Plant Circular RNA Database

Detail information of Os01g0703400_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os01g0703400_circ_g.4
					
						ID in PlantcircBase
						osa_circ_003542
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 29160711-29161978  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0703400						
					
						Parent gene annotation
						
							Similar to Farnesyl pyrophosphate synthetase (FPP synthetase) (F
PS) (Farnesyl diphosphate synthetase) [Includes: Dimethylallyltr
anstransferase (EC 2.5.1.1); Geranyltranstransferase (EC 2.5.1.1
0)]. (Os01t0703400-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0703400_circ_g.1 Os01g0703400_circ_g.2 Os01g0703400_circ_g.3 Os01g0703400_circ_g.5 Os01g0703400_circ_g.6 						
					
						Support reads
						1
					
						Tissues
						shoot
					
						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
						Os01t0703400-01:7

General Information
CircRNA Name	Os01g0703400_circ_g.4
ID in PlantcircBase	osa_circ_003542
Alias	NA
Organism	Oryza sativa
Position	chr1: 29160711-29161978 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0703400
Parent gene annotation	Similar to Farnesyl pyrophosphate synthetase (FPP synthetase) (F PS) (Farnesyl diphosphate synthetase) [Includes: Dimethylallyltr anstransferase (EC 2.5.1.1); Geranyltranstransferase (EC 2.5.1.1 0)]. (Os01t0703400-01)
Parent gene strand	+
Alternative splicing	Os01g0703400_circ_g.1 Os01g0703400_circ_g.2 Os01g0703400_circ_g.3 Os01g0703400_circ_g.5 Os01g0703400_circ_g.6
Support reads	1
Tissues	shoot
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	Os01t0703400-01:7

			
						 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  
						
							ATCTGAATCCTTTATGTCTAATTGACAGGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCA
AAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgttgggctcattgctgtaaatgatggta
ttatccttcgcaaccatatttcacgaattcttcaacgccattttaaaggaaagctgtattatgt
tgatctca

									
								

					

						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: 561
Transcript exons: 29160711-29160827,29160920-29161008,29161253-29161304,29
161410-29161505,29161578-29161622,29161745-29161834,2916
1907-29161978
GTTGGGCTCATTGCTGTAAATGATGGTATTATCCTTCGCAACCATATTTCACGAATTCTTCAAC
GCCATTTTAAAGGAAAGCTGTATTATGTTGATCTCATTGATTTGTTCAATGAGGTTGAGTTTAA
GACTGCTTCAGGTCAATTGTTGGATCTTATTACTACTCATGAGGGAGAAAAGGATCTCACAAAG
TACAACTTGACAGTTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTC
CGGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACAT
TCTTGTGGAAATGGGGACATACTTCCAAGTTCAGGATGATTATCTAGATTGTTATGGTGATCCT
GAGTTTATTGGCAAGATTGGAACGGACATTGAAGACTACAAGTGCTCATGGTTAGTTGTGCAAG
CTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTGAAAATTATGGGAAGCCAGATCC
TGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG
						
					

						Genomic sequence
						
							GTTGGGCTCATTGCTGTAAATGATGGTATTATCCTTCGCAACCATATTTCACGAATTCTTCAAC
GCCATTTTAAAGGAAAGCTGTATTATGTTGATCTCATTGATTTGTTCAATGAGGTAAGTTGTAT
CTTCTGACATGCACATATTGTTGGGAAAAAAATACTGTACGCTTCTCCCTGATGCCCAGTTGTA
TGTTTTTGTTTTGTTAGGTTGAGTTTAAGACTGCTTCAGGTCAATTGTTGGATCTTATTACTAC
TCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGTGTAAGTTCATTTTGCATTTACG
TGTTTGTTTCTTTCTTTCTTTGCATGATTTCCTGTCCATTTGTTTCTAAAAATAAGGTTCAAAC
AAAACAAAGGAACGGAAAAAATAACAGATAGTTCCTTTTCTGTGTTCCATGTGTAGTTTCTAGA
ATGAGTTGTATTTGCACTATATTTTATTTTAGCAGTTCAGAATTGGGTTATGATCTTCATTTAA
TGGTGTTCTTTTAACTGACATATTGTGCAGTCACCGCCGCATTGTTCAGTACAAGACAGCTTAC
TACTCATTCTATCTTCCGGTAGGATTTACCATTCTCCTATGGATTTTTTCCATCTTTAAACTCT
CACTTCGGTAATCTGCGAATAGTTGTCATCACTAGCAATAATATTTTTCTTTATCCAAGGTTGC
ATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACATTCTTGTG
GAAATGGGGACATACTTCCAAGTTCAGGTACCTTTTCACCTTGTTGGTTGTGAATTTATATATT
ACTGGACTACCGCACTAATACGAGTTTTCTCACAGGATGATTATCTAGATTGTTATGGTGATCC
TGAGTTTATTGGCAAGGTTAGTGTGCCCGTTGTGGTTGTACTAATCCCAATGAGTATGGCTACT
GCCAATCGGTCCATTGCTGTCCAGGCTTATTTTATCTGTAGCTTATGATCTGATCAGTAGAAAT
CTTAATGCAGATTGGAACGGACATTGAAGACTACAAGTGCTCATGGTTAGTTGTGCAAGCTCTC
GAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTGTAAGTATTATTAACTTTGTAGTTTTTA
TCAACCCATGGGCACCATCTGAATCCTTTATGTCTAATTGACAGGAAAATTATGGGAAGCCAGA
TCCTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG
						
