Plant Circular RNA Database

Detail information of Os04g0252200_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0252200_circ_g.3
					
						ID in PlantcircBase
						osa_circ_023188
					
						Alias
						Os04circ01744/Os_ciR726
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 9898548-9900259  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, find_circ
					
						Parent gene
						
							Os04g0252200						
					
						Parent gene annotation
						
							Similar to CPSF160; nucleic acid binding. (Os04t0252200-01);Simi
lar to CPSF160; nucleic acid binding. (Os04t0252200-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0252200_circ_g.1 Os04g0252200_circ_g.2 Os04g0252200_circ_g.4 Os04g0252200_circ_g.5 Os04g0252200_circ_g.6 Os04g0252200_circ_g.7 Os04g0252200_circ_g.8 Os04g0252200_circ_g.9 Os04g0252200_circ_g.10 Os04g0252200_circ_g.11 Os04g0252200_circ_g.12 Os04g0252200_circ_g.13 Os04g0252200_circ_g.14 Os04g0252200_circ_g.15 Os04g0252200_circ_g.16 Os04g0252200_circ_g.17 Os04g0252200_circ_g.18 						
					
						Support reads
						7/39/5
					
						Tissues
						leaf and panicle/root/shoot, root, seed, pistil
					
						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
						Os04t0252200-02:4

General Information
CircRNA Name	Os04g0252200_circ_g.3
ID in PlantcircBase	osa_circ_023188
Alias	Os04circ01744/Os_ciR726
Organism	Oryza sativa
Position	chr4: 9898548-9900259 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, find_circ
Parent gene	Os04g0252200
Parent gene annotation	Similar to CPSF160; nucleic acid binding. (Os04t0252200-01);Simi lar to CPSF160; nucleic acid binding. (Os04t0252200-02)
Parent gene strand	-
Alternative splicing	Os04g0252200_circ_g.1 Os04g0252200_circ_g.2 Os04g0252200_circ_g.4 Os04g0252200_circ_g.5 Os04g0252200_circ_g.6 Os04g0252200_circ_g.7 Os04g0252200_circ_g.8 Os04g0252200_circ_g.9 Os04g0252200_circ_g.10 Os04g0252200_circ_g.11 Os04g0252200_circ_g.12 Os04g0252200_circ_g.13 Os04g0252200_circ_g.14 Os04g0252200_circ_g.15 Os04g0252200_circ_g.16 Os04g0252200_circ_g.17 Os04g0252200_circ_g.18
Support reads	7/39/5
Tissues	leaf and panicle/root/shoot, root, seed, pistil
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	Os04t0252200-02:4

			
						 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  
						
							AATAACATATACTAATACTTACAGGAACAGACACTATTAGGGGATAAAGAGATTGCTCTGCATA
ATACGTGACCTGATGTGGGGTGCCATGCAAAGGGACaatgttcaggctcacaacatgcaaaggg
gcatcatagaatgcaacagcagtcaattcagcaccagtccacttgtttaatgtgatcttaggac
cagaagct

									
								

					

						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: 222
Transcript exons: 9898548-9898707,9900198-9900259
AATGTTCAGGCTCACAACATGCAAAGGGGCATCATAGAATGCAACAGCAGTCAATTCAGCACCA
GTCCACTTGTTTAATGTGATCTTAGGACCAGAAGCTATCAGCAGATGACCTTGAAGAGACGCAA
CAGCTGATACAGCACCTTTACTCTCTTTTGAGAGGGGATAAAGAGATTGCTCTGCATAATACGT
GACCTGATGTGGGGTGCCATGCAAAGGGAC
Transcript length: 354
Transcript exons: 9898548-9898697,9898820-9898945,9900182-9900259
AATGTTCAGGCTCACAACATGCAAAGGGGCATCATAGAATGCAACAGCAGTCAATTCAGCACCA
GTCCACTTGTTTAATGTGATCTTAGGACCAGAAGCTATCAGCAGATGACCTTGAAGAGACGCAA
CAGCTGATACAGCACCTTTACTTTGAGAATTTTCACTTTTCGTGAAAGAGAACAGAAGCACACG
TCCTCTAGCAGCTACATCCTCCCCAAGAACATAAGCAGTCCCAATGGCCAACAGGGTCTCATTT
TCCTTGGTGGTTGTATTCTGAGGAACAGACACTATTAGGGGATAAAGAGATTGCTCTGCATAAT
ACGTGACCTGATGTGGGGTGCCATGCAAAGGGAC
Transcript length: 608
Transcript exons: 9898548-9898721,9898814-9898942,9899309-9899535,9900182-
9900259
AATGTTCAGGCTCACAACATGCAAAGGGGCATCATAGAATGCAACAGCAGTCAATTCAGCACCA
GTCCACTTGTTTAATGTGATCTTAGGACCAGAAGCTATCAGCAGATGACCTTGAAGAGACGCAA
CAGCTGATACAGCACCTTTACTCTCTTTTGAGTAGACTTCAGTGACCAGATTTTGAGAATTTTC
ACTTTTCGTGAAAGAGAACAGAAGCACACGTCCTCTAGCAGCTACATCCTCCCCAAGAACATAA
GCAGTCCCAATGGCCAACAGGGTCTCATTTTCCTTGGTGGTTGTATTATGTAATGTAACAATGC
GCACGGTTAGAGCATTTTCAAACAATTGCATTGGAATTGTGGACTTCGTCTCCCAATGTCCACC
AGGTTTCTCCAGCTCCAAAATGCGGACCTCAAATTCATCAACAGTATATGTCTTATGAAGGGCA
TCAGTGCTTGTAACATCGTTATCCATGTGATGAACTGATTCTTGATCAGCCATAGAAGAAAGAA
CTTGATTTAGGGGACGAAAGGAACAGACACTATTAGGGGATAAAGAGATTGCTCTGCATAATAC
GTGACCTGATGTGGGGTGCCATGCAAAGGGAC
						
