Plant Circular RNA Database

Detail information of Os06g0598900_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os06g0598900_circ_g.1
					
						ID in PlantcircBase
						osa_circ_031297
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr6: 23614673-23615328  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os06g0598900						
					
						Parent gene annotation
						
							Similar to Serine-threonine kinase receptor-associated protein (
UNR-interacting protein) (WD-40 repeat protein PT-WD) (MAP activ
ator with WD repeats). (Os06t0598900-01);Hypothetical gene. (Os0
6t0598900-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os06g0598900_circ_g.2 Os06g0598900_circ_g.3 						
					
						Support reads
						2
					
						Tissues
						shoot, 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
						Os06t0598900-01:3

General Information
CircRNA Name	Os06g0598900_circ_g.1
ID in PlantcircBase	osa_circ_031297
Alias	NA
Organism	Oryza sativa
Position	chr6: 23614673-23615328 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os06g0598900
Parent gene annotation	Similar to Serine-threonine kinase receptor-associated protein ( UNR-interacting protein) (WD-40 repeat protein PT-WD) (MAP activ ator with WD repeats). (Os06t0598900-01);Hypothetical gene. (Os0 6t0598900-02)
Parent gene strand	-
Alternative splicing	Os06g0598900_circ_g.2 Os06g0598900_circ_g.3
Support reads	2
Tissues	shoot, 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	Os06t0598900-01:3

			
						 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  
						
							CAGGTGCTTTGTCAAGTTCTCTTGGTGCTGCATCTGGACGATTCATATCATAGACACGCAAAAT
CTTTTCTACGCCTCCAGTGAGCAACAGGTGGGTATCttatttcttcaccagtgaagaaatcaaa
tacatgaacccacatatcttctcccccaacaataaatttgctcccagattttggttccagggaa
gctgactc

						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: 454
Transcript exons: 23614673-23614812,23614909-23615046,23615153-23615328
TTATTTCTTCACCAGTGAAGAAATCAAATACATGAACCCACATATCTTCTCCCCCAACAATAAA
TTTGCTCCCAGATTTTGGTTCCAGGGAAGCTGACTCCACAGTGCAAGGCATATCATAGCTTTTA
ACAAGCCCAAAGTGATTAGCATCCCAAAATTTAACACTCGAGCCATCAGCTGTAGTGATGAACC
TGCTGTCTTGACTTACTTCTGCGCTAGTCACAGGCGCCTTGGTTTCAAGAGTTTGGACAATTTT
TCCAGTCCTCACATCCCACAATCTTACTCCTCCCATATCAGAGCACGAGCTTAGTATTGTTTGA
TCACTATGAAGCCAAGCAACAGTTCGCACGTTACCAGGTGCTTTGTCAAGTTCTCTTGGTGCTG
CATCTGGACGATTCATATCATAGACACGCAAAATCTTTTCTACGCCTCCAGTGAGCAACAGGTG
GGTATC
						
						Genomic sequence
						
							TTATTTCTTCACCAGTGAAGAAATCAAATACATGAACCCACATATCTTCTCCCCCAACAATAAA
TTTGCTCCCAGATTTTGGTTCCAGGGAAGCTGACTCCACAGTGCAAGGCATATCATAGCTTTTA
ACAAGCCCAAAGCTGCAAAATAACCAGCAAAAAATGTTTGTTGCAAAGGATTTAATAATTTTGT
ATGACACAGAACAACGGTATAATGATGATAGAAATAATACGTACTGATTAGCATCCCAAAATTT
AACACTCGAGCCATCAGCTGTAGTGATGAACCTGCTGTCTTGACTTACTTCTGCGCTAGTCACA
GGCGCCTTGGTTTCAAGAGTTTGGACAATTTTTCCAGTCCTCACATCCCACAATCTGTGCAGTG
CCATAACAATTAAATAAGAGGAACAAAATTACAATAAACTAGGAACAAATGGTAGCAGCTCTTC
CTATAGAATGAAGATATTTTTTCCAGACACACCTTACTCCTCCCATATCAGAGCACGAGCTTAG
TATTGTTTGATCACTATGAAGCCAAGCAACAGTTCGCACGTTACCAGGTGCTTTGTCAAGTTCT
CTTGGTGCTGCATCTGGACGATTCATATCATAGACACGCAAAATCTTTTCTACGCCTCCAGTGA
GCAACAGGTGGGTATC

