Plant Circular RNA Database

Detail information of Os01g0873800_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0873800_circ_g.3
					
						ID in PlantcircBase
						osa_circ_005039
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 37894663-37896477  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0873800						
					
						Parent gene annotation
						
							Conserved hypothetical protein. (Os01t0873800-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						1
					
						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  
						
							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
						Os01t0873800-01:4

General Information
CircRNA Name	Os01g0873800_circ_g.3
ID in PlantcircBase	osa_circ_005039
Alias	NA
Organism	Oryza sativa
Position	chr1: 37894663-37896477 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0873800
Parent gene annotation	Conserved hypothetical protein. (Os01t0873800-01)
Parent gene strand	-
Alternative splicing	NA
Support reads	1
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	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	Os01t0873800-01:4

			
						 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  
						
							TGCGTCCATCGGGAAAACCTTTTCTGGAATATTTGGTATCATCGGGAGTGTGTTGAGATCAGTC
TCCAATGGCAACATTTGATACCTTGGAGCTCCAGTTccaatatgcaccagggtcttgcttacag
ttatcttgcaggaacctcaggacagcaaggccattttgctggacaacttgtggatgaaatgcag
gtgtacca

									
								

					

						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: 1129
Transcript exons: 37894663-37894914,37894989-37895544,37895622-37895829,37
896365-37896477
CCAATATGCACCAGGGTCTTGCTTACAGTTATCTTGCAGGAACCTCAGGACAGCAAGGCCATTT
TGCTGGACAACTTGTGGATGAAATGCAGGTGTACCATCATCAGATACACCCTTAAGTAGAAAAA
TATCATCATTTTTCAAGAGCTCATAACCTTGCACAACACCATTTTGATGATAACATATAGCCAA
TTCTGGCACACTTGCCATTATATTATCTAGCCAAGCTTCAAGCCAGTTCAGTGGAGTAACCTGT
CTCGAAACATCCCAGAGGTGTAAGCTGACCGCCATATATTTCTCATTGCTAAATATAAGCAAGT
CGCTACCCAAAAGCATATGGAAATTATGAAACTGCCAAAAGCAAACCTTCCGAAATCCATTGTT
TCCCACCCTCCTACTTTTCTCGGATTCTTGCACGTCGCATCTGGGTTTGTCACCAACATGAGTG
GTTTTCTTAACAGGGTCAGACCCTTTAACTTTCTGCTTATTTTCCCTTGCACCCCAGTACAGGC
TTTCACGAGCACCATGTGATGTTTTTCTACTTTTACTGATATTCTGGTCCAGATAAGGTGAAGT
GCTAAAACTAGATGACGATGGCGAATCCAATGGACCCTCCCTTTGGCCAAATGGTCCACGCAAG
ATAGCGGATGCCGTTTGCTTCTCCTTTGATGGTTGATGACTTGGTGGGCAATCACAAGCTTCTG
CTCTCACTGAATGCATTGCAAAATTAAGAAACATTGAAGGATCAGATCCTTTGGGGTGGTTGCT
TTGTCTCCTGAATATCTTTTCACCTTCATCAACATCAGGACCTGTGTTTAGAATAAGTGTATCT
CCAATACGGTTAACAGCAATAGATACTTGTGCCTTGGAGTATGGTATTTTGAAAATCTGCTTTA
GGATATCAGTTGGAGCAACCACATCTATTTCATCACCATATTCAGCTAGGCCTGACACAGCCAG
TGCTTCACACTTCCTTGATAAGTTTTGGTTGGCAAGTCCACTTCCATATCGTGATCCTTCAGTA
CTCTTTGCGTCCATCGGGAAAACCTTTTCTGGAATATTTGGTATCATCGGGAGTGTGTTGAGAT
CAGTCTCCAATGGCAACATTTGATACCTTGGAGCTCCAGTT
						
					