					

			
		

Sequences
Splice junction sequence	ATCTGAATCCTTTATGTCTAATTGACAGGAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCA AAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgttgggctcattgctgtaaatgatggta ttatccttcgcaaccatatttcacgaattcttcaacgccattttaaaggaaagctgtattatgt tgatctca
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: 561 Transcript exons: 29160711-29160827,29160920-29161008,29161253-29161304,29 161410-29161505,29161578-29161622,29161745-29161834,2916 1907-29161978 GTTGGGCTCATTGCTGTAAATGATGGTATTATCCTTCGCAACCATATTTCACGAATTCTTCAAC GCCATTTTAAAGGAAAGCTGTATTATGTTGATCTCATTGATTTGTTCAATGAGGTTGAGTTTAA GACTGCTTCAGGTCAATTGTTGGATCTTATTACTACTCATGAGGGAGAAAAGGATCTCACAAAG TACAACTTGACAGTTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTC CGGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACAT TCTTGTGGAAATGGGGACATACTTCCAAGTTCAGGATGATTATCTAGATTGTTATGGTGATCCT GAGTTTATTGGCAAGATTGGAACGGACATTGAAGACTACAAGTGCTCATGGTTAGTTGTGCAAG CTCTCGAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTGAAAATTATGGGAAGCCAGATCC TGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG
Genomic sequence	GTTGGGCTCATTGCTGTAAATGATGGTATTATCCTTCGCAACCATATTTCACGAATTCTTCAAC GCCATTTTAAAGGAAAGCTGTATTATGTTGATCTCATTGATTTGTTCAATGAGGTAAGTTGTAT CTTCTGACATGCACATATTGTTGGGAAAAAAATACTGTACGCTTCTCCCTGATGCCCAGTTGTA TGTTTTTGTTTTGTTAGGTTGAGTTTAAGACTGCTTCAGGTCAATTGTTGGATCTTATTACTAC TCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGTGTAAGTTCATTTTGCATTTACG TGTTTGTTTCTTTCTTTCTTTGCATGATTTCCTGTCCATTTGTTTCTAAAAATAAGGTTCAAAC AAAACAAAGGAACGGAAAAAATAACAGATAGTTCCTTTTCTGTGTTCCATGTGTAGTTTCTAGA ATGAGTTGTATTTGCACTATATTTTATTTTAGCAGTTCAGAATTGGGTTATGATCTTCATTTAA TGGTGTTCTTTTAACTGACATATTGTGCAGTCACCGCCGCATTGTTCAGTACAAGACAGCTTAC TACTCATTCTATCTTCCGGTAGGATTTACCATTCTCCTATGGATTTTTTCCATCTTTAAACTCT CACTTCGGTAATCTGCGAATAGTTGTCATCACTAGCAATAATATTTTTCTTTATCCAAGGTTGC ATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACATTCTTGTG GAAATGGGGACATACTTCCAAGTTCAGGTACCTTTTCACCTTGTTGGTTGTGAATTTATATATT ACTGGACTACCGCACTAATACGAGTTTTCTCACAGGATGATTATCTAGATTGTTATGGTGATCC TGAGTTTATTGGCAAGGTTAGTGTGCCCGTTGTGGTTGTACTAATCCCAATGAGTATGGCTACT GCCAATCGGTCCATTGCTGTCCAGGCTTATTTTATCTGTAGCTTATGATCTGATCAGTAGAAAT CTTAATGCAGATTGGAACGGACATTGAAGACTACAAGTGCTCATGGTTAGTTGTGCAAGCTCTC GAGCGTGCTGACGAGAACCAAAAGCACATTCTATTTGTAAGTATTATTAACTTTGTAGTTTTTA TCAACCCATGGGCACCATCTGAATCCTTTATGTCTAATTGACAGGAAAATTATGGGAAGCCAGA TCCTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.24187385

