Plant Circular RNA Database

Detail information of Os05g0388400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os05g0388400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_027740
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 18782278-18783774  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							Os05g0388400						
					
						Parent gene annotation
						
							Similar to cDNA clone:J013089M16, full insert sequence. (Os05t03
88400-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os05g0388400_circ_g.2 						
					
						Support reads
						3
					
						Tissues
						shoot, root, seed
					
						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
						Os05t0388400-01:3

General Information
CircRNA Name	Os05g0388400_circ_g.3
ID in PlantcircBase	osa_circ_027740
Alias	NA
Organism	Oryza sativa
Position	chr5: 18782278-18783774 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	Os05g0388400
Parent gene annotation	Similar to cDNA clone:J013089M16, full insert sequence. (Os05t03 88400-01)
Parent gene strand	+
Alternative splicing	Os05g0388400_circ_g.2
Support reads	3
Tissues	shoot, root, seed
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	Os05t0388400-01:3

			
						 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  
						
							TCCAACTTACTGGAAATCTTTGACAGATGAGGAAATGAAGACATTACACACGAAGGTTGATCTC
ATTGTAACTCTTGGAGGTGATGGAACAGTTTTATGGgcaccatttaaactttcatggggatgca
atggggataataatggtcagcacaagcatgattttgtatccttcgaaaaaggggatataacaac
agctgaac

									
								

					

						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: 625
Transcript exons: 18782278-18782391,18782520-18782956,18783701-18783774
GCACCATTTAAACTTTCATGGGGATGCAATGGGGATAATAATGGTCAGCACAAGCATGATTTTG
TATCCTTCGAAAAAGGGGATATAACAACAGCTGAACGCAGCAATAAGCAGATTTTGCTAAAGTG
GGAATCCCCTCCACAAACTGTTCTTTTCGTGACTAAACCTAATTCCAACTCCGTGCACGCTCTC
TGTGCTGAAATGGTTAGGTATGTTTTCTTTCTGCTCTGTGTGCCAACATGGTCAGGTATGTCAA
AGGTTTTATATTTTATCAATCATCTGAGTTCGGCATTAAAAATAGCTTCTTTTTTGTTTCTGGA
ACTTGTCCTCTCCTAATTTACTTATGTTAAGCAGATTTTGTTGATAAATAATGTTGCATGGAAT
TGTATATTTTTCATTCAATATCGTTGTTTCACTTGTGCTAATGTCTGCCGTTCTCCGCAGATGG
CTTAAAGAGCACAATAATATAAACATCTTTGTAGAGCCACGAGTTAGCAAGGAACTAGTGACTG
AAGATTCATACTTCAACTTTATCCAAACATGGGATAATGATGAGGAAATGAAGACATTACACAC
GAAGGTTGATCTCATTGTAACTCTTGGAGGTGATGGAACAGTTTTATGG
						
					