						Genomic sequence
						
							CCAATATGCACCAGGGTCTTGCTTACAGTTATCTTGCAGGAACCTCAGGACAGCAAGGCCATTT
TGCTGGACAACTTGTGGATGAAATGCAGGTGTACCATCATCAGATACACCCTTAAGTAGAAAAA
TATCATCATTTTTCAAGAGCTCATAACCTTGCACAACACCATTTTGATGATAACATATAGCCAA
TTCTGGCACACTTGCCATTATATTATCTAGCCAAGCTTCAAGCCAGTTCAGTGGAGTAACCTAT
GAAACACATTTGTCAACAGAAAGAGTAAAAAATGAAATTGTGAAGCCATATTCAATAGAATAAA
ACATACCTGTCTCGAAACATCCCAGAGGTGTAAGCTGACCGCCATATATTTCTCATTGCTAAAT
ATAAGCAAGTCGCTACCCAAAAGCATATGGAAATTATGAAACTGCCAAAAGCAAACCTTCCGAA
ATCCATTGTTTCCCACCCTCCTACTTTTCTCGGATTCTTGCACGTCGCATCTGGGTTTGTCACC
AACATGAGTGGTTTTCTTAACAGGGTCAGACCCTTTAACTTTCTGCTTATTTTCCCTTGCACCC
CAGTACAGGCTTTCACGAGCACCATGTGATGTTTTTCTACTTTTACTGATATTCTGGTCCAGAT
AAGGTGAAGTGCTAAAACTAGATGACGATGGCGAATCCAATGGACCCTCCCTTTGGCCAAATGG
TCCACGCAAGATAGCGGATGCCGTTTGCTTCTCCTTTGATGGTTGATGACTTGGTGGGCAATCA
CAAGCTTCTGCTCTCACTGAATGCATTGCAAAATTAAGAAACATTGAAGGATCAGATCCTTTGG
GGTGGTTGCTTTGTCTCCTGAATATCTTTTCACCTTCATCAACATCAGGACTGCAACACGTACA
TTGCATTAGTATGAAGTACATAGAGCATGGTAGCTAGTTGCAACAATGAAACGGCCAATTTACC
CTGTGTTTAGAATAAGTGTATCTCCAATACGGTTAACAGCAATAGATACTTGTGCCTTGGAGTA
TGGTATTTTGAAAATCTGCTTTAGGATATCAGTTGGAGCAACCACATCTATTTCATCACCATAT
TCAGCTAGGCCTGACACAGCCAGTGCTTCACACTTCCTTGATAAGTTTTGGTTGGCAAGTCCAC
TTCCATATCGTGATCCTGAATAATATGAACAAAAATAACAATTAGAAATACATTGGCATGCCCA
GCAGATATAACCAACTGTGACTATTACATAGCTCAAACAGACTTATAGCCACATGTGGTCTTGC
AGCTGCAACAACAGCTTGTGCATGTGTGACGATAGAATAGAAAACCAAGGTATCGCATTTCCAT
TATTTTAGCTTCCTCTGACTATCCATTTGTTAATACTAATGGATGCATCAGGAGATATGAAGTC
TTCTATTGCAGCCGAAGAAAAAAATTTGGAATATAAATTTAGCTGGCCTTCTCATCTAGATTGC
ATAAATAAAGCTATTTAAAATACCAAATATAATCTACACATACAAGATGCAACCATGAAAACTT
GGATACAGTAGGAATCCTGATAGTAAGAGTGGCATGTATGGTAAAATTTACTTGCACCTACAAG
ATGTAATATTATCTATGTTTTCCCTATGGTAGAAGCTCTTAAGAAGCCTGCCATTTCTTTTGTG
AATCAAACTATAATGATCAAGCCTCAAGAAGAGATCACCTTCAGTACTCTTTGCGTCCATCGGG
AAAACCTTTTCTGGAATATTTGGTATCATCGGGAGTGTGTTGAGATCAGTCTCCAATGGCAACA
TTTGATACCTTGGAGCTCCAGTT
						
					

			
		

