Plant Circular RNA Database

Detail information of Os12g0163800_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os12g0163800_circ_g.4
					
						ID in PlantcircBase
						osa_circ_010560
					
						Alias
						Os_ciR3723
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 3237848-3239396  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os12g0163800						
					
						Parent gene annotation
						
							Similar to ATP binding protein. (Os12t0163800-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os12g0163800_circ_g.5 Os12g0163800_circ_g.6 Os12g0163800_circ_g.7 Os12g0163800_circ_g.8 Os12g0163800_circ_g.9 Os12g0163800_circ_g.10 						
					
						Support reads
						2
					
						Tissues
						root
					
						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
						Os12t0163800-01:6

General Information
CircRNA Name	Os12g0163800_circ_g.4
ID in PlantcircBase	osa_circ_010560
Alias	Os_ciR3723
Organism	Oryza sativa
Position	chr12: 3237848-3239396 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Os12g0163800
Parent gene annotation	Similar to ATP binding protein. (Os12t0163800-01)
Parent gene strand	-
Alternative splicing	Os12g0163800_circ_g.5 Os12g0163800_circ_g.6 Os12g0163800_circ_g.7 Os12g0163800_circ_g.8 Os12g0163800_circ_g.9 Os12g0163800_circ_g.10
Support reads	2
Tissues	root
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	Os12t0163800-01:6

			
						 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  
						
							ATGGAAAATGCTTATTGCTTAGACGATCATAATATATATCACAAGTTACCTCATTCCTTAAAAT
GGACGCTTCCAGTGCCTTGTGCAAACCATCAGTGTCctctggtgccatccatctgtatgttcca
gtttcagctgtcatgttacctccttgatcctgaaaacgagctacaccaaaatctgccactttca
caacctag

									
								

					

						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: 642
Transcript exons: 3237848-3237943,3238154-3238329,3238580-3238653,3238859-
3238966,3239050-3239186,3239346-3239396
CTCTGGTGCCATCCATCTGTATGTTCCAGTTTCAGCTGTCATGTTACCTCCTTGATCCTGAAAA
CGAGCTACACCAAAATCTGCCACTTTCACAACATGATCTTTGTCCATTAGAAGGTTTGCACTCT
TTAAATCTCTATGGATAATACCCCTCTGATGCAAGTAACACATCCCTCTGCATACATCAACTGC
AAACTTCAGCAGAGTTGGAAGGTCCAAGACATTATGCTGCTTGTGCACAAAGTCATACAGGCTT
CCTCCAGACATGTATTCAGTAATTATGCAAAATTGTGGTGGTTTTGTGCATGCACCAATGAATC
GCACAACATTAGTATGCTGAACTTCCCTTAGAATATATACTTCCTGTGTGAACTCATTCCAAAC
ATTCTTATTCAAATGCTCAGATCTTAGAATTTTAACAGCAACATCCTCACCGAGATAAGTCCCA
TGATACAAATCCCCACAAGATCCAGAAGCAATCATCCCTCCCATCTTCAGCAGTCGTTTGTCAA
TTTCCCATTCACCACCTTTTACTTGGAATGGCAGTGTTCTTTCTGCAGCTGATGAGTGAGATGA
ACCTGACCATGATCCCTCATTCCTTAAAATGGACGCTTCCAGTGCCTTGTGCAAACCATCAGTG
TC
						
					

