Plant Circular RNA Database

Detail information of Os10g0127700_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os10g0127700_circ_g.3
					
						ID in PlantcircBase
						osa_circ_006151
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr10: 1738246-1738813  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os10g0127700						
					
						Parent gene annotation
						
							Protein of unknown function DUF639 family protein. (Os10t0127700
-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os10g0126500_circ_ag.1 Os10g0126500_circ_igg.1 Os10g0126600_circ_ag.1 Os10g0127700_circ_g.1 Os10g0127700_circ_g.2 						
					
						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  
						
							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
						Os10t0127700-01:2

General Information
CircRNA Name	Os10g0127700_circ_g.3
ID in PlantcircBase	osa_circ_006151
Alias	NA
Organism	Oryza sativa
Position	chr10: 1738246-1738813 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os10g0127700
Parent gene annotation	Protein of unknown function DUF639 family protein. (Os10t0127700 -01)
Parent gene strand	-
Alternative splicing	Os10g0126500_circ_ag.1 Os10g0126500_circ_igg.1 Os10g0126600_circ_ag.1 Os10g0127700_circ_g.1 Os10g0127700_circ_g.2
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	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	Os10t0127700-01:2

			
						 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  
						
							TTCCAAAAAATTTCTTGCATAATTTCTTGGCTGCTTTATGGAATCAGATGCTTGCATATCAAAG
TCATACTGCAGCTCATCCGTGGAAGTACCAAGTACCctgtccaatcctgtaaggtacttatcat
atacaggaaatgtaagccggcctccacttgaagatgaaagtacatcaaatagatttgaacatgt
taccacat

						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: 405
Transcript exons: 1738246-1738415,1738579-1738813
CTGTCCAATCCTGTAAGGTACTTATCATATACAGGAAATGTAAGCCGGCCTCCACTTGAAGATG
AAAGTACATCAAATAGATTTGAACATGTTACCACATCAGTGATTGTTGGAATTGCAGGTGCTAT
TCTTGAAAAAGCCTCTAAACTGACTGTGTTGTCTACTTCAACCTTAACAGTGAGCTCGCTTGAA
GAAGAGGGAACTTCCCAAGCTAGCATCATATCAAAATTTAGGCGACGAAAGCTTTTGTCAGAAA
GATACCCTGCAACTTGTGAGGCATGTGCAAGTGCCCTCAAACAACAATATTCCAAAAAATTTCT
TGCATAATTTCTTGGCTGCTTTATGGAATCAGATGCTTGCATATCAAAGTCATACTGCAGCTCA
TCCGTGGAAGTACCAAGTACC
						
						Genomic sequence
						
							CTGTCCAATCCTGTAAGGTACTTATCATATACAGGAAATGTAAGCCGGCCTCCACTTGAAGATG
AAAGTACATCAAATAGATTTGAACATGTTACCACATCAGTGATTGTTGGAATTGCAGGTGCTAT
TCTTGAAAAAGCCTCTAAACTGACTGTGTTGTCTACTTCAACCTGCAAGGGAAAGGAGATGAAA
TTCAATATGTAGAAAGATTCTTAAAAGCCCTTAATACGAGGAAGTAACCTGGGAAAATTTTATT
AATGCAACGCTAACAAATTATATAAGGCGTGAACAAAAGAAAACTATTTAAGAAAGTAAAGAAA
GGAAAATTGTAACCTTAACAGTGAGCTCGCTTGAAGAAGAGGGAACTTCCCAAGCTAGCATCAT
ATCAAAATTTAGGCGACGAAAGCTTTTGTCAGAAAGATACCCTGCAACTTGTGAGGCATGTGCA
AGTGCCCTCAAACAACAATATTCCAAAAAATTTCTTGCATAATTTCTTGGCTGCTTTATGGAAT
CAGATGCTTGCATATCAAAGTCATACTGCAGCTCATCCGTGGAAGTACCAAGTACC

Sequences
Splice junction sequence	TTCCAAAAAATTTCTTGCATAATTTCTTGGCTGCTTTATGGAATCAGATGCTTGCATATCAAAG TCATACTGCAGCTCATCCGTGGAAGTACCAAGTACCctgtccaatcctgtaaggtacttatcat atacaggaaatgtaagccggcctccacttgaagatgaaagtacatcaaatagatttgaacatgt taccacat
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: 405 Transcript exons: 1738246-1738415,1738579-1738813 CTGTCCAATCCTGTAAGGTACTTATCATATACAGGAAATGTAAGCCGGCCTCCACTTGAAGATG AAAGTACATCAAATAGATTTGAACATGTTACCACATCAGTGATTGTTGGAATTGCAGGTGCTAT TCTTGAAAAAGCCTCTAAACTGACTGTGTTGTCTACTTCAACCTTAACAGTGAGCTCGCTTGAA GAAGAGGGAACTTCCCAAGCTAGCATCATATCAAAATTTAGGCGACGAAAGCTTTTGTCAGAAA GATACCCTGCAACTTGTGAGGCATGTGCAAGTGCCCTCAAACAACAATATTCCAAAAAATTTCT TGCATAATTTCTTGGCTGCTTTATGGAATCAGATGCTTGCATATCAAAGTCATACTGCAGCTCA TCCGTGGAAGTACCAAGTACC
Genomic sequence	CTGTCCAATCCTGTAAGGTACTTATCATATACAGGAAATGTAAGCCGGCCTCCACTTGAAGATG AAAGTACATCAAATAGATTTGAACATGTTACCACATCAGTGATTGTTGGAATTGCAGGTGCTAT TCTTGAAAAAGCCTCTAAACTGACTGTGTTGTCTACTTCAACCTGCAAGGGAAAGGAGATGAAA TTCAATATGTAGAAAGATTCTTAAAAGCCCTTAATACGAGGAAGTAACCTGGGAAAATTTTATT AATGCAACGCTAACAAATTATATAAGGCGTGAACAAAAGAAAACTATTTAAGAAAGTAAAGAAA GGAAAATTGTAACCTTAACAGTGAGCTCGCTTGAAGAAGAGGGAACTTCCCAAGCTAGCATCAT ATCAAAATTTAGGCGACGAAAGCTTTTGTCAGAAAGATACCCTGCAACTTGTGAGGCATGTGCA AGTGCCCTCAAACAACAATATTCCAAAAAATTTCTTGCATAATTTCTTGGCTGCTTTATGGAAT CAGATGCTTGCATATCAAAGTCATACTGCAGCTCATCCGTGGAAGTACCAAGTACC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.29318125