Sequences
Splice junction sequence	TGCGTCCATCGGGAAAACCTTTTCTGGAATATTTGGTATCATCGGGAGTGTGTTGAGATCAGTC TCCAATGGCAACATTTGATACCTTGGAGCTCCAGTTccaatatgcaccagggtcttgcttacag ttatcttgcaggaacctcaggacagcaaggccattttgctggacaacttgtggatgaaatgcag gtgtacca
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: 1129 Transcript exons: 37894663-37894914,37894989-37895544,37895622-37895829,37 896365-37896477 CCAATATGCACCAGGGTCTTGCTTACAGTTATCTTGCAGGAACCTCAGGACAGCAAGGCCATTT TGCTGGACAACTTGTGGATGAAATGCAGGTGTACCATCATCAGATACACCCTTAAGTAGAAAAA TATCATCATTTTTCAAGAGCTCATAACCTTGCACAACACCATTTTGATGATAACATATAGCCAA TTCTGGCACACTTGCCATTATATTATCTAGCCAAGCTTCAAGCCAGTTCAGTGGAGTAACCTGT CTCGAAACATCCCAGAGGTGTAAGCTGACCGCCATATATTTCTCATTGCTAAATATAAGCAAGT CGCTACCCAAAAGCATATGGAAATTATGAAACTGCCAAAAGCAAACCTTCCGAAATCCATTGTT TCCCACCCTCCTACTTTTCTCGGATTCTTGCACGTCGCATCTGGGTTTGTCACCAACATGAGTG GTTTTCTTAACAGGGTCAGACCCTTTAACTTTCTGCTTATTTTCCCTTGCACCCCAGTACAGGC TTTCACGAGCACCATGTGATGTTTTTCTACTTTTACTGATATTCTGGTCCAGATAAGGTGAAGT GCTAAAACTAGATGACGATGGCGAATCCAATGGACCCTCCCTTTGGCCAAATGGTCCACGCAAG ATAGCGGATGCCGTTTGCTTCTCCTTTGATGGTTGATGACTTGGTGGGCAATCACAAGCTTCTG CTCTCACTGAATGCATTGCAAAATTAAGAAACATTGAAGGATCAGATCCTTTGGGGTGGTTGCT TTGTCTCCTGAATATCTTTTCACCTTCATCAACATCAGGACCTGTGTTTAGAATAAGTGTATCT CCAATACGGTTAACAGCAATAGATACTTGTGCCTTGGAGTATGGTATTTTGAAAATCTGCTTTA GGATATCAGTTGGAGCAACCACATCTATTTCATCACCATATTCAGCTAGGCCTGACACAGCCAG TGCTTCACACTTCCTTGATAAGTTTTGGTTGGCAAGTCCACTTCCATATCGTGATCCTTCAGTA CTCTTTGCGTCCATCGGGAAAACCTTTTCTGGAATATTTGGTATCATCGGGAGTGTGTTGAGAT CAGTCTCCAATGGCAACATTTGATACCTTGGAGCTCCAGTT
Genomic sequence	CCAATATGCACCAGGGTCTTGCTTACAGTTATCTTGCAGGAACCTCAGGACAGCAAGGCCATTT TGCTGGACAACTTGTGGATGAAATGCAGGTGTACCATCATCAGATACACCCTTAAGTAGAAAAA TATCATCATTTTTCAAGAGCTCATAACCTTGCACAACACCATTTTGATGATAACATATAGCCAA TTCTGGCACACTTGCCATTATATTATCTAGCCAAGCTTCAAGCCAGTTCAGTGGAGTAACCTAT GAAACACATTTGTCAACAGAAAGAGTAAAAAATGAAATTGTGAAGCCATATTCAATAGAATAAA ACATACCTGTCTCGAAACATCCCAGAGGTGTAAGCTGACCGCCATATATTTCTCATTGCTAAAT ATAAGCAAGTCGCTACCCAAAAGCATATGGAAATTATGAAACTGCCAAAAGCAAACCTTCCGAA ATCCATTGTTTCCCACCCTCCTACTTTTCTCGGATTCTTGCACGTCGCATCTGGGTTTGTCACC AACATGAGTGGTTTTCTTAACAGGGTCAGACCCTTTAACTTTCTGCTTATTTTCCCTTGCACCC CAGTACAGGCTTTCACGAGCACCATGTGATGTTTTTCTACTTTTACTGATATTCTGGTCCAGAT AAGGTGAAGTGCTAAAACTAGATGACGATGGCGAATCCAATGGACCCTCCCTTTGGCCAAATGG TCCACGCAAGATAGCGGATGCCGTTTGCTTCTCCTTTGATGGTTGATGACTTGGTGGGCAATCA CAAGCTTCTGCTCTCACTGAATGCATTGCAAAATTAAGAAACATTGAAGGATCAGATCCTTTGG GGTGGTTGCTTTGTCTCCTGAATATCTTTTCACCTTCATCAACATCAGGACTGCAACACGTACA TTGCATTAGTATGAAGTACATAGAGCATGGTAGCTAGTTGCAACAATGAAACGGCCAATTTACC CTGTGTTTAGAATAAGTGTATCTCCAATACGGTTAACAGCAATAGATACTTGTGCCTTGGAGTA TGGTATTTTGAAAATCTGCTTTAGGATATCAGTTGGAGCAACCACATCTATTTCATCACCATAT TCAGCTAGGCCTGACACAGCCAGTGCTTCACACTTCCTTGATAAGTTTTGGTTGGCAAGTCCAC TTCCATATCGTGATCCTGAATAATATGAACAAAAATAACAATTAGAAATACATTGGCATGCCCA GCAGATATAACCAACTGTGACTATTACATAGCTCAAACAGACTTATAGCCACATGTGGTCTTGC AGCTGCAACAACAGCTTGTGCATGTGTGACGATAGAATAGAAAACCAAGGTATCGCATTTCCAT TATTTTAGCTTCCTCTGACTATCCATTTGTTAATACTAATGGATGCATCAGGAGATATGAAGTC TTCTATTGCAGCCGAAGAAAAAAATTTGGAATATAAATTTAGCTGGCCTTCTCATCTAGATTGC ATAAATAAAGCTATTTAAAATACCAAATATAATCTACACATACAAGATGCAACCATGAAAACTT GGATACAGTAGGAATCCTGATAGTAAGAGTGGCATGTATGGTAAAATTTACTTGCACCTACAAG ATGTAATATTATCTATGTTTTCCCTATGGTAGAAGCTCTTAAGAAGCCTGCCATTTCTTTTGTG AATCAAACTATAATGATCAAGCCTCAAGAAGAGATCACCTTCAGTACTCTTTGCGTCCATCGGG AAAACCTTTTCTGGAATATTTGGTATCATCGGGAGTGTGTTGAGATCAGTCTCCAATGGCAACA TTTGATACCTTGGAGCTCCAGTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.357994068

