Plant Circular RNA Database

Detail information of Os04g0492600_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0492600_circ_g.3
					
						ID in PlantcircBase
						osa_circ_024373
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 24632026-24633032  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							Os04g0492600						
					
						Parent gene annotation
						
							Anticodon-binding domain containing protein. (Os04t0492600-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0492600_circ_g.1 Os04g0492600_circ_g.2 						
					
						Support reads
						1
					
						Tissues
						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
						Os04t0492600-01:4

General Information
CircRNA Name	Os04g0492600_circ_g.3
ID in PlantcircBase	osa_circ_024373
Alias	NA
Organism	Oryza sativa
Position	chr4: 24632026-24633032 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	Os04g0492600
Parent gene annotation	Anticodon-binding domain containing protein. (Os04t0492600-01)
Parent gene strand	+
Alternative splicing	Os04g0492600_circ_g.1 Os04g0492600_circ_g.2
Support reads	1
Tissues	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	Os04t0492600-01:4

			
						 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  
						
							ATTTCTCAAATGTTTGAGAATATGGTCAATCGAAGAACATATTACTATTGATGTACTCATGCCT
CCTTCAGAATGTTACTACACAGATCTGTTTTTTCAGgtcactttggatgttggggcacactttt
atgatccgaaggcaataattatccgtctgaatcatagcaaacttgctgaagcagtttgttcctg
ggcaggag

									
								

					

						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: 465
Transcript exons: 24632026-24632157,24632238-24632324,24632703-24632811,24
632896-24633032
GTCACTTTGGATGTTGGGGCACACTTTTATGATCCGAAGGCAATAATTATCCGTCTGAATCATA
GCAAACTTGCTGAAGCAGTTTGTTCCTGGGCAGGAGTTCCTCAAGAACGGCGACAAAATGTTGC
TGAGTTTTTCTCTTCAACTCTTGTTCAGTATTGGCCAAATAAGGCTGATCGCAAGTCACAATGG
AGTTTGATTCGTGGGCAACTATTACAGGATCTTCGTCTTTCGGAAGAGGTGGTTGAGAAGCTAC
ATAAAGCTGATCAGAGATTTTGTGGTTCTGCAGATCAAGTACTTGCTAGATTAAGAGGGACCCT
GTTCTATGATAAATCTGCTTGCAAGGCTCTCGATGAGATCTCAGCATTTCTCAAATGTTTGAGA
ATATGGTCAATCGAAGAACATATTACTATTGATGTACTCATGCCTCCTTCAGAATGTTACTACA
CAGATCTGTTTTTTCAG
						
					

						Genomic sequence
						
							GTCACTTTGGATGTTGGGGCACACTTTTATGATCCGAAGGCAATAATTATCCGTCTGAATCATA
GCAAACTTGCTGAAGCAGTTTGTTCCTGGGCAGGAGTTCCTCAAGAACGGCGACAAAATGTTGC
TGAGGTACAGTACTTTGTCTCACCTGTTCCTCACATTTGTGGAATCATCTCAGCTGATACCTTT
TTTTTCTGTGTGTGTATCAGTTTTTCTCTTCAACTCTTGTTCAGTATTGGCCAAATAAGGCTGA
TCGCAAGTCACAATGGAGTTTGATTCGTGGGCAACTATTACAGGTACAAGCACCACAATACACA
ATCAAACCATGGTGGTACTTTAATAGTTGTTGTTTTATTGATTAATAAAGCATACTGAATACTA
CTACAGTGAAACTCCTGTATGAATAGTTTTTTTTGGTAAAAACAATATAATGCATCAACGTATT
ACTAATATTGAACAAGTTGGAAAAAATAATTCTGTTAACAATTTGCAAGATGCAAAGTTTTATC
CTATTTAATTAGGTTCGTTATTATACCTTTTCCCTTGTAAATGCTTGATTTACTGAGATGCATT
CACAAGATTCCCATGTGAATATTGAAAATGCTTCCATTACTAACAGTTTCCATCTTTCCATGTA
ATGGGTTAGTGTATAAAAATATTTATTGAATGCTCAGGATCTTCGTCTTTCGGAAGAGGTGGTT
GAGAAGCTACATAAAGCTGATCAGAGATTTTGTGGTTCTGCAGATCAAGTACTTGCTAGATTAA
GAGGGACCCTGTTCTATGGTAGTGATTAAGCCCCTCTACATTGTCTGCTGTAGTCTGCAAATAT
GTACTAAAATGTCAATCATTCTATGTTTCTTGTTGCAGATAAATCTGCTTGCAAGGCTCTCGAT
GAGATCTCAGCATTTCTCAAATGTTTGAGAATATGGTCAATCGAAGAACATATTACTATTGATG
TACTCATGCCTCCTTCAGAATGTTACTACACAGATCTGTTTTTTCAG
						
