Plant Circular RNA Database

Detail information of Os01g0118100_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0118100_circ_g.3
					
						ID in PlantcircBase
						osa_circ_000143
					
						Alias
						Os01circ01116
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 1026722-1027333  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl
					
						Parent gene
						
							Os01g0118100						
					
						Parent gene annotation
						
							Similar to Fructose-bisphosphate aldolase. (Os01t0118100-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0118100_circ_g.1 Os01g0118100_circ_g.2 Os01g0118100_circ_g.4 Os01g0118100_circ_g.5 						
					
						Support reads
						3/1
					
						Tissues
						leaf/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
						Os01t0118100-01:3

General Information
CircRNA Name	Os01g0118100_circ_g.3
ID in PlantcircBase	osa_circ_000143
Alias	Os01circ01116
Organism	Oryza sativa
Position	chr1: 1026722-1027333 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl
Parent gene	Os01g0118100
Parent gene annotation	Similar to Fructose-bisphosphate aldolase. (Os01t0118100-01)
Parent gene strand	+
Alternative splicing	Os01g0118100_circ_g.1 Os01g0118100_circ_g.2 Os01g0118100_circ_g.4 Os01g0118100_circ_g.5
Support reads	3/1
Tissues	leaf/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	Os01t0118100-01:3

			
						 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  
						
							GATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTCGGGACTTAGTGTG
AGAGATCCATTCTTGACTCCATTTGACAAGAAGGATagacgaggaagagctggtcgagtccaac
caggggagtgttaccatctatatccacaatgcgtgtatgaagcatttgctgactatcagttgcc
agaactcc

						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: 423
Transcript exons: 1026722-1026925,1027012-1027081,1027185-1027333
AGACGAGGAAGAGCTGGTCGAGTCCAACCAGGGGAGTGTTACCATCTATATCCACAATGCGTGT
ATGAAGCATTTGCTGACTATCAGTTGCCAGAACTCCTGAGAACTCCTCTGCAATCCCTCTGTTT
GCAAATAAAAAGCTTGCGCCTTGGGAGCATCTCTGAATTTTTATCCAGAGCTTTGCAATCACCT
GAGTCTCTATCGGTAGAAAATGCCATTGAATATCTCAAAGTCATTGGAGCGTTTGATCGTAATG
AAGAGTTAACAATTCTAGGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGAT
GCTGATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTCGGGACTTAGT
GTGAGAGATCCATTCTTGACTCCATTTGACAAGAAGGAT
						
						Genomic sequence
						
							AGACGAGGAAGAGCTGGTCGAGTCCAACCAGGGGAGTGTTACCATCTATATCCACAATGCGTGT
ATGAAGCATTTGCTGACTATCAGTTGCCAGAACTCCTGAGAACTCCTCTGCAATCCCTCTGTTT
GCAAATAAAAAGCTTGCGCCTTGGGAGCATCTCTGAATTTTTATCCAGAGCTTTGCAATCACCT
GAGTCTCTATCGGTACTTGATTTCCGTATTAATCACAAGCCGCAAAAGTCTATCCTGTGTCTTG
GAATGACTTGATAAATTAATTTGAATTTTTTCAGGTAGAAAATGCCATTGAATATCTCAAAGTC
ATTGGAGCGTTTGATCGTAATGAAGAGTTAACAATTCTAGGTATCAGATCCATCCTTCAAATCA
TCCGTTTATCACTGCTTTATTGAATCATCTTGAGCATTTGTAGCATGTGCTAACTATACCCACG
GATTGGCATTACCAGGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGATGCT
GATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTCGGGACTTAGTGTG
AGAGATCCATTCTTGACTCCATTTGACAAGAAGGAT

