Plant Circular RNA Database

Detail information of Os03g0136900_circ_g.10

			
						 General Information
					
						CircRNA Name
						Os03g0136900_circ_g.10
					
						ID in PlantcircBase
						osa_circ_017823
					
						Alias
						Os_ciR1646
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 2031824-2033098  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ
					
						Parent gene
						
							Os03g0136900						
					
						Parent gene annotation
						
							Similar to Aconitate hydratase, cytoplasmic (EC 4.2.1.3) (Citrat
e hydro-lyase) (Aconitase). (Os03t0136900-01);Similar to Aconita
te hydratase 2, mitochondrial. (Os03t0136900-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0136900_circ_g.5 Os03g0136900_circ_g.6 Os03g0136900_circ_g.7 Os03g0136900_circ_g.8 Os03g0136900_circ_g.9 Os03g0136900_circ_g.11 Os03g0136900_circ_g.12 Os03g0136900_circ_g.13 						
					
						Support reads
						7/3
					
						Tissues
						root/root, anther
					
						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
						Os03t0136900-01:3

General Information
CircRNA Name	Os03g0136900_circ_g.10
ID in PlantcircBase	osa_circ_017823
Alias	Os_ciR1646
Organism	Oryza sativa
Position	chr3: 2031824-2033098 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ
Parent gene	Os03g0136900
Parent gene annotation	Similar to Aconitate hydratase, cytoplasmic (EC 4.2.1.3) (Citrat e hydro-lyase) (Aconitase). (Os03t0136900-01);Similar to Aconita te hydratase 2, mitochondrial. (Os03t0136900-02)
Parent gene strand	-
Alternative splicing	Os03g0136900_circ_g.5 Os03g0136900_circ_g.6 Os03g0136900_circ_g.7 Os03g0136900_circ_g.8 Os03g0136900_circ_g.9 Os03g0136900_circ_g.11 Os03g0136900_circ_g.12 Os03g0136900_circ_g.13
Support reads	7/3
Tissues	root/root, anther
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	Os03t0136900-01:3

			
						 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  
						
							GGATCGGATAGCGCGGGCAGGCTGTAGTATTTCCCGAACTCCGCTCCGCCTCCCGGCTTCGCGA
GGCCCGTCAGGATTTCATCGTACGAGTTCTTCGCCGcagaggattaattttgtttgggtcactg
ccaagtttgctcatagcatccctcatgcacgcaagatcaaccactgctggaacaccagtgaaat
cctgtaat

									
								

					

						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: 362
Transcript exons: 2031824-2031916,2032444-2032604,2032991-2033098
CAGAGGATTAATTTTGTTTGGGTCACTGCCAAGTTTGCTCATAGCATCCCTCATGCACGCAAGA
TCAACCACTGCTGGAACACCAGTGAAATCCTGGAGGAGGACACGGGCTGGCTTAAATGGGATTT
CGACTTGCTTTGGTGCGCTGTTCTCCCAGTCCAGGATTTTCTCAACGTCCTTCCCGGTGACCTG
GAACTCATCACAGTTTCTGATTGCCGACTCGAGAAGAATCCTTATCGAGTAAGGGAGTCGCTCG
ATCCGCGGATCGGATAGCGCGGGCAGGCTGTAGTATTTCCCGAACTCCGCTCCGCCTCCCGGCT
TCGCGAGGCCCGTCAGGATTTCATCGTACGAGTTCTTCGCCG
						
					

						Genomic sequence
						
							CAGAGGATTAATTTTGTTTGGGTCACTGCCAAGTTTGCTCATAGCATCCCTCATGCACGCAAGA
TCAACCACTGCTGGAACACCAGTGAAATCCTGTAATGTGTAAATCAGGTAAAAGGTTAGCTGGC
TGAGTCATCATCAAGGTAGCTTCAACAACTCAGTTACAACAACTGAGAAAGCAGAACACATTTG
CATCGACACATCATCAGAAAATGTGACATCAGATATAAATAATAAGCAATATATCCAGCTATCA
CTAGCCACATGCCAGACTAAAATAGAATGATTGACTTTCATTGTTGTCTAGAGAATAAGAATAT
AATATGGAGATGCAGGTAATTTTGTACAGCCACCAGCACCTTCTGCCTTGTTGTTTCCATATCT
ATCATTAAACAACATTACATACAGTAGCAATCATAGATCAGAAAAACGAACAAAAGATAAGCCA
TGTGCAACTCCACTTCCTTGAAAGGATAGGTTCGTAAGAAAGTGGGAACTACAGTTCCAATATT
CCTGTCATCAAAGGCTATTGACTGAAACTTTTCCAGCTCACAATTATTCTATCAACAGCAATCG
AACAAAGTAGATCAAAAAGCATGAGACGGTGCCAGGATTAGTACCTGGAGGAGGACACGGGCTG
GCTTAAATGGGATTTCGACTTGCTTTGGTGCGCTGTTCTCCCAGTCCAGGATTTTCTCAACGTC
CTTCCCGGTGACCTGGAACTCATCACAGTTTCTGATTGCCGACTCGAGAAGAATCCTTATCGAG
TAAGGGAGTCGCTCTGATCAAAACCACCAAAACATGGATCAAATCATCGTTGTTCTAATAATTC
GGCAGCAGAGGTAGATCAAAACCTTCAAAGGAAATTCTATATAAGGAAAGCACAAATGCATCAA
AATTCCTTGGTCTGAACACATCTAAACCTCCAATTTCACAACCACATTACGCTCTAACCGGAGG
TCAGAGCCCTCGAACAAAACCAAACAATTCGTCCAATTCAAATCTTCACAAACGATTGACCGAC
CGAAAGAGATGAAAGCGTCAACCCCTCGTTGAATGCCCAATTCAACCATCACGAACTAACAATC
AAACAAAAAAAAACACACATCCAACACCAAATAGTGGATCGGGGCGTCCAACAATACTGGAAGG
CATCAAAACACTCACCGATCCGCGGATCGGATAGCGCGGGCAGGCTGTAGTATTTCCCGAACTC
CGCTCCGCCTCCCGGCTTCGCGAGGCCCGTCAGGATTTCATCGTACGAGTTCTTCGCCG
						