					

						Genomic sequence
						
							AATGTTCAGGCTCACAACATGCAAAGGGGCATCATAGAATGCAACAGCAGTCAATTCAGCACCA
GTCCACTTGTTTAATGTGATCTTAGGACCAGAAGCTATCAGCAGATGACCTTGAAGAGACGCAA
CAGCTGATACAGCACCTTTACTCTCTTTTGAGTAGACTTCAGTGACCTGCAATTAGTGTTTACA
TGTTATCAAATCAATCGATACGTAACGGAAGTAATAACCTTTTTCCCAATTGCAATAATGCTCC
CTCACAGTACCAGATTTTGAGAATTTTCACTTTTCGTGAAAGAGAACAGAAGCACACGTCCTCT
AGCAGCTACATCCTCCCCAAGAACATAAGCAGTCCCAATGGCCAACAGGGTCTCATTTTCCTTG
GTGGTTGTATTCTGAAGTAAAAATGCATAACTGTTCAGTGAATAATATAATTAAACCTACAGAC
ATGTGTACCTTTGATCATTAAATTTTCAAACAAGATAAATCTCAAGCATAGAAATGACATGGCA
ACCATGCATTTGGAAGAAAAGAAGATAGAAAAAGGAAGTAATGATGACTTTATTATAGCTGACA
GTTTATGCTAACAGCTCCATAATTGAATTATAAAGGGTCAAATATAGAGTATAGAGGGCATTTA
GTTTGCAAAAATGTGCTTGTGGGTTGCTAAAATATGGTGTCTTCAACCAGACAGGTTCACTTGG
TTTGTCACAGAAGTTCATATAGTTTGGTTTCAAGTGGGAATGAGAAAAGACGCATACATGTAAT
GTAACAATGCGCACGGTTAGAGCATTTTCAAACAATTGCATTGGAATTGTGGACTTCGTCTCCC
AATGTCCACCAGGTTTCTCCAGCTCCAAAATGCGGACCTCAAATTCATCAACAGTATATGTCTT
ATGAAGGGCATCAGTGCTTGTAACATCGTTATCCATGTGATGAACTGATTCTTGATCAGCCATA
GAAGAAAGAACTTGATTTAGGGGACGAACTACCTGCAGGACCAAAATGAGAATATTGTACTAGA
TAGTTGTACATAGGAAGAAGTCCAAATACCCTGAACTTTATAACTGGACATCCAACCCCCCCCC
CCCCCCCCCGTCCCCCAAAAAAAAAAAAAAAAAAAAAACTTTGCAATACCATTCGTATTACCCC
CTAGGGTAGTTTGCACATTTGGAAGCTTAAATGAGCAGCTTTGAATAACTGATACAACATATTT
ACATATCATTAATAGTAGGTCATAAATTTCTTCTTACATAGTGATGTGACACTTTCACAATGTT
GTTGCAGCGAATAAGGGAGTGAAAAAAAAGTTTTGCATGGAGATTTTTAACATATATATGTCTA
ATACGTATGTCATGTGATCAAACTCATCCAACATACATGCAAATTAGATGAAAAACCACTTTGC
AAAATCACCTTAGGGGGTTGTATAAACTGTATTGTTTAGTTTGGGGGTTTGAACGTCCGGTTTT
AAAGTTCAATATGCTAGATGGACTCTCAATCAAAGTTTAGGTGGCGGAGGGTGTTATTTGGACT
TTATGTGTTGAACATATTCGAAAATGCCTCAAAAACATAATTAGATGCCAATGATAAATTATGT
TAGAATTGCAGTAATAACATATACTAATACTTACAGGAACAGACACTATTAGGGGATAAAGAGA
TTGCTCTGCATAATACGTGACCTGATGTGGGGTGCCATGCAAAGGGAC
						