Conservation Information
Conserved circRNAs	NA
PMCS	0.357994068

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							37896447-37894744(+)
37896457-37896438(-)
						
						Potential amino acid sequence
						
							MATFDTLELQFQYAPGSCLQLSCRNLRTARPFCWTTCG*(+)
MLPLETDLNTLPMIPNIPEKVFPMDAKSTEGSRYGSGLANQNLSRKCEALAVSGLAEYGDEIDV
VAPTDILKQIFKIPYSKAQVSIAVNRIGDTLILNTGPDVDEGEKIFRRQSNHPKGSDPSMFLNF
AMHSVRAEACDCPPSHQPSKEKQTASAILRGPFGQREGPLDSPSSSSFSTSPYLDQNISKSRKT
SHGARESLYWGARENKQKVKGSDPVKKTTHVGDKPRCDVQESEKSRRVGNNGFRKVCFWQFHNF
HMLLGSDLLIFSNEKYMAVSLHLWDVSRQVTPLNWLEAWLDNIMASVPELAICYHQNGVVQGYE
LLKNDDIFLLKGVSDDGTPAFHPQVVQQNGLAVLRFLQDNCKQDPGAYWNWSSKVSNVAIGD*(
-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	37896447-37894744(+) 37896457-37896438(-)
Potential amino acid sequence	MATFDTLELQFQYAPGSCLQLSCRNLRTARPFCWTTCG(+) MLPLETDLNTLPMIPNIPEKVFPMDAKSTEGSRYGSGLANQNLSRKCEALAVSGLAEYGDEIDV VAPTDILKQIFKIPYSKAQVSIAVNRIGDTLILNTGPDVDEGEKIFRRQSNHPKGSDPSMFLNF AMHSVRAEACDCPPSHQPSKEKQTASAILRGPFGQREGPLDSPSSSSFSTSPYLDQNISKSRKT SHGARESLYWGARENKQKVKGSDPVKKTTHVGDKPRCDVQESEKSRRVGNNGFRKVCFWQFHNF HMLLGSDLLIFSNEKYMAVSLHLWDVSRQVTPLNWLEAWLDNIMASVPELAICYHQNGVVQGYE LLKNDDIFLLKGVSDDGTPAFHPQVVQQNGLAVLRFLQDNCKQDPGAYWNWSSKVSNVAIGD( -)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0873800_circ_g.3

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