Plant Circular RNA Database

Detail information of Os01g0886600_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0886600_circ_g.3
					
						ID in PlantcircBase
						osa_circ_005139
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 38521288-38522327  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0886600						
					
						Parent gene annotation
						
							Similar to CLP protease regulatory subunit CLPX precursor. (Os01
t0886600-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0886600_circ_g.1 Os01g0886600_circ_g.2 Os01g0886600_circ_g.4 Os01g0886600_circ_g.5 Os01g0886600_circ_g.6 Os01g0886600_circ_g.7 						
					
						Support reads
						1
					
						Tissues
						shoot
					
						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
						Os01t0886600-01:5

General Information
CircRNA Name	Os01g0886600_circ_g.3
ID in PlantcircBase	osa_circ_005139
Alias	NA
Organism	Oryza sativa
Position	chr1: 38521288-38522327 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0886600
Parent gene annotation	Similar to CLP protease regulatory subunit CLPX precursor. (Os01 t0886600-01)
Parent gene strand	-
Alternative splicing	Os01g0886600_circ_g.1 Os01g0886600_circ_g.2 Os01g0886600_circ_g.4 Os01g0886600_circ_g.5 Os01g0886600_circ_g.6 Os01g0886600_circ_g.7
Support reads	1
Tissues	shoot
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	Os01t0886600-01:5

			
						 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  
						
							AGATTCCAACAATGATGAAGTGACCATTGGATCAGTCACTTCAGAACTTCTCATGTTTATCCGA
ATGGGTGCCCCAAAACCTATAGATGAATCTTGGCGCcatggaattcttcatgttagtgtttgtt
atgtactgctccaatgcaccgtcaccccgaagaattttggctccacatcctggcctatcaattg
aacctatt

									
								

					

						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: 550
Transcript exons: 38521288-38521446,38521517-38521639,38521726-38521788,38
521989-38522093,38522228-38522327
CATGGAATTCTTCATGTTAGTGTTTGTTATGTACTGCTCCAATGCACCGTCACCCCGAAGAATT
TTGGCTCCACATCCTGGCCTATCAATTGAACCTATTGCCTCCTCATCCACCACAACAGCGTCTA
CTCGTTCGCTTCCTGTTTTCTCGTCTGGGATCTCATACATGGCCTCCAATAGAAGGCTTTCCAA
GATGGCTCTCAGACCACGTGCACCAGTATTTCTGGCTATAGCCTTCTTGGCTACTATTCTAAGT
GCACCATCAGTAAAGTGTAACTTAACTTTGTTCAGGCTAAACATTTTCCTGTATTGTCTGGAAA
GAGAATTCTTTGGTTCTGTAAGAACCTGAACAAGCTGATCTTCATTGAGAGCTGTCAAACTAAC
TAGGATGGGCAAGCGTCCAATAAACTCTGGTATCAAACCATATCTTGCAAGATCGCCACTCTCA
ACAGATTCCAACAATGATGAAGTGACCATTGGATCAGTCACTTCAGAACTTCTCATGTTTATCC
GAATGGGTGCCCCAAAACCTATAGATGAATCTTGGCGC
						
					