					

			
		

Sequences
Splice junction sequence	AATAACATATACTAATACTTACAGGAACAGACACTATTAGGGGATAAAGAGATTGCTCTGCATA ATACGTGACCTGATGTGGGGTGCCATGCAAAGGGACaatgttcaggctcacaacatgcaaaggg gcatcatagaatgcaacagcagtcaattcagcaccagtccacttgtttaatgtgatcttaggac cagaagct
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: 222 Transcript exons: 9898548-9898707,9900198-9900259 AATGTTCAGGCTCACAACATGCAAAGGGGCATCATAGAATGCAACAGCAGTCAATTCAGCACCA GTCCACTTGTTTAATGTGATCTTAGGACCAGAAGCTATCAGCAGATGACCTTGAAGAGACGCAA CAGCTGATACAGCACCTTTACTCTCTTTTGAGAGGGGATAAAGAGATTGCTCTGCATAATACGT GACCTGATGTGGGGTGCCATGCAAAGGGAC Transcript length: 354 Transcript exons: 9898548-9898697,9898820-9898945,9900182-9900259 AATGTTCAGGCTCACAACATGCAAAGGGGCATCATAGAATGCAACAGCAGTCAATTCAGCACCA GTCCACTTGTTTAATGTGATCTTAGGACCAGAAGCTATCAGCAGATGACCTTGAAGAGACGCAA CAGCTGATACAGCACCTTTACTTTGAGAATTTTCACTTTTCGTGAAAGAGAACAGAAGCACACG TCCTCTAGCAGCTACATCCTCCCCAAGAACATAAGCAGTCCCAATGGCCAACAGGGTCTCATTT TCCTTGGTGGTTGTATTCTGAGGAACAGACACTATTAGGGGATAAAGAGATTGCTCTGCATAAT ACGTGACCTGATGTGGGGTGCCATGCAAAGGGAC Transcript length: 608 Transcript exons: 9898548-9898721,9898814-9898942,9899309-9899535,9900182- 9900259 AATGTTCAGGCTCACAACATGCAAAGGGGCATCATAGAATGCAACAGCAGTCAATTCAGCACCA GTCCACTTGTTTAATGTGATCTTAGGACCAGAAGCTATCAGCAGATGACCTTGAAGAGACGCAA CAGCTGATACAGCACCTTTACTCTCTTTTGAGTAGACTTCAGTGACCAGATTTTGAGAATTTTC ACTTTTCGTGAAAGAGAACAGAAGCACACGTCCTCTAGCAGCTACATCCTCCCCAAGAACATAA GCAGTCCCAATGGCCAACAGGGTCTCATTTTCCTTGGTGGTTGTATTATGTAATGTAACAATGC GCACGGTTAGAGCATTTTCAAACAATTGCATTGGAATTGTGGACTTCGTCTCCCAATGTCCACC AGGTTTCTCCAGCTCCAAAATGCGGACCTCAAATTCATCAACAGTATATGTCTTATGAAGGGCA TCAGTGCTTGTAACATCGTTATCCATGTGATGAACTGATTCTTGATCAGCCATAGAAGAAAGAA CTTGATTTAGGGGACGAAAGGAACAGACACTATTAGGGGATAAAGAGATTGCTCTGCATAATAC GTGACCTGATGTGGGGTGCCATGCAAAGGGAC
Genomic sequence	AATGTTCAGGCTCACAACATGCAAAGGGGCATCATAGAATGCAACAGCAGTCAATTCAGCACCA GTCCACTTGTTTAATGTGATCTTAGGACCAGAAGCTATCAGCAGATGACCTTGAAGAGACGCAA CAGCTGATACAGCACCTTTACTCTCTTTTGAGTAGACTTCAGTGACCTGCAATTAGTGTTTACA TGTTATCAAATCAATCGATACGTAACGGAAGTAATAACCTTTTTCCCAATTGCAATAATGCTCC CTCACAGTACCAGATTTTGAGAATTTTCACTTTTCGTGAAAGAGAACAGAAGCACACGTCCTCT AGCAGCTACATCCTCCCCAAGAACATAAGCAGTCCCAATGGCCAACAGGGTCTCATTTTCCTTG GTGGTTGTATTCTGAAGTAAAAATGCATAACTGTTCAGTGAATAATATAATTAAACCTACAGAC ATGTGTACCTTTGATCATTAAATTTTCAAACAAGATAAATCTCAAGCATAGAAATGACATGGCA ACCATGCATTTGGAAGAAAAGAAGATAGAAAAAGGAAGTAATGATGACTTTATTATAGCTGACA GTTTATGCTAACAGCTCCATAATTGAATTATAAAGGGTCAAATATAGAGTATAGAGGGCATTTA GTTTGCAAAAATGTGCTTGTGGGTTGCTAAAATATGGTGTCTTCAACCAGACAGGTTCACTTGG TTTGTCACAGAAGTTCATATAGTTTGGTTTCAAGTGGGAATGAGAAAAGACGCATACATGTAAT GTAACAATGCGCACGGTTAGAGCATTTTCAAACAATTGCATTGGAATTGTGGACTTCGTCTCCC AATGTCCACCAGGTTTCTCCAGCTCCAAAATGCGGACCTCAAATTCATCAACAGTATATGTCTT ATGAAGGGCATCAGTGCTTGTAACATCGTTATCCATGTGATGAACTGATTCTTGATCAGCCATA GAAGAAAGAACTTGATTTAGGGGACGAACTACCTGCAGGACCAAAATGAGAATATTGTACTAGA TAGTTGTACATAGGAAGAAGTCCAAATACCCTGAACTTTATAACTGGACATCCAACCCCCCCCC CCCCCCCCCGTCCCCCAAAAAAAAAAAAAAAAAAAAAACTTTGCAATACCATTCGTATTACCCC CTAGGGTAGTTTGCACATTTGGAAGCTTAAATGAGCAGCTTTGAATAACTGATACAACATATTT ACATATCATTAATAGTAGGTCATAAATTTCTTCTTACATAGTGATGTGACACTTTCACAATGTT GTTGCAGCGAATAAGGGAGTGAAAAAAAAGTTTTGCATGGAGATTTTTAACATATATATGTCTA ATACGTATGTCATGTGATCAAACTCATCCAACATACATGCAAATTAGATGAAAAACCACTTTGC AAAATCACCTTAGGGGGTTGTATAAACTGTATTGTTTAGTTTGGGGGTTTGAACGTCCGGTTTT AAAGTTCAATATGCTAGATGGACTCTCAATCAAAGTTTAGGTGGCGGAGGGTGTTATTTGGACT TTATGTGTTGAACATATTCGAAAATGCCTCAAAAACATAATTAGATGCCAATGATAAATTATGT TAGAATTGCAGTAATAACATATACTAATACTTACAGGAACAGACACTATTAGGGGATAAAGAGA TTGCTCTGCATAATACGTGACCTGATGTGGGGTGCCATGCAAAGGGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005337* osi_circ_015133 						
					
