Plant Circular RNA Database

Detail information of Os04g0489600_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0489600_circ_g.2
					
						ID in PlantcircBase
						osa_circ_024317
					
						Alias
						Os_ciR9412
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 24466451-24467090  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os04g0489600						
					
						Parent gene annotation
						
							Hypothetical conserved gene. (Os04t0489600-01);Helix-loop-helix 
DNA-binding domain containing protein. (Os04t0489600-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0489600_circ_g.3 Os04g0489600_circ_g.4 						
					
						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  
						
							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
						Os04t0489600-02:2

General Information
CircRNA Name	Os04g0489600_circ_g.2
ID in PlantcircBase	osa_circ_024317
Alias	Os_ciR9412
Organism	Oryza sativa
Position	chr4: 24466451-24467090 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Os04g0489600
Parent gene annotation	Hypothetical conserved gene. (Os04t0489600-01);Helix-loop-helix DNA-binding domain containing protein. (Os04t0489600-02)
Parent gene strand	+
Alternative splicing	Os04g0489600_circ_g.3 Os04g0489600_circ_g.4
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	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	Os04t0489600-02:2

			
						 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  
						
							TGGCGTAGAGAAATACCTGCAGATGCAGCACGACCAGGTGCCATTCAGAGTACGGGCCAAGCGT
GGATGCGCGACGCACCCACGGAGCATCGCAGAGAGGgtttctcatcgagtgctagaccagcagg
atcatcactcggtgaggttcgccatggcgccatgagcagcagcagcaacaacaacaagaagatg
aaggcccc

						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: 509
Transcript exons: 24466451-24466836,24466968-24467090
GTTTCTCATCGAGTGCTAGACCAGCAGGATCATCACTCGGTGAGGTTCGCCATGGCGCCATGAG
CAGCAGCAGCAACAACAACAAGAAGATGAAGGCCCCACTGAGCTTCGCTAGCAGCAGGCAGGGC
TCCGGCGGCCTCTCCCAGATATCCGAGGACGGCATCCCGGACCTCACTGACAGCATCCATGGCG
CCGCTCATCATCATGGGCGCTCCGAGGAGAACGTCTCCACCCACGACCACGTCGTCCGCTCCTT
CTCCTCCGGTGGGTTCTCGATCGGGTCATGGGAGGACTCCAACTCCATCGTGTTCTCCACGTCG
ACGGGCAAATCAGGAGCGCACGGCAACGACGACATCATCGCCACCCTTAGCAACTACGAATCTC
AGCTTGTTGCGCCCAGGGAGATGGCTGGCGTAGAGAAATACCTGCAGATGCAGCACGACCAGGT
GCCATTCAGAGTACGGGCCAAGCGTGGATGCGCGACGCACCCACGGAGCATCGCAGAGAGG
						
						Genomic sequence
						
							GTTTCTCATCGAGTGCTAGACCAGCAGGATCATCACTCGGTGAGGTTCGCCATGGCGCCATGAG
CAGCAGCAGCAACAACAACAAGAAGATGAAGGCCCCACTGAGCTTCGCTAGCAGCAGGCAGGGC
TCCGGCGGCCTCTCCCAGATATCCGAGGACGGCATCCCGGACCTCACTGACAGCATCCATGGCG
CCGCTCATCATCATGGGCGCTCCGAGGAGAACGTCTCCACCCACGACCACGTCGTCCGCTCCTT
CTCCTCCGGTGGGTTCTCGATCGGGTCATGGGAGGACTCCAACTCCATCGTGTTCTCCACGTCG
ACGGGCAAATCAGGAGCGCACGGCAACGACGACATCATCGCCACCCTTAGCAACTACGAATCTC
AGGTGTATATATATATGCGTTTTATCTTTATTTTTCATTTTTCGTATTTATAGTTTGATTTATT
AGTGTGTGTGTGTACAATGTGAGGGATGATTTCATGTCTAATTTGTATATACATGCATCTGCGA
TGCAGCTTGTTGCGCCCAGGGAGATGGCTGGCGTAGAGAAATACCTGCAGATGCAGCACGACCA
GGTGCCATTCAGAGTACGGGCCAAGCGTGGATGCGCGACGCACCCACGGAGCATCGCAGAGAGG