					

			
		

Sequences
Splice junction sequence	ATTTCTCAAATGTTTGAGAATATGGTCAATCGAAGAACATATTACTATTGATGTACTCATGCCT CCTTCAGAATGTTACTACACAGATCTGTTTTTTCAGgtcactttggatgttggggcacactttt atgatccgaaggcaataattatccgtctgaatcatagcaaacttgctgaagcagtttgttcctg ggcaggag
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: 465 Transcript exons: 24632026-24632157,24632238-24632324,24632703-24632811,24 632896-24633032 GTCACTTTGGATGTTGGGGCACACTTTTATGATCCGAAGGCAATAATTATCCGTCTGAATCATA GCAAACTTGCTGAAGCAGTTTGTTCCTGGGCAGGAGTTCCTCAAGAACGGCGACAAAATGTTGC TGAGTTTTTCTCTTCAACTCTTGTTCAGTATTGGCCAAATAAGGCTGATCGCAAGTCACAATGG AGTTTGATTCGTGGGCAACTATTACAGGATCTTCGTCTTTCGGAAGAGGTGGTTGAGAAGCTAC ATAAAGCTGATCAGAGATTTTGTGGTTCTGCAGATCAAGTACTTGCTAGATTAAGAGGGACCCT GTTCTATGATAAATCTGCTTGCAAGGCTCTCGATGAGATCTCAGCATTTCTCAAATGTTTGAGA ATATGGTCAATCGAAGAACATATTACTATTGATGTACTCATGCCTCCTTCAGAATGTTACTACA CAGATCTGTTTTTTCAG
Genomic sequence	GTCACTTTGGATGTTGGGGCACACTTTTATGATCCGAAGGCAATAATTATCCGTCTGAATCATA GCAAACTTGCTGAAGCAGTTTGTTCCTGGGCAGGAGTTCCTCAAGAACGGCGACAAAATGTTGC TGAGGTACAGTACTTTGTCTCACCTGTTCCTCACATTTGTGGAATCATCTCAGCTGATACCTTT TTTTTCTGTGTGTGTATCAGTTTTTCTCTTCAACTCTTGTTCAGTATTGGCCAAATAAGGCTGA TCGCAAGTCACAATGGAGTTTGATTCGTGGGCAACTATTACAGGTACAAGCACCACAATACACA ATCAAACCATGGTGGTACTTTAATAGTTGTTGTTTTATTGATTAATAAAGCATACTGAATACTA CTACAGTGAAACTCCTGTATGAATAGTTTTTTTTGGTAAAAACAATATAATGCATCAACGTATT ACTAATATTGAACAAGTTGGAAAAAATAATTCTGTTAACAATTTGCAAGATGCAAAGTTTTATC CTATTTAATTAGGTTCGTTATTATACCTTTTCCCTTGTAAATGCTTGATTTACTGAGATGCATT CACAAGATTCCCATGTGAATATTGAAAATGCTTCCATTACTAACAGTTTCCATCTTTCCATGTA ATGGGTTAGTGTATAAAAATATTTATTGAATGCTCAGGATCTTCGTCTTTCGGAAGAGGTGGTT GAGAAGCTACATAAAGCTGATCAGAGATTTTGTGGTTCTGCAGATCAAGTACTTGCTAGATTAA GAGGGACCCTGTTCTATGGTAGTGATTAAGCCCCTCTACATTGTCTGCTGTAGTCTGCAAATAT GTACTAAAATGTCAATCATTCTATGTTTCTTGTTGCAGATAAATCTGCTTGCAAGGCTCTCGAT GAGATCTCAGCATTTCTCAAATGTTTGAGAATATGGTCAATCGAAGAACATATTACTATTGATG TACTCATGCCTCCTTCAGAATGTTACTACACAGATCTGTTTTTTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_014497 						
					