					

			
		

Sequences
Splice junction sequence	GGATCGGATAGCGCGGGCAGGCTGTAGTATTTCCCGAACTCCGCTCCGCCTCCCGGCTTCGCGA GGCCCGTCAGGATTTCATCGTACGAGTTCTTCGCCGcagaggattaattttgtttgggtcactg ccaagtttgctcatagcatccctcatgcacgcaagatcaaccactgctggaacaccagtgaaat cctgtaat
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: 362 Transcript exons: 2031824-2031916,2032444-2032604,2032991-2033098 CAGAGGATTAATTTTGTTTGGGTCACTGCCAAGTTTGCTCATAGCATCCCTCATGCACGCAAGA TCAACCACTGCTGGAACACCAGTGAAATCCTGGAGGAGGACACGGGCTGGCTTAAATGGGATTT CGACTTGCTTTGGTGCGCTGTTCTCCCAGTCCAGGATTTTCTCAACGTCCTTCCCGGTGACCTG GAACTCATCACAGTTTCTGATTGCCGACTCGAGAAGAATCCTTATCGAGTAAGGGAGTCGCTCG ATCCGCGGATCGGATAGCGCGGGCAGGCTGTAGTATTTCCCGAACTCCGCTCCGCCTCCCGGCT TCGCGAGGCCCGTCAGGATTTCATCGTACGAGTTCTTCGCCG
Genomic sequence	CAGAGGATTAATTTTGTTTGGGTCACTGCCAAGTTTGCTCATAGCATCCCTCATGCACGCAAGA TCAACCACTGCTGGAACACCAGTGAAATCCTGTAATGTGTAAATCAGGTAAAAGGTTAGCTGGC TGAGTCATCATCAAGGTAGCTTCAACAACTCAGTTACAACAACTGAGAAAGCAGAACACATTTG CATCGACACATCATCAGAAAATGTGACATCAGATATAAATAATAAGCAATATATCCAGCTATCA CTAGCCACATGCCAGACTAAAATAGAATGATTGACTTTCATTGTTGTCTAGAGAATAAGAATAT AATATGGAGATGCAGGTAATTTTGTACAGCCACCAGCACCTTCTGCCTTGTTGTTTCCATATCT ATCATTAAACAACATTACATACAGTAGCAATCATAGATCAGAAAAACGAACAAAAGATAAGCCA TGTGCAACTCCACTTCCTTGAAAGGATAGGTTCGTAAGAAAGTGGGAACTACAGTTCCAATATT CCTGTCATCAAAGGCTATTGACTGAAACTTTTCCAGCTCACAATTATTCTATCAACAGCAATCG AACAAAGTAGATCAAAAAGCATGAGACGGTGCCAGGATTAGTACCTGGAGGAGGACACGGGCTG GCTTAAATGGGATTTCGACTTGCTTTGGTGCGCTGTTCTCCCAGTCCAGGATTTTCTCAACGTC CTTCCCGGTGACCTGGAACTCATCACAGTTTCTGATTGCCGACTCGAGAAGAATCCTTATCGAG TAAGGGAGTCGCTCTGATCAAAACCACCAAAACATGGATCAAATCATCGTTGTTCTAATAATTC GGCAGCAGAGGTAGATCAAAACCTTCAAAGGAAATTCTATATAAGGAAAGCACAAATGCATCAA AATTCCTTGGTCTGAACACATCTAAACCTCCAATTTCACAACCACATTACGCTCTAACCGGAGG TCAGAGCCCTCGAACAAAACCAAACAATTCGTCCAATTCAAATCTTCACAAACGATTGACCGAC CGAAAGAGATGAAAGCGTCAACCCCTCGTTGAATGCCCAATTCAACCATCACGAACTAACAATC AAACAAAAAAAAACACACATCCAACACCAAATAGTGGATCGGGGCGTCCAACAATACTGGAAGG CATCAAAACACTCACCGATCCGCGGATCGGATAGCGCGGGCAGGCTGTAGTATTTCCCGAACTC CGCTCCGCCTCCCGGCTTCGCGAGGCCCGTCAGGATTTCATCGTACGAGTTCTTCGCCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.247625856

Conservation Information
Conserved circRNAs	NA
PMCS	0.247625856

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2031879-2033071(-)
						
						Potential amino acid sequence
						
							MRDAMSKLGSDPNKINPLRRRTRTMKS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2031879-2033071(-)
Potential amino acid sequence	MRDAMSKLGSDPNKINPLRRRTRTMKS*(-)
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 Os03g0136900_circ_g.10

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