Sequences
Splice junction sequence	CAGGTGCTTTGTCAAGTTCTCTTGGTGCTGCATCTGGACGATTCATATCATAGACACGCAAAAT CTTTTCTACGCCTCCAGTGAGCAACAGGTGGGTATCttatttcttcaccagtgaagaaatcaaa tacatgaacccacatatcttctcccccaacaataaatttgctcccagattttggttccagggaa gctgactc
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: 454 Transcript exons: 23614673-23614812,23614909-23615046,23615153-23615328 TTATTTCTTCACCAGTGAAGAAATCAAATACATGAACCCACATATCTTCTCCCCCAACAATAAA TTTGCTCCCAGATTTTGGTTCCAGGGAAGCTGACTCCACAGTGCAAGGCATATCATAGCTTTTA ACAAGCCCAAAGTGATTAGCATCCCAAAATTTAACACTCGAGCCATCAGCTGTAGTGATGAACC TGCTGTCTTGACTTACTTCTGCGCTAGTCACAGGCGCCTTGGTTTCAAGAGTTTGGACAATTTT TCCAGTCCTCACATCCCACAATCTTACTCCTCCCATATCAGAGCACGAGCTTAGTATTGTTTGA TCACTATGAAGCCAAGCAACAGTTCGCACGTTACCAGGTGCTTTGTCAAGTTCTCTTGGTGCTG CATCTGGACGATTCATATCATAGACACGCAAAATCTTTTCTACGCCTCCAGTGAGCAACAGGTG GGTATC
Genomic sequence	TTATTTCTTCACCAGTGAAGAAATCAAATACATGAACCCACATATCTTCTCCCCCAACAATAAA TTTGCTCCCAGATTTTGGTTCCAGGGAAGCTGACTCCACAGTGCAAGGCATATCATAGCTTTTA ACAAGCCCAAAGCTGCAAAATAACCAGCAAAAAATGTTTGTTGCAAAGGATTTAATAATTTTGT ATGACACAGAACAACGGTATAATGATGATAGAAATAATACGTACTGATTAGCATCCCAAAATTT AACACTCGAGCCATCAGCTGTAGTGATGAACCTGCTGTCTTGACTTACTTCTGCGCTAGTCACA GGCGCCTTGGTTTCAAGAGTTTGGACAATTTTTCCAGTCCTCACATCCCACAATCTGTGCAGTG CCATAACAATTAAATAAGAGGAACAAAATTACAATAAACTAGGAACAAATGGTAGCAGCTCTTC CTATAGAATGAAGATATTTTTTCCAGACACACCTTACTCCTCCCATATCAGAGCACGAGCTTAG TATTGTTTGATCACTATGAAGCCAAGCAACAGTTCGCACGTTACCAGGTGCTTTGTCAAGTTCT CTTGGTGCTGCATCTGGACGATTCATATCATAGACACGCAAAATCTTTTCTACGCCTCCAGTGA GCAACAGGTGGGTATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_016388 						
					
						PMCS
						0.404791463

Conservation Information
Conserved circRNAs	osi_circ_016388
PMCS	0.404791463

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							23615201-23614687(+)
23615276-23615278(-)
						
						Potential amino acid sequence
						
							MKPSNSSHVTRCFVKFSWCCIWTIHIIDTQNLFYASSEQQVGILFLHQ*(+)
MNRPDAAPRELDKAPGNVRTVAWLHSDQTILSSCSDMGGVRLWDVRTGKIVQTLETKAPVTSAE
VSQDSRFITTADGSSVKFWDANHFGLVKSYDMPCTVESASLEPKSGSKFIVGGEDMWVHVFDFF
TGEEIRYPPVAHWRRRKDFACL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	23615201-23614687(+) 23615276-23615278(-)
Potential amino acid sequence	MKPSNSSHVTRCFVKFSWCCIWTIHIIDTQNLFYASSEQQVGILFLHQ(+) MNRPDAAPRELDKAPGNVRTVAWLHSDQTILSSCSDMGGVRLWDVRTGKIVQTLETKAPVTSAE VSQDSRFITTADGSSVKFWDANHFGLVKSYDMPCTVESASLEPKSGSKFIVGGEDMWVHVFDFF TGEEIRYPPVAHWRRRKDFACL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os06g0598900_circ_g.1

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