Conservation Information
Conserved circRNAs	NA
PMCS	0.29318125

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1738752-1738732(+)
1738762-1738258(+)
1738688-1738301(+)
1738772-1738248(-)
1738320-1738751(-)
						
						Potential amino acid sequence
						
							MESDACISKSYCSSSVEVPSTLSNPVRYLSYTGNVSRPPLEDESTSNRFEHVTTSVIVGIAGAI
LEKASKLTVLSTSTLTVSSLEEEGTSQASIISKFRRRKLLSERYPATCEACASALKQQYSKKFL
A*(+)
MLAYQSHTAAHPWKYQVPCPIL*(+)
MCKCPQTTIFQKISCIISWLLYGIRCLHIKVILQLIRGSTKYPVQSCKVLIIYRKCKPAST*(+
)
MQASDSIKQPRNYARNFLEYCCLRALAHASQVAGYLSDKSFRRLNFDMMLAWEVPSSSSELTVK
VEVDNTVSLEAFSRIAPAIPTITDVVTCSNLFDVLSSSSGGRLTFPVYDKYLTGLDRVLGTSTD
ELQYDFDMQASDSIKQPRNYARNFLEYCCLRALAHASQVAGYLSDKSFRRLNFDMMLAWEVPSS
SSELTVKVEVDNTVSLEAFSRIAPAIPTITDVVTCSNLFDVLSSSSGGRLTFPVYDKYLTGLDR
VLGTSTDELQYDFDMQASDSIKQPRNYARNFLEYCCLRALAHASQVAGYLSDKSFRRLNFDMML
AWEVPSSSSELTVKVEVDNTVSLEAFSRIAPAIPTITDVVTCSNLFDVLSSSSGGRLTFPVYDK
YLTGLDRVLGTSTDELQYDFDMQASDSIKQPRNYARNFLEYCCLRALAHASQVAGYLSDKSFRR
LNFDMMLAWEVPSSSSELTVKVEVDNTVSLEAFSRIAPAIPTITDVVTCSNLFDVLSSSSGGRL
TFPVYDKYLTGLD(-)
MYFHLQVEAGLHFLYMISTLQDWTGYLVLPRMSCSMTLICKHLIP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1738752-1738732(+) 1738762-1738258(+) 1738688-1738301(+) 1738772-1738248(-) 1738320-1738751(-)
Potential amino acid sequence	MESDACISKSYCSSSVEVPSTLSNPVRYLSYTGNVSRPPLEDESTSNRFEHVTTSVIVGIAGAI LEKASKLTVLSTSTLTVSSLEEEGTSQASIISKFRRRKLLSERYPATCEACASALKQQYSKKFL A(+) MLAYQSHTAAHPWKYQVPCPIL(+) MCKCPQTTIFQKISCIISWLLYGIRCLHIKVILQLIRGSTKYPVQSCKVLIIYRKCKPAST(+ ) MQASDSIKQPRNYARNFLEYCCLRALAHASQVAGYLSDKSFRRLNFDMMLAWEVPSSSSELTVK VEVDNTVSLEAFSRIAPAIPTITDVVTCSNLFDVLSSSSGGRLTFPVYDKYLTGLDRVLGTSTD ELQYDFDMQASDSIKQPRNYARNFLEYCCLRALAHASQVAGYLSDKSFRRLNFDMMLAWEVPSS SSELTVKVEVDNTVSLEAFSRIAPAIPTITDVVTCSNLFDVLSSSSGGRLTFPVYDKYLTGLDR VLGTSTDELQYDFDMQASDSIKQPRNYARNFLEYCCLRALAHASQVAGYLSDKSFRRLNFDMML AWEVPSSSSELTVKVEVDNTVSLEAFSRIAPAIPTITDVVTCSNLFDVLSSSSGGRLTFPVYDK YLTGLDRVLGTSTDELQYDFDMQASDSIKQPRNYARNFLEYCCLRALAHASQVAGYLSDKSFRR LNFDMMLAWEVPSSSSELTVKVEVDNTVSLEAFSRIAPAIPTITDVVTCSNLFDVLSSSSGGRL TFPVYDKYLTGLD(-) MYFHLQVEAGLHFLYMISTLQDWTGYLVLPRMSCSMTLICKHLIP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os10g0127700_circ_g.3

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