Plant Circular RNA Database

Detail information of Os06g0129400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os06g0129400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_029506
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr6: 1556450-1557650  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							Os06g0129400						
					
						Parent gene annotation
						
							Splicing variant of SPX-MFS protein 3 (Os06t0129400-01);Vacuolar
 phosphate efflux transporter, Pi homeostasis (Os06t0129400-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os06g0129400_circ_g.1 Os06g0129400_circ_g.2 Os06g0129400_circ_g.4 Os06g0129400_circ_g.5 Os06g0129400_circ_g.6 Os06g0129400_circ_g.7 Os06g0129400_circ_g.8 Os06g0129400_circ_g.9 						
					
						Support reads
						1
					
						Tissues
						root, 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  
						
							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
						Os06t0129400-01:3
Os06t0129400-02:3

General Information
CircRNA Name	Os06g0129400_circ_g.3
ID in PlantcircBase	osa_circ_029506
Alias	NA
Organism	Oryza sativa
Position	chr6: 1556450-1557650 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	Os06g0129400
Parent gene annotation	Splicing variant of SPX-MFS protein 3 (Os06t0129400-01);Vacuolar phosphate efflux transporter, Pi homeostasis (Os06t0129400-02)
Parent gene strand	+
Alternative splicing	Os06g0129400_circ_g.1 Os06g0129400_circ_g.2 Os06g0129400_circ_g.4 Os06g0129400_circ_g.5 Os06g0129400_circ_g.6 Os06g0129400_circ_g.7 Os06g0129400_circ_g.8 Os06g0129400_circ_g.9
Support reads	1
Tissues	root, 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	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	Os06t0129400-01:3 Os06t0129400-02:3

			
						 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  
						
							GAAGTTTGACAAGCGTTTCGGCTACAGATTTACTGATTACTATGTGACAAGTAGATCGAATCAC
CCATATTCTCAGCTACAGCAGGTCTTCAAGCATGTGtttaatatctccaagtcaagatggttaa
ctttgggaagaaattgatggctgatcaaattccggaatggaaagggtatgattcagggctttta
ttacttta

									
								

					

						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: 506
Transcript exons: 1556450-1556522,1556742-1556862,1557339-1557650
TTTAATATCTCCAAGTCAAGATGGTTAACTTTGGGAAGAAATTGATGGCTGATCAAATTCCGGA
ATGGAAAGGGTACTACATAAACTACAAGTTGATGAAGAAGAAAGTAAAACAGTACGGGCAGCAG
GTTCAACAGGGTGAGAAAGATCGTCGCCGGGTTCTTAAGGATTTCTCGAAGATGCTTGATGATC
AGATTGAGAAGATTGTCCTATTTCTGTTGGAGCAACAAGGAGCGTTGGCAAGCAGGATAGAGAA
ATTAGGAAAGCAAAGGGCAATATTAGCAGAACAGCCAGATATATCTGCCATTGCTGAGTTGCGA
GAAGCTTACAGGGAAGTTGGCCTGGATCTTATCAAACTTCTCAAATTTGTTGATCTCAATGCGA
CTGGCATTCGGAAAATTTTGAAGAAGTTTGACAAGCGTTTCGGCTACAGATTTACTGATTACTA
TGTGACAAGTAGATCGAATCACCCATATTCTCAGCTACAGCAGGTCTTCAAGCATGTG
						
					

						Genomic sequence
						
							TTTAATATCTCCAAGTCAAGATGGTTAACTTTGGGAAGAAATTGATGGCTGATCAAATTCCGGA
ATGGAAAGGGTATGATTCAGGGCTTTTATTACTTTAATTTTTATGGACCATTCTACGCTTACCA
GTTCTGTAAATATCATCAGTCTTCCACCCCTCACCAGATAATTTTTTCTATGGAAACTTATTAT
TTTTTTCTTAACAAACCTGATAGTCTAATGATACATTGAAATAGTTGATACTTAGTTACCGAAA
TTTAGCTTTGCCTCTTTTTTATACCGATGTTTCCAGGTACTACATAAACTACAAGTTGATGAAG
AAGAAAGTAAAACAGTACGGGCAGCAGGTTCAACAGGGTGAGAAAGATCGTCGCCGGGTTCTTA
AGGATTTCTCGAAGATGCTTGATGATCAGGTAATGCCAAGAGATAGATGCTATGAAAAGCCATT
ACTTCATTCTCCCTGATCTGCTTTAATTGCAGACTTTAGCTTCTCTGTGGATATTTAGCTTGCT
GAGTGTAGCATCAACATGGTGAGCATGTGTAATCTGTATGTCAGTGTTTACCCACATATGCTCA
TATATCAAATTATCCATGCATGGCCTTTCTAAGCAAAGGAATTTCAATAGTTTTATTTTAAATA
AACTGTAGCGGAGTTTTGTCACCAATTTTCTTGTAGAAACTGAGTAATACTATCAAAATGTTAC
AAGCCAACAGTTCTAGTTGACGACTTACTGTTCTTTATTTTTTTTCTTTCTGGTGCTCACATGT
GAGCCCTGTTTTCACCTGGTTCCATCCCTTGTGCGAGATTTTGATGCAACAAATTTATCTAATT
GACCATACTAAAATTTGTGTTTTACATTACTGATGTTCTGTTTTCCTGTGGCATCAGATTGAGA
AGATTGTCCTATTTCTGTTGGAGCAACAAGGAGCGTTGGCAAGCAGGATAGAGAAATTAGGAAA
GCAAAGGGCAATATTAGCAGAACAGCCAGATATATCTGCCATTGCTGAGTTGCGAGAAGCTTAC
AGGGAAGTTGGCCTGGATCTTATCAAACTTCTCAAATTTGTTGATCTCAATGCGACTGGCATTC
GGAAAATTTTGAAGAAGTTTGACAAGCGTTTCGGCTACAGATTTACTGATTACTATGTGACAAG
TAGATCGAATCACCCATATTCTCAGCTACAGCAGGTCTTCAAGCATGTG
						
