Plant Circular RNA Database

Detail information of Os07g0479200_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os07g0479200_circ_g.1
					
						ID in PlantcircBase
						osa_circ_033789
					
						Alias
						Os07circ08039/Os_ciR529
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr7: 17407832-17408700  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, PcircRNA_finder, SMALT, Segemehl, circseq_cup, find_circ
					
						Parent gene
						
							Os07g0479200						
					
						Parent gene annotation
						
							Similar to SL15-like (Fragment). (Os07t0479200-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						3/62/37/44
					
						Tissues
						leaf/root/root/shoot, 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
						Os07t0479200-01:4

General Information
CircRNA Name	Os07g0479200_circ_g.1
ID in PlantcircBase	osa_circ_033789
Alias	Os07circ08039/Os_ciR529
Organism	Oryza sativa
Position	chr7: 17407832-17408700 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, PcircRNA_finder, SMALT, Segemehl, circseq_cup, find_circ
Parent gene	Os07g0479200
Parent gene annotation	Similar to SL15-like (Fragment). (Os07t0479200-01)
Parent gene strand	+
Alternative splicing	NA
Support reads	3/62/37/44
Tissues	leaf/root/root/shoot, 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	Os07t0479200-01:4

			
						 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  
						
							TTTCCTTTTATATGATGTGTTTAAAGCTAGCTAAACTTTATCTGATATTCTGTTGCAGTAAGAG
TGTTCACCAGCATCCAGGAGAAGACTCCCTTAAGTGatattgcggactggctccaacagtattg
ggtgggaaaattgaccctgctctttttgaagtcctctatgtaagttataaatgaaagattattt
tgtgtagc

						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: 230
Transcript exons: 17407832-17407898,17407986-17408045,17408324-17408384,17
408659-17408700
ATATTGCGGACTGGCTCCAACAGTATTGGGTGGGAAAATTGACCCTGCTCTTTTTGAAGTCCTC
TATGCTTCTCAGCATGCTATCTTCTTCTTTGCTAGGCTTCCACAGATATGGAAGAATTTTATGA
ACAAGGGCACTGGCGAGCTGAGCTTTCTGACCTGTTTCATGAACTTTGCTGGTTCCATAGTAAG
AGTGTTCACCAGCATCCAGGAGAAGACTCCCTTAAGTG
						
						Genomic sequence
						
							ATATTGCGGACTGGCTCCAACAGTATTGGGTGGGAAAATTGACCCTGCTCTTTTTGAAGTCCTC
TATGTAAGTTATAAATGAAAGATTATTTTGTGTAGCACTTGATATATTCGTATATGCTTGTCTT
TTGATTGTGTGTAATATATTTTGCAGGCTTCTCAGCATGCTATCTTCTTCTTTGCTAGGCTTCC
ACAGATATGGAAGAATTTTATGGTTCGTTGTTAGATTTCTGTACATCTAGCTATATTAGGTTTA
TCTTTTCATGGAAAGTTGCTGTAACTAGGTGTACTAAATAGTAAAATGGTAACCTTAAATTTAA
ATGAATCTTATGGTCTGGACCTTAGAATAAATAATTTGGGATTGACTAGTATGACAATGAACTT
TTCATCTATCAGTCAGCATTTTGTACCAATTTTGTGAGTGGAGGCTTCTAACAAGTCGTTTGAC
AATTTGCATGTACAAACTTTCTGACCTGTTGCTACGATACGCAGAACAAGGGCACTGGCGAGCT
GAGCTTTCTGACCTGTTTCATGAACTTTGCTGGTTCCATAGGTAAGCTTAAGTACATGCCAGAT
TAGTTACCAAGGCATTACTTTTTTACTTCACAATCCATTTTATTCTCTTCTTTGTTTGAAATTA
AGTAGTATAAGCACAAAGTAGTCAAATGTTCTGAATACTGAATAGGGAGCATGGCTTGAAATAA
TCACATCCTTATTCGGCTGAGTAGATCCTTCTGTGCAGCCAGTATACCTGTCCTGTGTTATACT
TTTTCCTTTTATATGATGTGTTTAAAGCTAGCTAAACTTTATCTGATATTCTGTTGCAGTAAGA
GTGTTCACCAGCATCCAGGAGAAGACTCCCTTAAGTG