Sequences
Splice junction sequence	GATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTCGGGACTTAGTGTG AGAGATCCATTCTTGACTCCATTTGACAAGAAGGATagacgaggaagagctggtcgagtccaac caggggagtgttaccatctatatccacaatgcgtgtatgaagcatttgctgactatcagttgcc agaactcc
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: 423 Transcript exons: 1026722-1026925,1027012-1027081,1027185-1027333 AGACGAGGAAGAGCTGGTCGAGTCCAACCAGGGGAGTGTTACCATCTATATCCACAATGCGTGT ATGAAGCATTTGCTGACTATCAGTTGCCAGAACTCCTGAGAACTCCTCTGCAATCCCTCTGTTT GCAAATAAAAAGCTTGCGCCTTGGGAGCATCTCTGAATTTTTATCCAGAGCTTTGCAATCACCT GAGTCTCTATCGGTAGAAAATGCCATTGAATATCTCAAAGTCATTGGAGCGTTTGATCGTAATG AAGAGTTAACAATTCTAGGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGAT GCTGATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTCGGGACTTAGT GTGAGAGATCCATTCTTGACTCCATTTGACAAGAAGGAT
Genomic sequence	AGACGAGGAAGAGCTGGTCGAGTCCAACCAGGGGAGTGTTACCATCTATATCCACAATGCGTGT ATGAAGCATTTGCTGACTATCAGTTGCCAGAACTCCTGAGAACTCCTCTGCAATCCCTCTGTTT GCAAATAAAAAGCTTGCGCCTTGGGAGCATCTCTGAATTTTTATCCAGAGCTTTGCAATCACCT GAGTCTCTATCGGTACTTGATTTCCGTATTAATCACAAGCCGCAAAAGTCTATCCTGTGTCTTG GAATGACTTGATAAATTAATTTGAATTTTTTCAGGTAGAAAATGCCATTGAATATCTCAAAGTC ATTGGAGCGTTTGATCGTAATGAAGAGTTAACAATTCTAGGTATCAGATCCATCCTTCAAATCA TCCGTTTATCACTGCTTTATTGAATCATCTTGAGCATTTGTAGCATGTGCTAACTATACCCACG GATTGGCATTACCAGGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGATGCT GATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTCGGGACTTAGTGTG AGAGATCCATTCTTGACTCCATTTGACAAGAAGGAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_001770* osi_circ_008946 						
					
						PMCS
						0.480562977

Conservation Information
Conserved circRNAs	osi_circ_001770* osi_circ_008946
PMCS	0.480562977

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1027200-1027330(+)
1026768-1027273(-)
1026796-1027292(-)
						
						Potential amino acid sequence
						
							MLPVEPKLGKMLIFGAIFNCLDPILTIVSGLSVRDPFLTPFDKKDRRGRAGRVQPGECYHLYPQ
CVYEAFADYQLPELLRTPLQSLCLQIKSLRLGSISEFLSRALQSPESLSVENAIEYLKVIGAFD
RNEELTILGKHLSMLPVEPKLGKMLIFGAIFNCLDPILTIVSGLSVRDPFLTPFDKKDRRGRAG
RVQPGECYHLYPQCVYEAFADYQLPELLRTPLQSLCLQIKSLRLGSISEFLSRALQSPESLSVE
NAIEYLKVIGAFDRNEELTILGKHLSMLPVEPKLGKMLIFGAIFNCLDPILTIVSGLSVRDPFL
TPFDKKDRRGRAGRVQPGECYHLYPQCVYEAFADYQLPELLRTPLQSLCLQIKSLRLGSISEFL
SRALQSPESLSVENAIEYLKVIGAFDRNEELTILGKHLSMLPVEPKLGKMLIFGAIFNCLDPIL
TIVSGLSVRDPFLTPFDKKD(+)
MVTLPWLDSTSSSSSILLVKWSQEWISHTKSRNNG*(-)
MLHTRIVDIDGNTPLVGLDQLFLVYPSCQMESRMDLSH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1027200-1027330(+) 1026768-1027273(-) 1026796-1027292(-)
Potential amino acid sequence	MLPVEPKLGKMLIFGAIFNCLDPILTIVSGLSVRDPFLTPFDKKDRRGRAGRVQPGECYHLYPQ CVYEAFADYQLPELLRTPLQSLCLQIKSLRLGSISEFLSRALQSPESLSVENAIEYLKVIGAFD RNEELTILGKHLSMLPVEPKLGKMLIFGAIFNCLDPILTIVSGLSVRDPFLTPFDKKDRRGRAG RVQPGECYHLYPQCVYEAFADYQLPELLRTPLQSLCLQIKSLRLGSISEFLSRALQSPESLSVE NAIEYLKVIGAFDRNEELTILGKHLSMLPVEPKLGKMLIFGAIFNCLDPILTIVSGLSVRDPFL TPFDKKDRRGRAGRVQPGECYHLYPQCVYEAFADYQLPELLRTPLQSLCLQIKSLRLGSISEFL SRALQSPESLSVENAIEYLKVIGAFDRNEELTILGKHLSMLPVEPKLGKMLIFGAIFNCLDPIL TIVSGLSVRDPFLTPFDKKD(+) MVTLPWLDSTSSSSSILLVKWSQEWISHTKSRNNG(-) MLHTRIVDIDGNTPLVGLDQLFLVYPSCQMESRMDLSH(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Chu et al., 2017

circRNA

Detail information of Os01g0118100_circ_g.3

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