					

			
		

Sequences
Splice junction sequence	GAAGTTTGACAAGCGTTTCGGCTACAGATTTACTGATTACTATGTGACAAGTAGATCGAATCAC CCATATTCTCAGCTACAGCAGGTCTTCAAGCATGTGtttaatatctccaagtcaagatggttaa ctttgggaagaaattgatggctgatcaaattccggaatggaaagggtatgattcagggctttta ttacttta
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: 506 Transcript exons: 1556450-1556522,1556742-1556862,1557339-1557650 TTTAATATCTCCAAGTCAAGATGGTTAACTTTGGGAAGAAATTGATGGCTGATCAAATTCCGGA ATGGAAAGGGTACTACATAAACTACAAGTTGATGAAGAAGAAAGTAAAACAGTACGGGCAGCAG GTTCAACAGGGTGAGAAAGATCGTCGCCGGGTTCTTAAGGATTTCTCGAAGATGCTTGATGATC AGATTGAGAAGATTGTCCTATTTCTGTTGGAGCAACAAGGAGCGTTGGCAAGCAGGATAGAGAA ATTAGGAAAGCAAAGGGCAATATTAGCAGAACAGCCAGATATATCTGCCATTGCTGAGTTGCGA GAAGCTTACAGGGAAGTTGGCCTGGATCTTATCAAACTTCTCAAATTTGTTGATCTCAATGCGA CTGGCATTCGGAAAATTTTGAAGAAGTTTGACAAGCGTTTCGGCTACAGATTTACTGATTACTA TGTGACAAGTAGATCGAATCACCCATATTCTCAGCTACAGCAGGTCTTCAAGCATGTG
Genomic sequence	TTTAATATCTCCAAGTCAAGATGGTTAACTTTGGGAAGAAATTGATGGCTGATCAAATTCCGGA ATGGAAAGGGTATGATTCAGGGCTTTTATTACTTTAATTTTTATGGACCATTCTACGCTTACCA GTTCTGTAAATATCATCAGTCTTCCACCCCTCACCAGATAATTTTTTCTATGGAAACTTATTAT TTTTTTCTTAACAAACCTGATAGTCTAATGATACATTGAAATAGTTGATACTTAGTTACCGAAA TTTAGCTTTGCCTCTTTTTTATACCGATGTTTCCAGGTACTACATAAACTACAAGTTGATGAAG AAGAAAGTAAAACAGTACGGGCAGCAGGTTCAACAGGGTGAGAAAGATCGTCGCCGGGTTCTTA AGGATTTCTCGAAGATGCTTGATGATCAGGTAATGCCAAGAGATAGATGCTATGAAAAGCCATT ACTTCATTCTCCCTGATCTGCTTTAATTGCAGACTTTAGCTTCTCTGTGGATATTTAGCTTGCT GAGTGTAGCATCAACATGGTGAGCATGTGTAATCTGTATGTCAGTGTTTACCCACATATGCTCA TATATCAAATTATCCATGCATGGCCTTTCTAAGCAAAGGAATTTCAATAGTTTTATTTTAAATA AACTGTAGCGGAGTTTTGTCACCAATTTTCTTGTAGAAACTGAGTAATACTATCAAAATGTTAC AAGCCAACAGTTCTAGTTGACGACTTACTGTTCTTTATTTTTTTTCTTTCTGGTGCTCACATGT GAGCCCTGTTTTCACCTGGTTCCATCCCTTGTGCGAGATTTTGATGCAACAAATTTATCTAATT GACCATACTAAAATTTGTGTTTTACATTACTGATGTTCTGTTTTCCTGTGGCATCAGATTGAGA AGATTGTCCTATTTCTGTTGGAGCAACAAGGAGCGTTGGCAAGCAGGATAGAGAAATTAGGAAA GCAAAGGGCAATATTAGCAGAACAGCCAGATATATCTGCCATTGCTGAGTTGCGAGAAGCTTAC AGGGAAGTTGGCCTGGATCTTATCAAACTTCTCAAATTTGTTGATCTCAATGCGACTGGCATTC GGAAAATTTTGAAGAAGTTTGACAAGCGTTTCGGCTACAGATTTACTGATTACTATGTGACAAG TAGATCGAATCACCCATATTCTCAGCTACAGCAGGTCTTCAAGCATGTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.27946079

Conservation Information
Conserved circRNAs	NA
PMCS	0.27946079

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1556471-1556491(+)
						
						Potential amino acid sequence
						
							MVNFGKKLMADQIPEWKGYYINYKLMKKKVKQYGQQVQQGEKDRRRVLKDFSKMLDDQIEKIVL
FLLEQQGALASRIEKLGKQRAILAEQPDISAIAELREAYREVGLDLIKLLKFVDLNATGIRKIL
KKFDKRFGYRFTDYYVTSRSNHPYSQLQQVFKHVFNISKSRWLTLGRN*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1556471-1556491(+)
Potential amino acid sequence	MVNFGKKLMADQIPEWKGYYINYKLMKKKVKQYGQQVQQGEKDRRRVLKDFSKMLDDQIEKIVL FLLEQQGALASRIEKLGKQRAILAEQPDISAIAELREAYREVGLDLIKLLKFVDLNATGIRKIL KKFDKRFGYRFTDYYVTSRSNHPYSQLQQVFKHVFNISKSRWLTLGRN*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os06g0129400_circ_g.3

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