVPFIMILKLARRTPQK MVSAVTSYVIQNQGTRLK(-) MSQSTDLVAWPGSSLVWLTLTAFSMMKSSQATLSSIQTISGGEPEEAWCTT(-)
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 Os03g0784700_circ_g.4

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