						Genomic sequence
						
							CATGGAATTCTTCATGTTAGTGTTTGTTATGTACTGCTCCAATGCACCGTCACCCCGAAGAATT
TTGGCTCCACATCCTGGCCTATCAATTGAACCTATTGCCTCCTCATCCACCACAACAGCGTCTA
CTCGTTCGCTTCCTGTTTTCTCGTCTGGGATCTGATTAAAAGAAGCGTCAGAATGTATAACTAA
GCTTTGTGTCACTATTTACAGAACAATAGAACGCTACCTCATACATGGCCTCCAATAGAAGGCT
TTCCAAGATGGCTCTCAGACCACGTGCACCAGTATTTCTGGCTATAGCCTTCTTGGCTACTATT
CTAAGTGCACCATCAGTAAAGTGTAACTTAACCTGAAGGAAAAAAACAAGATTGAGGATTAGAT
ATTACTGAATATAAGAAAACCTTAAGCCTATCACCTAAGTTCATGTGAACTCACTTTGTTCAGG
CTAAACATTTTCCTGTATTGTCTGGAAAGAGAATTCTTTGGTTCTGTAAGAACCTGAATGCAGA
TGAAATCATTTCAGTTAGCTACAGCAGGCAAGTACAAAAGAATACATAAAATAGATTTCTTCAT
GGCCATAGAAGTTTATGTGATGGAGAAGAATAAACATGATTTTGAACTAAGATGACATTAAAGG
CATAAACCATCAACATTATGCATATTTTTTTCTCTGCATAAGTCTTCCTGAACAAGCTAACCTG
AACAAGCTGATCTTCATTGAGAGCTGTCAAACTAACTAGGATGGGCAAGCGTCCAATAAACTCT
GGTATCAAACCATATCTTGCAAGATCGCCACTCTCAACCTGCCAAAGGAGCACGTGGTTTCGTA
TTCATGACCATGTGATAGTTTTTTTAAGATGAAACACAGCTCCATGGTATTGGTGGTACCAAGT
AGACCATAAGGAGTTCAGTTAGCCAAAGGTTCCAAAATGCTTACAGATTCCAACAATGATGAAG
TGACCATTGGATCAGTCACTTCAGAACTTCTCATGTTTATCCGAATGGGTGCCCCAAAACCTAT
AGATGAATCTTGGCGC
						
					

			
		

Sequences
Splice junction sequence	AGATTCCAACAATGATGAAGTGACCATTGGATCAGTCACTTCAGAACTTCTCATGTTTATCCGA ATGGGTGCCCCAAAACCTATAGATGAATCTTGGCGCcatggaattcttcatgttagtgtttgtt atgtactgctccaatgcaccgtcaccccgaagaattttggctccacatcctggcctatcaattg aacctatt
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: 550 Transcript exons: 38521288-38521446,38521517-38521639,38521726-38521788,38 521989-38522093,38522228-38522327 CATGGAATTCTTCATGTTAGTGTTTGTTATGTACTGCTCCAATGCACCGTCACCCCGAAGAATT TTGGCTCCACATCCTGGCCTATCAATTGAACCTATTGCCTCCTCATCCACCACAACAGCGTCTA CTCGTTCGCTTCCTGTTTTCTCGTCTGGGATCTCATACATGGCCTCCAATAGAAGGCTTTCCAA GATGGCTCTCAGACCACGTGCACCAGTATTTCTGGCTATAGCCTTCTTGGCTACTATTCTAAGT GCACCATCAGTAAAGTGTAACTTAACTTTGTTCAGGCTAAACATTTTCCTGTATTGTCTGGAAA GAGAATTCTTTGGTTCTGTAAGAACCTGAACAAGCTGATCTTCATTGAGAGCTGTCAAACTAAC TAGGATGGGCAAGCGTCCAATAAACTCTGGTATCAAACCATATCTTGCAAGATCGCCACTCTCA ACAGATTCCAACAATGATGAAGTGACCATTGGATCAGTCACTTCAGAACTTCTCATGTTTATCC GAATGGGTGCCCCAAAACCTATAGATGAATCTTGGCGC
Genomic sequence	CATGGAATTCTTCATGTTAGTGTTTGTTATGTACTGCTCCAATGCACCGTCACCCCGAAGAATT TTGGCTCCACATCCTGGCCTATCAATTGAACCTATTGCCTCCTCATCCACCACAACAGCGTCTA CTCGTTCGCTTCCTGTTTTCTCGTCTGGGATCTGATTAAAAGAAGCGTCAGAATGTATAACTAA GCTTTGTGTCACTATTTACAGAACAATAGAACGCTACCTCATACATGGCCTCCAATAGAAGGCT TTCCAAGATGGCTCTCAGACCACGTGCACCAGTATTTCTGGCTATAGCCTTCTTGGCTACTATT CTAAGTGCACCATCAGTAAAGTGTAACTTAACCTGAAGGAAAAAAACAAGATTGAGGATTAGAT ATTACTGAATATAAGAAAACCTTAAGCCTATCACCTAAGTTCATGTGAACTCACTTTGTTCAGG CTAAACATTTTCCTGTATTGTCTGGAAAGAGAATTCTTTGGTTCTGTAAGAACCTGAATGCAGA TGAAATCATTTCAGTTAGCTACAGCAGGCAAGTACAAAAGAATACATAAAATAGATTTCTTCAT GGCCATAGAAGTTTATGTGATGGAGAAGAATAAACATGATTTTGAACTAAGATGACATTAAAGG CATAAACCATCAACATTATGCATATTTTTTTCTCTGCATAAGTCTTCCTGAACAAGCTAACCTG AACAAGCTGATCTTCATTGAGAGCTGTCAAACTAACTAGGATGGGCAAGCGTCCAATAAACTCT GGTATCAAACCATATCTTGCAAGATCGCCACTCTCAACCTGCCAAAGGAGCACGTGGTTTCGTA TTCATGACCATGTGATAGTTTTTTTAAGATGAAACACAGCTCCATGGTATTGGTGGTACCAAGT AGACCATAAGGAGTTCAGTTAGCCAAAGGTTCCAAAATGCTTACAGATTCCAACAATGATGAAG TGACCATTGGATCAGTCACTTCAGAACTTCTCATGTTTATCCGAATGGGTGCCCCAAAACCTAT AGATGAATCTTGGCGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.29099391

