Plant Circular RNA Database

Detail information of Os05g0519500_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os05g0519500_circ_g.1
					
						ID in PlantcircBase
						osa_circ_028551
					
						Alias
						Os_ciR3070
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 25791255-25791699  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os05g0519500						
					
						Parent gene annotation
						
							Similar to Periodic tryptophan protein-associated region; WD40-l
ike. (Os05t0519500-01);WD40/YVTN repeat-like domain containing p
rotein. (Os05t0519500-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						4/2
					
						Tissues
						root/shoot, 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
						Os05t0519500-02:2
Os05t0519500-01:2

General Information
CircRNA Name	Os05g0519500_circ_g.1
ID in PlantcircBase	osa_circ_028551
Alias	Os_ciR3070
Organism	Oryza sativa
Position	chr5: 25791255-25791699 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os05g0519500
Parent gene annotation	Similar to Periodic tryptophan protein-associated region; WD40-l ike. (Os05t0519500-01);WD40/YVTN repeat-like domain containing p rotein. (Os05t0519500-02)
Parent gene strand	-
Alternative splicing	NA
Support reads	4/2
Tissues	root/shoot, 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	Os05t0519500-02:2 Os05t0519500-01:2

			
						 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  
						
							TGAGAAGAGAATGATTATTGGCCATAAAATGAACTGCAGTAACAGCGTTTGTATGCTCCGAAAA
TGTTATGAAACAGAACCCAGAGGAGACTGTCCAGACattgattggcgaaaacattaggccatga
actggtccttggtgaccactgagtatatccaacaaacgaccagtcttcattgaccaaacaaata
tctgcatg

						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: 345
Transcript exons: 25791255-25791347,25791448-25791699
ATTGATTGGCGAAAACATTAGGCCATGAACTGGTCCTTGGTGACCACTGAGTATATCCAACAAA
CGACCAGTCTTCATTGACCAAACAAATATCTCAAATGAATCAAGTGTTCCAGCACATATTACTT
CTCCACTCTGATCTGCCGTTAAAGAAACAAATTGTCTGGGCAATGCAGTAGTAAATGTCTTGAA
ATTTCGATAGCGGAACAGATCCCATGCTCGAATAGTCCCATCAAGGGAGGCACTGAGAAGAGAA
TGATTATTGGCCATAAAATGAACTGCAGTAACAGCGTTTGTATGCTCCGAAAATGTTATGAAAC
AGAACCCAGAGGAGACTGTCCAGAC
						
						Genomic sequence
						
							ATTGATTGGCGAAAACATTAGGCCATGAACTGGTCCTTGGTGACCACTGAGTATATCCAACAAA
CGACCAGTCTTCATTGACCAAACAAATATCTGCATGAAGATGTTTTGACAGTCAAAAAAATGAG
AGAAAAAGAGAAGCATATGCACGGGGAAAAAAACTGCAGCAAAAAGGTTGACTTCACACACACA
CCTCAAATGAATCAAGTGTTCCAGCACATATTACTTCTCCACTCTGATCTGCCGTTAAAGAAAC
AAATTGTCTGGGCAATGCAGTAGTAAATGTCTTGAAATTTCGATAGCGGAACAGATCCCATGCT
CGAATAGTCCCATCAAGGGAGGCACTGAGAAGAGAATGATTATTGGCCATAAAATGAACTGCAG
TAACAGCGTTTGTATGCTCCGAAAATGTTATGAAACAGAACCCAGAGGAGACTGTCCAGAC