						Genomic sequence
						
							CTCTGGTGCCATCCATCTGTATGTTCCAGTTTCAGCTGTCATGTTACCTCCTTGATCCTGAAAA
CGAGCTACACCAAAATCTGCCACTTTCACAACCTAGAAAAATAATAATGAAGTTATTTATCAGT
TCATAGATATTTTCTCTCAAGTGCAAAGCAGATGGCTCCTGCACATACAAAAACACAAATGAAG
CATGATTATATTGCATCAGTACCATTTGCCCACTTGCATAAACTATACTATCTTGTCTTATTTT
TTCCCCTCATATGTTCATCAATAAAATGTTAAAGATTATAGGCTACGTACATGATCTTTGTCCA
TTAGAAGGTTTGCACTCTTTAAATCTCTATGGATAATACCCCTCTGATGCAAGTAACACATCCC
TCTGCATACATCAACTGCAAACTTCAGCAGAGTTGGAAGGTCCAAGACATTATGCTGCTTGTGC
ACAAAGTCATACAGGCTTCCTCCAGACATGTATTCTGAAAGATATAAAAGTAGATGATGAGCAT
TAGTAGGAATCTTCCAGTCACCAAGATATAAATTAAGCAAGAACCCGCTCTTTGTCACATAATA
ACAAGCATAATTATATGGAATTAAAAATTACATCTCACCAATATTGTGAAATTAATTAGCATTG
TGTAATAATTATTCAGCACATGCTTTATTTTTAGGAACAAACTATTCTTTGCAAATTCCCCGGT
GAGAACCAATTGATGTCATAAATCTTACCAGTAATTATGCAAAATTGTGGTGGTTTTGTGCATG
CACCAATGAATCGCACAACATTAGTATGCTGAACTTCCCTGAAAACAAGTATGGGAGATCAAGG
CAAGGCATAAATATTTAGTTATTGGTACTTGCATGAACTGGGTAATTTCAGACATTCTTAATCT
AAGAGCAGTAATATGCTCATGGCTAAGAATTGGATATGCTTAAACTATTCATTCACAATGGTAA
ATGCTAAAAAAGAATTATATAAACAAAACACCTTATTATAATGTTAAATACCTTAGAATATATA
CTTCCTGTGTGAACTCATTCCAAACATTCTTATTCAAATGCTCAGATCTTAGAATTTTAACAGC
AACATCCTCACCGAGATAAGTCCCATGATACCTTGACATAAGGATAACACACCATAAAAACAAA
GTGCAATAAATACAGTGATAAAACAACTCAGCAGTATACAATTGACTTACAAATCCCCACAAGA
TCCAGAAGCAATCATCCCTCCCATCTTCAGCAGTCGTTTGTCAATTTCCCATTCACCACCTTTT
ACTTGGAATGGCAGTGTTCTTTCTGCAGCTGATGAGTGAGATGAACCTGACCATGATCCCTGCA
TTTTCAGAGAGCACCAGCAAATATGCTGTTAGATTTGTCAAATGGAACAAGACATTGTATCATG
CATCAACTCCTTGCAAAAATACAAAATAGGATTATATCCGCATGGAAAATGCTTATTGCTTAGA
CGATCATAATATATATCACAAGTTACCTCATTCCTTAAAATGGACGCTTCCAGTGCCTTGTGCA
AACCATCAGTGTC
						
					

			
		