						PMCS
						0.383567197

Conservation Information
Conserved circRNAs	osi_circ_005337* osi_circ_015133
PMCS	0.383567197

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9900237-9898622(+)
9899508-9899526(-)
						
						Potential amino acid sequence
						
							MWGAMQRDNVQAHNMQRGIIECNSSQFSTSPLV*(+)
MADQESVHHMDNDVTSTDALHKTYTVDEFEVRILELEKPGGHWETKSTIPMQLFENALTVRIVT
LHNTTTKENETLLAIGTAYVLGEDVAARGRVLLFSFTKSENSQNLVTEVYSKESKGAVSAVASL
QGHLLIASGPKITLNKWTGAELTAVAFYDAPLHVVSLNIVPLHGTPHQVTYYAEQSLYPLIVSV
PFVP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9900237-9898622(+) 9899508-9899526(-)
Potential amino acid sequence	MWGAMQRDNVQAHNMQRGIIECNSSQFSTSPLV(+) MADQESVHHMDNDVTSTDALHKTYTVDEFEVRILELEKPGGHWETKSTIPMQLFENALTVRIVT LHNTTTKENETLLAIGTAYVLGEDVAARGRVLLFSFTKSENSQNLVTEVYSKESKGAVSAVASL QGHLLIASGPKITLNKWTGAELTAVAFYDAPLHVVSLNIVPLHGTPHQVTYYAEQSLYPLIVSV PFVP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os04g0252200_circ_g.3

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