						PMCS
						0.167408664

Conservation Information
Conserved circRNAs	osi_circ_014497
PMCS	0.167408664

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24632992-24633029(+)
24632984-24632068(+)
24632090-24633002(-)
						
						Potential amino acid sequence
						
							MPPSECYYTDLFFQVTLDVGAHFYDPKAIIIRLNHSKLAEAVCSWAGVPQERRQNVAEFFSSTL
VQYWPNKADRKSQWSLIRGQLLQDLRLSEEVVEKLHKADQRFCGSADQVLARLRGTLFYDKSAC
KALDEISAFLKCLRIWSIEEHITIDVLMPPSECYYTDLFFQVTLDVGAHFYDPKAIIIRLNHSK
LAEAVCSWAGVPQERRQNVAEFFSSTLVQYWPNKADRKSQWSLIRGQLLQDLRLSEEVVEKLHK
ADQRFCGSADQVLARLRGTLFYDKSACKALDEISAFLKCLRIWSIEEHITIDVLMPPSECYYTD
LFFQVTLDVGAHFYDPKAIIIRLNHSKLAEAVCSWAGVPQERRQNVAEFFSSTLVQYWPNKADR
KSQWSLIRGQLLQDLRLSEEVVEKLHKADQRFCGSADQVLARLRGTLFYDKSACKALDEISAFL
KCLRIWSIEEHITIDVLMPPSECYYTDLFFQ(+)
MYSCLLQNVTTQICFFRSLWMLGHTFMIRRQ*(+)
MIQTDNYCLRIIKVCPNIQSDLKKQICVVTF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24632992-24633029(+) 24632984-24632068(+) 24632090-24633002(-)
Potential amino acid sequence	MPPSECYYTDLFFQVTLDVGAHFYDPKAIIIRLNHSKLAEAVCSWAGVPQERRQNVAEFFSSTL VQYWPNKADRKSQWSLIRGQLLQDLRLSEEVVEKLHKADQRFCGSADQVLARLRGTLFYDKSAC KALDEISAFLKCLRIWSIEEHITIDVLMPPSECYYTDLFFQVTLDVGAHFYDPKAIIIRLNHSK LAEAVCSWAGVPQERRQNVAEFFSSTLVQYWPNKADRKSQWSLIRGQLLQDLRLSEEVVEKLHK ADQRFCGSADQVLARLRGTLFYDKSACKALDEISAFLKCLRIWSIEEHITIDVLMPPSECYYTD LFFQVTLDVGAHFYDPKAIIIRLNHSKLAEAVCSWAGVPQERRQNVAEFFSSTLVQYWPNKADR KSQWSLIRGQLLQDLRLSEEVVEKLHKADQRFCGSADQVLARLRGTLFYDKSACKALDEISAFL KCLRIWSIEEHITIDVLMPPSECYYTDLFFQ(+) MYSCLLQNVTTQICFFRSLWMLGHTFMIRRQ(+) MIQTDNYCLRIIKVCPNIQSDLKKQICVVTF(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0492600_circ_g.3

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