Sequences
Splice junction sequence	ATGGAAAATGCTTATTGCTTAGACGATCATAATATATATCACAAGTTACCTCATTCCTTAAAAT GGACGCTTCCAGTGCCTTGTGCAAACCATCAGTGTCctctggtgccatccatctgtatgttcca gtttcagctgtcatgttacctccttgatcctgaaaacgagctacaccaaaatctgccactttca caacctag
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: 642 Transcript exons: 3237848-3237943,3238154-3238329,3238580-3238653,3238859- 3238966,3239050-3239186,3239346-3239396 CTCTGGTGCCATCCATCTGTATGTTCCAGTTTCAGCTGTCATGTTACCTCCTTGATCCTGAAAA CGAGCTACACCAAAATCTGCCACTTTCACAACATGATCTTTGTCCATTAGAAGGTTTGCACTCT TTAAATCTCTATGGATAATACCCCTCTGATGCAAGTAACACATCCCTCTGCATACATCAACTGC AAACTTCAGCAGAGTTGGAAGGTCCAAGACATTATGCTGCTTGTGCACAAAGTCATACAGGCTT CCTCCAGACATGTATTCAGTAATTATGCAAAATTGTGGTGGTTTTGTGCATGCACCAATGAATC GCACAACATTAGTATGCTGAACTTCCCTTAGAATATATACTTCCTGTGTGAACTCATTCCAAAC ATTCTTATTCAAATGCTCAGATCTTAGAATTTTAACAGCAACATCCTCACCGAGATAAGTCCCA TGATACAAATCCCCACAAGATCCAGAAGCAATCATCCCTCCCATCTTCAGCAGTCGTTTGTCAA TTTCCCATTCACCACCTTTTACTTGGAATGGCAGTGTTCTTTCTGCAGCTGATGAGTGAGATGA ACCTGACCATGATCCCTCATTCCTTAAAATGGACGCTTCCAGTGCCTTGTGCAAACCATCAGTG TC
Genomic sequence	CTCTGGTGCCATCCATCTGTATGTTCCAGTTTCAGCTGTCATGTTACCTCCTTGATCCTGAAAA CGAGCTACACCAAAATCTGCCACTTTCACAACCTAGAAAAATAATAATGAAGTTATTTATCAGT TCATAGATATTTTCTCTCAAGTGCAAAGCAGATGGCTCCTGCACATACAAAAACACAAATGAAG CATGATTATATTGCATCAGTACCATTTGCCCACTTGCATAAACTATACTATCTTGTCTTATTTT TTCCCCTCATATGTTCATCAATAAAATGTTAAAGATTATAGGCTACGTACATGATCTTTGTCCA TTAGAAGGTTTGCACTCTTTAAATCTCTATGGATAATACCCCTCTGATGCAAGTAACACATCCC TCTGCATACATCAACTGCAAACTTCAGCAGAGTTGGAAGGTCCAAGACATTATGCTGCTTGTGC ACAAAGTCATACAGGCTTCCTCCAGACATGTATTCTGAAAGATATAAAAGTAGATGATGAGCAT TAGTAGGAATCTTCCAGTCACCAAGATATAAATTAAGCAAGAACCCGCTCTTTGTCACATAATA ACAAGCATAATTATATGGAATTAAAAATTACATCTCACCAATATTGTGAAATTAATTAGCATTG TGTAATAATTATTCAGCACATGCTTTATTTTTAGGAACAAACTATTCTTTGCAAATTCCCCGGT GAGAACCAATTGATGTCATAAATCTTACCAGTAATTATGCAAAATTGTGGTGGTTTTGTGCATG CACCAATGAATCGCACAACATTAGTATGCTGAACTTCCCTGAAAACAAGTATGGGAGATCAAGG CAAGGCATAAATATTTAGTTATTGGTACTTGCATGAACTGGGTAATTTCAGACATTCTTAATCT AAGAGCAGTAATATGCTCATGGCTAAGAATTGGATATGCTTAAACTATTCATTCACAATGGTAA ATGCTAAAAAAGAATTATATAAACAAAACACCTTATTATAATGTTAAATACCTTAGAATATATA CTTCCTGTGTGAACTCATTCCAAACATTCTTATTCAAATGCTCAGATCTTAGAATTTTAACAGC AACATCCTCACCGAGATAAGTCCCATGATACCTTGACATAAGGATAACACACCATAAAAACAAA GTGCAATAAATACAGTGATAAAACAACTCAGCAGTATACAATTGACTTACAAATCCCCACAAGA TCCAGAAGCAATCATCCCTCCCATCTTCAGCAGTCGTTTGTCAATTTCCCATTCACCACCTTTT ACTTGGAATGGCAGTGTTCTTTCTGCAGCTGATGAGTGAGATGAACCTGACCATGATCCCTGCA TTTTCAGAGAGCACCAGCAAATATGCTGTTAGATTTGTCAAATGGAACAAGACATTGTATCATG CATCAACTCCTTGCAAAAATACAAAATAGGATTATATCCGCATGGAAAATGCTTATTGCTTAGA CGATCATAATATATATCACAAGTTACCTCATTCCTTAAAATGGACGCTTCCAGTGCCTTGTGCA AACCATCAGTGTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.258245874

Conservation Information
Conserved circRNAs	NA
PMCS	0.258245874

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3239360-3237899(+)
3239136-3238200(+)
3239089-3237850(-)
						
