Plant Circular RNA Database

Detail information of Os06g0245800_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os06g0245800_circ_g.3
					
						ID in PlantcircBase
						osa_circ_030363
					
						Alias
						Os06circ06471
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr6: 7578267-7579187  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl
					
						Parent gene
						
							Os06g0245800						
					
						Parent gene annotation
						
							Similar to Alanyl-tRNA synthetase. (Os06t0245800-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os06g0245800_circ_g.1 Os06g0245800_circ_g.2 Os06g0245800_circ_g.4 						
					
						Support reads
						2/1
					
						Tissues
						leaf/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  
						
							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
						Os06t0245800-01:2

General Information
CircRNA Name	Os06g0245800_circ_g.3
ID in PlantcircBase	osa_circ_030363
Alias	Os06circ06471
Organism	Oryza sativa
Position	chr6: 7578267-7579187 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl
Parent gene	Os06g0245800
Parent gene annotation	Similar to Alanyl-tRNA synthetase. (Os06t0245800-01)
Parent gene strand	+
Alternative splicing	Os06g0245800_circ_g.1 Os06g0245800_circ_g.2 Os06g0245800_circ_g.4
Support reads	2/1
Tissues	leaf/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	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	Os06t0245800-01:2

			
						 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  
						
							GAATATCTTTGTTCACAAAGGCACAATTAAACAGGGGTCCGTAGAAGTTGGGAAGGAAATCGAT
GCTGCTGTTGATGCAAAATTGAGGCAGGGGGCTAAGataattggggatcacatgagagcagttg
tttatctcatatcagatggagtcattccctcaaatattgggagaggatatgttgtccgaaggct
tataagaa

									
								

					

						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: 820
Transcript exons: 7578267-7578859,7578961-7579187
ATAATTGGGGATCACATGAGAGCAGTTGTTTATCTCATATCAGATGGAGTCATTCCCTCAAATA
TTGGGAGAGGATATGTTGTCCGAAGGCTTATAAGAAGAGTAGTTCGAACTGGTAGACTGATAGG
TATAAGAGGTGATGGGCATGGAAATTCAGAAGGTGCCTTTTTACCTTCACTAGCTGAGGTAGCA
ATCAGTCTTAGCACTGAGATAGATCCGGATGTTGAATCTAGAAGGAAATCAATTCTTGGAGAAC
TTCAAAGGGAAGAACTGCGATTTGTGCAGACTTTGGAAAGAGGTGAAAAATTATTGGACGAACT
TCTGGATGAGGCATTATCAAGTGCTGGTAATAATGGTGGTAAACCTTGTCTATCTGGAAAAGAT
GTTTTCCTTTTGTATGATACATATGGTTTTCCAGTAGAGATTACAGCTGAAATATCAGGTGAAC
GAGGTGTAATTGTTGACATGAAGGGATTTGATATGGAAATGGAAAACCAAAGGAAACAATCTCA
GGCTGCTCATAATGTAGTTAAACTTTCTGTAGGAAATGAGACTGAGATTGTCAAGAGTATCCCC
GATACTGAATTTCTGGGATCGGACACCATTTTATGCTGAATCAGGTGGTCAAGTGGGAGATAAT
GGTTTCTTGTATGTCTATGGAGAAGAAGATGCAAAACAGAAGGCAGTCATAGAAATCAATGACG
TCCAAAAATCCCTGGGGAATATCTTTGTTCACAAAGGCACAATTAAACAGGGGTCCGTAGAAGT
TGGGAAGGAAATCGATGCTGCTGTTGATGCAAAATTGAGGCAGGGGGCTAAG
						
					