Conservation Information
Conserved circRNAs	NA
PMCS	0.24187385

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							29161483-29161975(+)
29160757-29161831(-)
29160723-29161914(-)
						
						Potential amino acid sequence
						
							MGTYFQVQDDYLDCYGDPEFIGKIGTDIEDYKCSWLVVQALERADENQKHILFENYGKPDPECV
AKVKDLYKELNLEVGLIAVNDGIILRNHISRILQRHFKGKLYYVDLIDLFNEVEFKTASGQLLD
LITTHEGEKDLTKYNLTVHRRIVQYKTAYYSFYLPVACALLLSGENLDNFGDVKNILVEMGTYF
QVQDDYLDCYGDPEFIGKIGTDIEDYKCSWLVVQALERADENQKHILFENYGKPDPECVAKVKD
LYKELNLEVGLIAVNDGIILRNHISRILQRHFKGKLYYVDLIDLFNEVEFKTASGQLLDLITTH
EGEKDLTKYNLTVHRRIVQYKTAYYSFYLPVACALLLSGENLDNFGDVKNILVEMGTYFQVQDD
YLDCYGDPEFIGKIGTDIEDYKCSWLVVQALERADENQKHILFENYGKPDPECVAKVKDLYKEL
NLEVGLIAVNDGIILRNHISRILQRHFKGKLYYVDLIDLFNEVEFKTASGQLLDLITTHEGEKD
LTKYNLTVHRRIVQYKTAYYSFYLPVACALLLSGENLDNFGDVKNILVEMGTYFQVQDDYLDCY
GDPEFIGKIGTDIEDYKCSWLVVQALERADENQKHILFENYGKPDPECVAKVKDLYKELNLE(+
)
MVAKDNTIIYSNEPNLQIKFFIQILHFCNTFRIWLPIIFK*(-)
MSPTSRLSSLYRSFTFATHSGSGFP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	29161483-29161975(+) 29160757-29161831(-) 29160723-29161914(-)
Potential amino acid sequence	MGTYFQVQDDYLDCYGDPEFIGKIGTDIEDYKCSWLVVQALERADENQKHILFENYGKPDPECV AKVKDLYKELNLEVGLIAVNDGIILRNHISRILQRHFKGKLYYVDLIDLFNEVEFKTASGQLLD LITTHEGEKDLTKYNLTVHRRIVQYKTAYYSFYLPVACALLLSGENLDNFGDVKNILVEMGTYF QVQDDYLDCYGDPEFIGKIGTDIEDYKCSWLVVQALERADENQKHILFENYGKPDPECVAKVKD LYKELNLEVGLIAVNDGIILRNHISRILQRHFKGKLYYVDLIDLFNEVEFKTASGQLLDLITTH EGEKDLTKYNLTVHRRIVQYKTAYYSFYLPVACALLLSGENLDNFGDVKNILVEMGTYFQVQDD YLDCYGDPEFIGKIGTDIEDYKCSWLVVQALERADENQKHILFENYGKPDPECVAKVKDLYKEL NLEVGLIAVNDGIILRNHISRILQRHFKGKLYYVDLIDLFNEVEFKTASGQLLDLITTHEGEKD LTKYNLTVHRRIVQYKTAYYSFYLPVACALLLSGENLDNFGDVKNILVEMGTYFQVQDDYLDCY GDPEFIGKIGTDIEDYKCSWLVVQALERADENQKHILFENYGKPDPECVAKVKDLYKELNLE(+ ) MVAKDNTIIYSNEPNLQIKFFIQILHFCNTFRIWLPIIFK(-) MSPTSRLSSLYRSFTFATHSGSGFP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0703400_circ_g.4

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