Sequences
Splice junction sequence	TGGCGTAGAGAAATACCTGCAGATGCAGCACGACCAGGTGCCATTCAGAGTACGGGCCAAGCGT GGATGCGCGACGCACCCACGGAGCATCGCAGAGAGGgtttctcatcgagtgctagaccagcagg atcatcactcggtgaggttcgccatggcgccatgagcagcagcagcaacaacaacaagaagatg aaggcccc
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: 509 Transcript exons: 24466451-24466836,24466968-24467090 GTTTCTCATCGAGTGCTAGACCAGCAGGATCATCACTCGGTGAGGTTCGCCATGGCGCCATGAG CAGCAGCAGCAACAACAACAAGAAGATGAAGGCCCCACTGAGCTTCGCTAGCAGCAGGCAGGGC TCCGGCGGCCTCTCCCAGATATCCGAGGACGGCATCCCGGACCTCACTGACAGCATCCATGGCG CCGCTCATCATCATGGGCGCTCCGAGGAGAACGTCTCCACCCACGACCACGTCGTCCGCTCCTT CTCCTCCGGTGGGTTCTCGATCGGGTCATGGGAGGACTCCAACTCCATCGTGTTCTCCACGTCG ACGGGCAAATCAGGAGCGCACGGCAACGACGACATCATCGCCACCCTTAGCAACTACGAATCTC AGCTTGTTGCGCCCAGGGAGATGGCTGGCGTAGAGAAATACCTGCAGATGCAGCACGACCAGGT GCCATTCAGAGTACGGGCCAAGCGTGGATGCGCGACGCACCCACGGAGCATCGCAGAGAGG
Genomic sequence	GTTTCTCATCGAGTGCTAGACCAGCAGGATCATCACTCGGTGAGGTTCGCCATGGCGCCATGAG CAGCAGCAGCAACAACAACAAGAAGATGAAGGCCCCACTGAGCTTCGCTAGCAGCAGGCAGGGC TCCGGCGGCCTCTCCCAGATATCCGAGGACGGCATCCCGGACCTCACTGACAGCATCCATGGCG CCGCTCATCATCATGGGCGCTCCGAGGAGAACGTCTCCACCCACGACCACGTCGTCCGCTCCTT CTCCTCCGGTGGGTTCTCGATCGGGTCATGGGAGGACTCCAACTCCATCGTGTTCTCCACGTCG ACGGGCAAATCAGGAGCGCACGGCAACGACGACATCATCGCCACCCTTAGCAACTACGAATCTC AGGTGTATATATATATGCGTTTTATCTTTATTTTTCATTTTTCGTATTTATAGTTTGATTTATT AGTGTGTGTGTGTACAATGTGAGGGATGATTTCATGTCTAATTTGTATATACATGCATCTGCGA TGCAGCTTGTTGCGCCCAGGGAGATGGCTGGCGTAGAGAAATACCTGCAGATGCAGCACGACCA GGTGCCATTCAGAGTACGGGCCAAGCGTGGATGCGCGACGCACCCACGGAGCATCGCAGAGAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.332200742

Conservation Information
Conserved circRNAs	NA
PMCS	0.332200742

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24467058-24466510(+)
24466511-24466510(+)
24466636-24467037(-)
24466461-24466782(-)
						
						Potential amino acid sequence
						
							MRDAPTEHRREGFSSSARPAGSSLGEVRHGAMSSSSNNNKKMKAPLSFASSRQGSGGLSQISED
GIPDLTDSIHGAAHHHGRSEENVSTHDHVVRSFSSGGFSIGSWEDSNSIVFSTSTGKSGAHGND
DIIATLSNYESQLVAPREMAGVEKYLQMQHDQVPFRVRAKRGCATHPRSIAERVSHRVLDQQDH
HSVRFAMAP*(+)
MSSSSNNNKKMKAPLSFASSRQGSGGLSQISEDGIPDLTDSIHGAAHHHGRSEENVSTHDHVVR
SFSSGGFSIGSWEDSNSIVFSTSTGKSGAHGNDDIIATLSNYESQLVAPREMAGVEKYLQMQHD
QVPFRVRAKRGCATHPRSIAERVSHRVLDQQDHHSVRFAMAP*(+)
MLSVRSGMPSSDIWERPPEPCLLLAKLSGAFIFLLLLLLLLMAPWRTSPSDDPAGLALDEKPSL
RCSVGASRIHAWPVL*(-)
MRNPLCDAPWVRRASTLGPYSEWHLVVLHLQVFLYASHLPGRNKLRFVVAKGGDDVVVAVRS*(
-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24467058-24466510(+) 24466511-24466510(+) 24466636-24467037(-) 24466461-24466782(-)
Potential amino acid sequence	MRDAPTEHRREGFSSSARPAGSSLGEVRHGAMSSSSNNNKKMKAPLSFASSRQGSGGLSQISED GIPDLTDSIHGAAHHHGRSEENVSTHDHVVRSFSSGGFSIGSWEDSNSIVFSTSTGKSGAHGND DIIATLSNYESQLVAPREMAGVEKYLQMQHDQVPFRVRAKRGCATHPRSIAERVSHRVLDQQDH HSVRFAMAP(+) MSSSSNNNKKMKAPLSFASSRQGSGGLSQISEDGIPDLTDSIHGAAHHHGRSEENVSTHDHVVR SFSSGGFSIGSWEDSNSIVFSTSTGKSGAHGNDDIIATLSNYESQLVAPREMAGVEKYLQMQHD QVPFRVRAKRGCATHPRSIAERVSHRVLDQQDHHSVRFAMAP(+) MLSVRSGMPSSDIWERPPEPCLLLAKLSGAFIFLLLLLLLLMAPWRTSPSDDPAGLALDEKPSL RCSVGASRIHAWPVL(-) MRNPLCDAPWVRRASTLGPYSEWHLVVLHLQVFLYASHLPGRNKLRFVVAKGGDDVVVAVRS( -)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os04g0489600_circ_g.2

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