						Genomic sequence
						
							ATAATTGGGGATCACATGAGAGCAGTTGTTTATCTCATATCAGATGGAGTCATTCCCTCAAATA
TTGGGAGAGGATATGTTGTCCGAAGGCTTATAAGAAGAGTAGTTCGAACTGGTAGACTGATAGG
TATAAGAGGTGATGGGCATGGAAATTCAGAAGGTGCCTTTTTACCTTCACTAGCTGAGGTAGCA
ATCAGTCTTAGCACTGAGATAGATCCGGATGTTGAATCTAGAAGGAAATCAATTCTTGGAGAAC
TTCAAAGGGAAGAACTGCGATTTGTGCAGACTTTGGAAAGAGGTGAAAAATTATTGGACGAACT
TCTGGATGAGGCATTATCAAGTGCTGGTAATAATGGTGGTAAACCTTGTCTATCTGGAAAAGAT
GTTTTCCTTTTGTATGATACATATGGTTTTCCAGTAGAGATTACAGCTGAAATATCAGGTGAAC
GAGGTGTAATTGTTGACATGAAGGGATTTGATATGGAAATGGAAAACCAAAGGAAACAATCTCA
GGCTGCTCATAATGTAGTTAAACTTTCTGTAGGAAATGAGACTGAGATTGTCAAGAGTATCCCC
GATACTGAATTTCTGGGGTACGACTCTCTTTCTGCCACTGCTGTTGTTAAAGGTCTTTTAGTTA
ATGGAAACTCAGTGAATGTAGTTTCAGAAGGTTCTGATGTAGAAATATTTTTAGATCGGACACC
ATTTTATGCTGAATCAGGTGGTCAAGTGGGAGATAATGGTTTCTTGTATGTCTATGGAGAAGAA
GATGCAAAACAGAAGGCAGTCATAGAAATCAATGACGTCCAAAAATCCCTGGGGAATATCTTTG
TTCACAAAGGCACAATTAAACAGGGGTCCGTAGAAGTTGGGAAGGAAATCGATGCTGCTGTTGA
TGCAAAATTGAGGCAGGGGGCTAAG
						
					

			
		