Conservation Information
Conserved circRNAs	NA
PMCS	0.29099391

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							38522033-38521377(+)
38522315-38521989(+)
38522283-38522270(-)
						
						Potential amino acid sequence
						
							MGKRPINSGIKPYLARSPLSTDSNNDEVTIGSVTSELLMFIRMGAPKPIDESWRHGILHVSVCY
VLLQCTVTPKNFGSTSWPIN*(+)
MNLGAMEFFMLVFVMYCSNAPSPRRILAPHPGLSIEPIASSSTTTASTRSLPVFSSGISYMASN
RRLSKMALRPRAPVFLAIAFLATILSAPSVKCNLTLFRLNIFLYCLEREFFGSVRT*(+)
MRSSEVTDPMVTSSLLESVESGDLARYGLIPEFIGRLPILVSLTALNEDQLVQVLTEPKNSLSR
QYRKMFSLNKVKLHFTDGALRIVAKKAIARNTGARGLRAILESLLLEAMYEIPDEKTGSERVDA
VVVDEEAIGSIDRPGCGAKILRGDGALEQYITNTNMKNSMAPRFIYRFWGTHSDKHEKF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	38522033-38521377(+) 38522315-38521989(+) 38522283-38522270(-)
Potential amino acid sequence	MGKRPINSGIKPYLARSPLSTDSNNDEVTIGSVTSELLMFIRMGAPKPIDESWRHGILHVSVCY VLLQCTVTPKNFGSTSWPIN(+) MNLGAMEFFMLVFVMYCSNAPSPRRILAPHPGLSIEPIASSSTTTASTRSLPVFSSGISYMASN RRLSKMALRPRAPVFLAIAFLATILSAPSVKCNLTLFRLNIFLYCLEREFFGSVRT(+) MRSSEVTDPMVTSSLLESVESGDLARYGLIPEFIGRLPILVSLTALNEDQLVQVLTEPKNSLSR QYRKMFSLNKVKLHFTDGALRIVAKKAIARNTGARGLRAILESLLLEAMYEIPDEKTGSERVDA VVVDEEAIGSIDRPGCGAKILRGDGALEQYITNTNMKNSMAPRFIYRFWGTHSDKHEKF*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0886600_circ_g.3

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