Sequences
Splice junction sequence	TGAGAAGAGAATGATTATTGGCCATAAAATGAACTGCAGTAACAGCGTTTGTATGCTCCGAAAA TGTTATGAAACAGAACCCAGAGGAGACTGTCCAGACattgattggcgaaaacattaggccatga actggtccttggtgaccactgagtatatccaacaaacgaccagtcttcattgaccaaacaaata tctgcatg
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: 345 Transcript exons: 25791255-25791347,25791448-25791699 ATTGATTGGCGAAAACATTAGGCCATGAACTGGTCCTTGGTGACCACTGAGTATATCCAACAAA CGACCAGTCTTCATTGACCAAACAAATATCTCAAATGAATCAAGTGTTCCAGCACATATTACTT CTCCACTCTGATCTGCCGTTAAAGAAACAAATTGTCTGGGCAATGCAGTAGTAAATGTCTTGAA ATTTCGATAGCGGAACAGATCCCATGCTCGAATAGTCCCATCAAGGGAGGCACTGAGAAGAGAA TGATTATTGGCCATAAAATGAACTGCAGTAACAGCGTTTGTATGCTCCGAAAATGTTATGAAAC AGAACCCAGAGGAGACTGTCCAGAC
Genomic sequence	ATTGATTGGCGAAAACATTAGGCCATGAACTGGTCCTTGGTGACCACTGAGTATATCCAACAAA CGACCAGTCTTCATTGACCAAACAAATATCTGCATGAAGATGTTTTGACAGTCAAAAAAATGAG AGAAAAAGAGAAGCATATGCACGGGGAAAAAAACTGCAGCAAAAAGGTTGACTTCACACACACA CCTCAAATGAATCAAGTGTTCCAGCACATATTACTTCTCCACTCTGATCTGCCGTTAAAGAAAC AAATTGTCTGGGCAATGCAGTAGTAAATGTCTTGAAATTTCGATAGCGGAACAGATCCCATGCT CGAATAGTCCCATCAAGGGAGGCACTGAGAAGAGAATGATTATTGGCCATAAAATGAACTGCAG TAACAGCGTTTGTATGCTCCGAAAATGTTATGAAACAGAACCCAGAGGAGACTGTCCAGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_015659 						
					
						PMCS
						0.454156498

Conservation Information
Conserved circRNAs	osi_circ_015659
PMCS	0.454156498

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25791611-25791272(+)
25791626-25791257(-)
						
						Potential amino acid sequence
						
							MIIGHKMNCSNSVCMLRKCYETEPRGDCPDIDWRKH*(+)
MANNHSLLSASLDGTIRAWDLFRYRNFKTFTTALPRQFVSLTADQSGEVICAGTLDSFEIFVWS
MKTGRLLDILSGHQGPVHGLMFSPINVWTVSSGFCFITFSEHTNAVTAVHFMANNHSLLSASLD
GTIRAWDLFRYRNFKTFTTALPRQFVSLTADQSGEVICAGTLDSFEIFVWSMKTGRLLDILSGH
QGPVHGLMFSPINVWTVSSGFCFITFSEHTNAVTAVHFMANNHSLLSASLDGTIRAWDLFRYRN
FKTFTTALPRQFVSLTADQSGEVICAGTLDSFEIFVWSMKTGRLLDILSGHQGPVHGLMFSPIN
VWTVSSGFCFITFSEHTNAVTAVHFMANNHSLLSASLDGTIRAWDLFRYRNFKTFTTALPRQFV
SLTADQSGEVICAGTLDSFEIFVWSMKTGRLLDILSGHQGPVHGLMFSPIN(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	25791611-25791272(+) 25791626-25791257(-)
Potential amino acid sequence	MIIGHKMNCSNSVCMLRKCYETEPRGDCPDIDWRKH*(+) MANNHSLLSASLDGTIRAWDLFRYRNFKTFTTALPRQFVSLTADQSGEVICAGTLDSFEIFVWS MKTGRLLDILSGHQGPVHGLMFSPINVWTVSSGFCFITFSEHTNAVTAVHFMANNHSLLSASLD GTIRAWDLFRYRNFKTFTTALPRQFVSLTADQSGEVICAGTLDSFEIFVWSMKTGRLLDILSGH QGPVHGLMFSPINVWTVSSGFCFITFSEHTNAVTAVHFMANNHSLLSASLDGTIRAWDLFRYRN FKTFTTALPRQFVSLTADQSGEVICAGTLDSFEIFVWSMKTGRLLDILSGHQGPVHGLMFSPIN VWTVSSGFCFITFSEHTNAVTAVHFMANNHSLLSASLDGTIRAWDLFRYRNFKTFTTALPRQFV SLTADQSGEVICAGTLDSFEIFVWSMKTGRLLDILSGHQGPVHGLMFSPIN(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os05g0519500_circ_g.1

Address

Any questions?

Supported by