						Potential amino acid sequence
						
							MDASSALCKPSVSSGAIHLYVPVSAVMLPP*(+)
MAVFFLQLMSEMNLTMIPHSLKWTLPVPCANHQCPLVPSICMFQFQLSCYLLDPENELHQNLPL
SQHDLCPLEGLHSLNLYG*(+)
MGGMIASGSCGDLYHGTYLGEDVAVKILRSEHLNKNVWNEFTQEVYILREVQHTNVVRFIGACT
KPPQFCIITEYMSGGSLYDFVHKQHNVLDLPTLLKFAVDVCRGMCYLHQRGIIHRDLKSANLLM
DKDHVVKVADFGVARFQDQGGNMTAETGTYRWMAPEDTDGLHKALEASILRNEGSWSGSSHSSA
AERTLPFQVKGGEWEIDKRLLKMGGMIASGSCGDLYHGTYLGEDVAVKILRSEHLNKNVWNEFT
QEVYILREVQHTNVVRFIGACTKPPQFCIITEYMSGGSLYDFVHKQHNVLDLPTLLKFAVDVCR
GMCYLHQRGIIHRDLKSANLLMDKDHVVKVADFGVARFQDQGGNMTAETGTYRWMAPEDTDGLH
KALEASILRNEGSWSGSSHSSAAERTLPFQVKGGEWEIDKRLLKMGGMIASGSCGDLYHGTYLG
EDVAVKILRSEHLNKNVWNEFTQEVYILREVQHTNVVRFIGACTKPPQFCIITEYMSGGSLYDF
VHKQHNVLDLPTLLKFAVDVCRGMCYLHQRGIIHRDLKSANLLMDKDHVVKVADFGVARFQDQG
GNMTAETGTYRWMAPEDTDGLHKALEASILRNEGSWSGSSHSSAAERTLPFQVKGGEWEIDKRL
LKMGGMIASGSCGDLYHGTYLGEDVAVKILRSEHLNKNVWNEFTQEVYILREVQHTNVVRFIGA
CTKPPQFCIITEYMSGGSLYDFVHKQHNVLDLPTLLKFAVDVCRGMCYLHQRGIIHRDLKSANL
LMDKDHVVKVADFGVARFQDQGGNMTAETGTYRWMAPE(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3239360-3237899(+) 3239136-3238200(+) 3239089-3237850(-)
Potential amino acid sequence	MDASSALCKPSVSSGAIHLYVPVSAVMLPP(+) MAVFFLQLMSEMNLTMIPHSLKWTLPVPCANHQCPLVPSICMFQFQLSCYLLDPENELHQNLPL SQHDLCPLEGLHSLNLYG(+) MGGMIASGSCGDLYHGTYLGEDVAVKILRSEHLNKNVWNEFTQEVYILREVQHTNVVRFIGACT KPPQFCIITEYMSGGSLYDFVHKQHNVLDLPTLLKFAVDVCRGMCYLHQRGIIHRDLKSANLLM DKDHVVKVADFGVARFQDQGGNMTAETGTYRWMAPEDTDGLHKALEASILRNEGSWSGSSHSSA AERTLPFQVKGGEWEIDKRLLKMGGMIASGSCGDLYHGTYLGEDVAVKILRSEHLNKNVWNEFT QEVYILREVQHTNVVRFIGACTKPPQFCIITEYMSGGSLYDFVHKQHNVLDLPTLLKFAVDVCR GMCYLHQRGIIHRDLKSANLLMDKDHVVKVADFGVARFQDQGGNMTAETGTYRWMAPEDTDGLH KALEASILRNEGSWSGSSHSSAAERTLPFQVKGGEWEIDKRLLKMGGMIASGSCGDLYHGTYLG EDVAVKILRSEHLNKNVWNEFTQEVYILREVQHTNVVRFIGACTKPPQFCIITEYMSGGSLYDF VHKQHNVLDLPTLLKFAVDVCRGMCYLHQRGIIHRDLKSANLLMDKDHVVKVADFGVARFQDQG GNMTAETGTYRWMAPEDTDGLHKALEASILRNEGSWSGSSHSSAAERTLPFQVKGGEWEIDKRL LKMGGMIASGSCGDLYHGTYLGEDVAVKILRSEHLNKNVWNEFTQEVYILREVQHTNVVRFIGA CTKPPQFCIITEYMSGGSLYDFVHKQHNVLDLPTLLKFAVDVCRGMCYLHQRGIIHRDLKSANL LMDKDHVVKVADFGVARFQDQGGNMTAETGTYRWMAPE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os12g0163800_circ_g.4

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