						Genomic sequence
						
							GCACCATTTAAACTTTCATGGGGATGCAATGGGGATAATAATGGTCAGCACAAGCATGATTTTG
TATCCTTCGAAAAAGGGGATATAACAACAGCTGAACGCAGCAATAAGCAGGTAGCTATTTGAGG
TTTGAGCTATATGATCCATTTTTTAAAAAAATTGTCTTAACTAGTTGGAAATGATTGTTGGATA
ATTCCATTGCTGCCGTATTTTTTTAATGGCAAAAAATTACCGTGCCTCAGATTTTGCTAAAGTG
GGAATCCCCTCCACAAACTGTTCTTTTCGTGACTAAACCTAATTCCAACTCCGTGCACGCTCTC
TGTGCTGAAATGGTTAGGTATGTTTTCTTTCTGCTCTGTGTGCCAACATGGTCAGGTATGTCAA
AGGTTTTATATTTTATCAATCATCTGAGTTCGGCATTAAAAATAGCTTCTTTTTTGTTTCTGGA
ACTTGTCCTCTCCTAATTTACTTATGTTAAGCAGATTTTGTTGATAAATAATGTTGCATGGAAT
TGTATATTTTTCATTCAATATCGTTGTTTCACTTGTGCTAATGTCTGCCGTTCTCCGCAGATGG
CTTAAAGAGCACAATAATATAAACATCTTTGTAGAGCCACGAGTTAGCAAGGAACTAGTGACTG
AAGATTCATACTTCAACTTTATCCAAACATGGGATAATGGTAATTATTTTTGCCTATATTAGAA
TCATTAGACTTTGTATCTTGGAACGTCAGGGTGTGAAGAATATCTTGTCACAACCTAGATAACC
TGATATCTGATTTATTTTTTTAAATATCAATAATCTGGCACTGAAATAAATGGTTATGGTCACT
GTTTATGAGAATGAAAAGCAGTATGCTGTGATAATTTCATAATTTAAGGACTACATTGGTTCAT
TTAACTCATGGACAACCAATAGACATTCCCCTCTACTTTTAAGTAACCTGCTAAATTTCTTCTC
ATTGGCCCTTGCAATGAAGTTCTTCTTTCATACCTAATGACCCTTGCAATGAAGTTTTCTTTCA
TACCTAATGACATGCTGCTGCTGGTGGCTGTGTGTTTGTTAATGTGATAAATTCATTACAGTGG
TCTAATATCTACTACGAGAAATGTATCCTTTCCTTTAGCATTATACATTAAGTTGGTTAATGTT
AATTTCCTTTACCGATAAAATACTAAAAACAAAACAGTCTAGTGTCTCAACTCTCAACAGTTGC
TTGAGTTTCTATTAGTGCTTGAATGGATCGTCTATCATTAAATAGCTCCTTTTCTGTTGATGAG
TTCTGTCAATAGAGTTCCCTTGCGCTGTCTTTCTCTGTGGTTTAAAATATCCCCATTCCATAAT
ATACTTGTTTTGTTAACCTATGCCCTTAGAAATATGCCCCTTTGTTTTTGGTGTCCAACTTACT
GGAAATCTTTGACAGATGAGGAAATGAAGACATTACACACGAAGGTTGATCTCATTGTAACTCT
TGGAGGTGATGGAACAGTTTTATGG
						
					

			
		