Sequences
Splice junction sequence	GAATATCTTTGTTCACAAAGGCACAATTAAACAGGGGTCCGTAGAAGTTGGGAAGGAAATCGAT GCTGCTGTTGATGCAAAATTGAGGCAGGGGGCTAAGataattggggatcacatgagagcagttg tttatctcatatcagatggagtcattccctcaaatattgggagaggatatgttgtccgaaggct tataagaa
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: 820 Transcript exons: 7578267-7578859,7578961-7579187 ATAATTGGGGATCACATGAGAGCAGTTGTTTATCTCATATCAGATGGAGTCATTCCCTCAAATA TTGGGAGAGGATATGTTGTCCGAAGGCTTATAAGAAGAGTAGTTCGAACTGGTAGACTGATAGG TATAAGAGGTGATGGGCATGGAAATTCAGAAGGTGCCTTTTTACCTTCACTAGCTGAGGTAGCA ATCAGTCTTAGCACTGAGATAGATCCGGATGTTGAATCTAGAAGGAAATCAATTCTTGGAGAAC TTCAAAGGGAAGAACTGCGATTTGTGCAGACTTTGGAAAGAGGTGAAAAATTATTGGACGAACT TCTGGATGAGGCATTATCAAGTGCTGGTAATAATGGTGGTAAACCTTGTCTATCTGGAAAAGAT GTTTTCCTTTTGTATGATACATATGGTTTTCCAGTAGAGATTACAGCTGAAATATCAGGTGAAC GAGGTGTAATTGTTGACATGAAGGGATTTGATATGGAAATGGAAAACCAAAGGAAACAATCTCA GGCTGCTCATAATGTAGTTAAACTTTCTGTAGGAAATGAGACTGAGATTGTCAAGAGTATCCCC GATACTGAATTTCTGGGATCGGACACCATTTTATGCTGAATCAGGTGGTCAAGTGGGAGATAAT GGTTTCTTGTATGTCTATGGAGAAGAAGATGCAAAACAGAAGGCAGTCATAGAAATCAATGACG TCCAAAAATCCCTGGGGAATATCTTTGTTCACAAAGGCACAATTAAACAGGGGTCCGTAGAAGT TGGGAAGGAAATCGATGCTGCTGTTGATGCAAAATTGAGGCAGGGGGCTAAG
Genomic sequence	ATAATTGGGGATCACATGAGAGCAGTTGTTTATCTCATATCAGATGGAGTCATTCCCTCAAATA TTGGGAGAGGATATGTTGTCCGAAGGCTTATAAGAAGAGTAGTTCGAACTGGTAGACTGATAGG TATAAGAGGTGATGGGCATGGAAATTCAGAAGGTGCCTTTTTACCTTCACTAGCTGAGGTAGCA ATCAGTCTTAGCACTGAGATAGATCCGGATGTTGAATCTAGAAGGAAATCAATTCTTGGAGAAC TTCAAAGGGAAGAACTGCGATTTGTGCAGACTTTGGAAAGAGGTGAAAAATTATTGGACGAACT TCTGGATGAGGCATTATCAAGTGCTGGTAATAATGGTGGTAAACCTTGTCTATCTGGAAAAGAT GTTTTCCTTTTGTATGATACATATGGTTTTCCAGTAGAGATTACAGCTGAAATATCAGGTGAAC GAGGTGTAATTGTTGACATGAAGGGATTTGATATGGAAATGGAAAACCAAAGGAAACAATCTCA GGCTGCTCATAATGTAGTTAAACTTTCTGTAGGAAATGAGACTGAGATTGTCAAGAGTATCCCC GATACTGAATTTCTGGGGTACGACTCTCTTTCTGCCACTGCTGTTGTTAAAGGTCTTTTAGTTA ATGGAAACTCAGTGAATGTAGTTTCAGAAGGTTCTGATGTAGAAATATTTTTAGATCGGACACC ATTTTATGCTGAATCAGGTGGTCAAGTGGGAGATAATGGTTTCTTGTATGTCTATGGAGAAGAA GATGCAAAACAGAAGGCAGTCATAGAAATCAATGACGTCCAAAAATCCCTGGGGAATATCTTTG TTCACAAAGGCACAATTAAACAGGGGTCCGTAGAAGTTGGGAAGGAAATCGATGCTGCTGTTGA TGCAAAATTGAGGCAGGGGGCTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_006618* osi_circ_016856 						
					
						PMCS
						0.323892581

Conservation Information
Conserved circRNAs	osi_circ_006618* osi_circ_016856
PMCS	0.323892581

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7578815-7578979(+)
						
						Potential amino acid sequence
						
							MRLRLSRVSPILNFWDRTPFYAESGGQVGDNGFLYVYGEEDAKQKAVIEINDVQKSLGNIFVHK
GTIKQGSVEVGKEIDAAVDAKLRQGAKIIGDHMRAVVYLISDGVIPSNIGRGYVVRRLIRRVVR
TGRLIGIRGDGHGNSEGAFLPSLAEVAISLSTEIDPDVESRRKSILGELQREELRFVQTLERGE
KLLDELLDEALSSAGNNGGKPCLSGKDVFLLYDTYGFPVEITAEISGERGVIVDMKGFDMEMEN
QRKQSQAAHNVVKLSVGNETEIVKSIPDTEFLGSDTILC*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7578815-7578979(+)
Potential amino acid sequence	MRLRLSRVSPILNFWDRTPFYAESGGQVGDNGFLYVYGEEDAKQKAVIEINDVQKSLGNIFVHK GTIKQGSVEVGKEIDAAVDAKLRQGAKIIGDHMRAVVYLISDGVIPSNIGRGYVVRRLIRRVVR TGRLIGIRGDGHGNSEGAFLPSLAEVAISLSTEIDPDVESRRKSILGELQREELRFVQTLERGE KLLDELLDEALSSAGNNGGKPCLSGKDVFLLYDTYGFPVEITAEISGERGVIVDMKGFDMEMEN QRKQSQAAHNVVKLSVGNETEIVKSIPDTEFLGSDTILC*(+)
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 Os06g0245800_circ_g.3

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