Sequences
Splice junction sequence	TTTCCTTTTATATGATGTGTTTAAAGCTAGCTAAACTTTATCTGATATTCTGTTGCAGTAAGAG TGTTCACCAGCATCCAGGAGAAGACTCCCTTAAGTGatattgcggactggctccaacagtattg ggtgggaaaattgaccctgctctttttgaagtcctctatgtaagttataaatgaaagattattt tgtgtagc
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: 230 Transcript exons: 17407832-17407898,17407986-17408045,17408324-17408384,17 408659-17408700 ATATTGCGGACTGGCTCCAACAGTATTGGGTGGGAAAATTGACCCTGCTCTTTTTGAAGTCCTC TATGCTTCTCAGCATGCTATCTTCTTCTTTGCTAGGCTTCCACAGATATGGAAGAATTTTATGA ACAAGGGCACTGGCGAGCTGAGCTTTCTGACCTGTTTCATGAACTTTGCTGGTTCCATAGTAAG AGTGTTCACCAGCATCCAGGAGAAGACTCCCTTAAGTG
Genomic sequence	ATATTGCGGACTGGCTCCAACAGTATTGGGTGGGAAAATTGACCCTGCTCTTTTTGAAGTCCTC TATGTAAGTTATAAATGAAAGATTATTTTGTGTAGCACTTGATATATTCGTATATGCTTGTCTT TTGATTGTGTGTAATATATTTTGCAGGCTTCTCAGCATGCTATCTTCTTCTTTGCTAGGCTTCC ACAGATATGGAAGAATTTTATGGTTCGTTGTTAGATTTCTGTACATCTAGCTATATTAGGTTTA TCTTTTCATGGAAAGTTGCTGTAACTAGGTGTACTAAATAGTAAAATGGTAACCTTAAATTTAA ATGAATCTTATGGTCTGGACCTTAGAATAAATAATTTGGGATTGACTAGTATGACAATGAACTT TTCATCTATCAGTCAGCATTTTGTACCAATTTTGTGAGTGGAGGCTTCTAACAAGTCGTTTGAC AATTTGCATGTACAAACTTTCTGACCTGTTGCTACGATACGCAGAACAAGGGCACTGGCGAGCT GAGCTTTCTGACCTGTTTCATGAACTTTGCTGGTTCCATAGGTAAGCTTAAGTACATGCCAGAT TAGTTACCAAGGCATTACTTTTTTACTTCACAATCCATTTTATTCTCTTCTTTGTTTGAAATTA AGTAGTATAAGCACAAAGTAGTCAAATGTTCTGAATACTGAATAGGGAGCATGGCTTGAAATAA TCACATCCTTATTCGGCTGAGTAGATCCTTCTGTGCAGCCAGTATACCTGTCCTGTGTTATACT TTTTCCTTTTATATGATGTGTTTAAAGCTAGCTAAACTTTATCTGATATTCTGTTGCAGTAAGA GTGTTCACCAGCATCCAGGAGAAGACTCCCTTAAGTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_017062 						
					
						PMCS
						0.221083439

Conservation Information
Conserved circRNAs	osi_circ_017062
PMCS	0.221083439

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							17408044-17408043(+)
17407999-17407993(-)
						
						Potential amino acid sequence
						
							MNKGTGELSFLTCFMNFAGSIVRVFTSIQEKTPLSDIADWLQQYWVGKLTLLFLKSSMLLSMLS
SSLLGFHRYGRIL*(+)
MLRSIEDFKKSRVNFPTQYCWSQSAISLKGVFSWMLVNTLTMEPAKFMKQVRKLSSPVPLFIKF
FHICGSLAKKKIAC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	17408044-17408043(+) 17407999-17407993(-)
Potential amino acid sequence	MNKGTGELSFLTCFMNFAGSIVRVFTSIQEKTPLSDIADWLQQYWVGKLTLLFLKSSMLLSMLS SSLLGFHRYGRIL(+) MLRSIEDFKKSRVNFPTQYCWSQSAISLKGVFSWMLVNTLTMEPAKFMKQVRKLSSPVPLFIKF FHICGSLAKKKIAC(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015;Ye et al., 2016;Chu et al., 2017

circRNA

Detail information of Os07g0479200_circ_g.1

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