Sequences
Splice junction sequence	TCCAACTTACTGGAAATCTTTGACAGATGAGGAAATGAAGACATTACACACGAAGGTTGATCTC ATTGTAACTCTTGGAGGTGATGGAACAGTTTTATGGgcaccatttaaactttcatggggatgca atggggataataatggtcagcacaagcatgattttgtatccttcgaaaaaggggatataacaac agctgaac
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: 625 Transcript exons: 18782278-18782391,18782520-18782956,18783701-18783774 GCACCATTTAAACTTTCATGGGGATGCAATGGGGATAATAATGGTCAGCACAAGCATGATTTTG TATCCTTCGAAAAAGGGGATATAACAACAGCTGAACGCAGCAATAAGCAGATTTTGCTAAAGTG GGAATCCCCTCCACAAACTGTTCTTTTCGTGACTAAACCTAATTCCAACTCCGTGCACGCTCTC TGTGCTGAAATGGTTAGGTATGTTTTCTTTCTGCTCTGTGTGCCAACATGGTCAGGTATGTCAA AGGTTTTATATTTTATCAATCATCTGAGTTCGGCATTAAAAATAGCTTCTTTTTTGTTTCTGGA ACTTGTCCTCTCCTAATTTACTTATGTTAAGCAGATTTTGTTGATAAATAATGTTGCATGGAAT TGTATATTTTTCATTCAATATCGTTGTTTCACTTGTGCTAATGTCTGCCGTTCTCCGCAGATGG CTTAAAGAGCACAATAATATAAACATCTTTGTAGAGCCACGAGTTAGCAAGGAACTAGTGACTG AAGATTCATACTTCAACTTTATCCAAACATGGGATAATGATGAGGAAATGAAGACATTACACAC GAAGGTTGATCTCATTGTAACTCTTGGAGGTGATGGAACAGTTTTATGG
Genomic sequence	GCACCATTTAAACTTTCATGGGGATGCAATGGGGATAATAATGGTCAGCACAAGCATGATTTTG TATCCTTCGAAAAAGGGGATATAACAACAGCTGAACGCAGCAATAAGCAGGTAGCTATTTGAGG TTTGAGCTATATGATCCATTTTTTAAAAAAATTGTCTTAACTAGTTGGAAATGATTGTTGGATA ATTCCATTGCTGCCGTATTTTTTTAATGGCAAAAAATTACCGTGCCTCAGATTTTGCTAAAGTG GGAATCCCCTCCACAAACTGTTCTTTTCGTGACTAAACCTAATTCCAACTCCGTGCACGCTCTC TGTGCTGAAATGGTTAGGTATGTTTTCTTTCTGCTCTGTGTGCCAACATGGTCAGGTATGTCAA AGGTTTTATATTTTATCAATCATCTGAGTTCGGCATTAAAAATAGCTTCTTTTTTGTTTCTGGA ACTTGTCCTCTCCTAATTTACTTATGTTAAGCAGATTTTGTTGATAAATAATGTTGCATGGAAT TGTATATTTTTCATTCAATATCGTTGTTTCACTTGTGCTAATGTCTGCCGTTCTCCGCAGATGG CTTAAAGAGCACAATAATATAAACATCTTTGTAGAGCCACGAGTTAGCAAGGAACTAGTGACTG AAGATTCATACTTCAACTTTATCCAAACATGGGATAATGGTAATTATTTTTGCCTATATTAGAA TCATTAGACTTTGTATCTTGGAACGTCAGGGTGTGAAGAATATCTTGTCACAACCTAGATAACC TGATATCTGATTTATTTTTTTAAATATCAATAATCTGGCACTGAAATAAATGGTTATGGTCACT GTTTATGAGAATGAAAAGCAGTATGCTGTGATAATTTCATAATTTAAGGACTACATTGGTTCAT TTAACTCATGGACAACCAATAGACATTCCCCTCTACTTTTAAGTAACCTGCTAAATTTCTTCTC ATTGGCCCTTGCAATGAAGTTCTTCTTTCATACCTAATGACCCTTGCAATGAAGTTTTCTTTCA TACCTAATGACATGCTGCTGCTGGTGGCTGTGTGTTTGTTAATGTGATAAATTCATTACAGTGG TCTAATATCTACTACGAGAAATGTATCCTTTCCTTTAGCATTATACATTAAGTTGGTTAATGTT AATTTCCTTTACCGATAAAATACTAAAAACAAAACAGTCTAGTGTCTCAACTCTCAACAGTTGC TTGAGTTTCTATTAGTGCTTGAATGGATCGTCTATCATTAAATAGCTCCTTTTCTGTTGATGAG TTCTGTCAATAGAGTTCCCTTGCGCTGTCTTTCTCTGTGGTTTAAAATATCCCCATTCCATAAT ATACTTGTTTTGTTAACCTATGCCCTTAGAAATATGCCCCTTTGTTTTTGGTGTCCAACTTACT GGAAATCTTTGACAGATGAGGAAATGAAGACATTACACACGAAGGTTGATCTCATTGTAACTCT TGGAGGTGATGGAACAGTTTTATGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_006213* osi_circ_015406 						
					
						PMCS
						0.240299332

Conservation Information
Conserved circRNAs	osi_circ_006213* osi_circ_015406
PMCS	0.240299332

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							18782777-18782738(+)
18783759-18782362(+)
						
						Potential amino acid sequence
						
							MLHGIVYFSFNIVVSLVLMSAVLRRWLKEHNNINIFVEPRVSKELVTEDSYFNFIQTWDNDEEM
KTLHTKVDLIVTLGGDGTVLWAPFKLSWGCNGDNNGQHKHDFVSFEKGDITTAERSNKQILLKW
ESPPQTVLFVTKPNSNSVHALCAEMVRYVFFLLCVPTWSGMSKVLYFINHLSSALKIASFLFLE
LVLS*(+)
MEQFYGHHLNFHGDAMGIIMVSTSMILYPSKKGI*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	18782777-18782738(+) 18783759-18782362(+)
Potential amino acid sequence	MLHGIVYFSFNIVVSLVLMSAVLRRWLKEHNNINIFVEPRVSKELVTEDSYFNFIQTWDNDEEM KTLHTKVDLIVTLGGDGTVLWAPFKLSWGCNGDNNGQHKHDFVSFEKGDITTAERSNKQILLKW ESPPQTVLFVTKPNSNSVHALCAEMVRYVFFLLCVPTWSGMSKVLYFINHLSSALKIASFLFLE LVLS(+) MEQFYGHHLNFHGDAMGIIMVSTSMILYPSKKGI(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os05g0388400_circ_g.3

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