Plant Circular RNA Database

Detail information of Os12g0174800_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os12g0174800_circ_g.2
					
						ID in PlantcircBase
						osa_circ_010663
					
						Alias
						Os12circ01415/Os_ciR741
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 3795289-3795604  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, SMALT, Segemehl, circseq_cup, find_circ
					
						Parent gene
						
							Os12g0174800						
					
						Parent gene annotation
						
							Protein-tyrosine phosphatase, receptor/non-receptor type domain 
containing protein. (Os12t0174800-01);Protein-tyrosine phosphata
se, receptor/non-receptor type domain containing protein. (Os12t
0174800-02);Conserved hypothetical protein. (Os12t0174800-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						3/40/4/13
					
						Tissues
						leaf and panicle/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  
						
							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
						Os12t0174800-01:2
Os12t0174800-02:2

General Information
CircRNA Name	Os12g0174800_circ_g.2
ID in PlantcircBase	osa_circ_010663
Alias	Os12circ01415/Os_ciR741
Organism	Oryza sativa
Position	chr12: 3795289-3795604 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, SMALT, Segemehl, circseq_cup, find_circ
Parent gene	Os12g0174800
Parent gene annotation	Protein-tyrosine phosphatase, receptor/non-receptor type domain containing protein. (Os12t0174800-01);Protein-tyrosine phosphata se, receptor/non-receptor type domain containing protein. (Os12t 0174800-02);Conserved hypothetical protein. (Os12t0174800-03)
Parent gene strand	-
Alternative splicing	NA
Support reads	3/40/4/13
Tissues	leaf and panicle/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	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	Os12t0174800-01:2 Os12t0174800-02:2

			
						 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   
						
							Yes							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   
						
							F: TGGACCTTGAGTGGAAATAA
 R: AAGGTCCACTAGCCAAGACA
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	Yes 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	F: TGGACCTTGAGTGGAAATAA R: AAGGTCCACTAGCCAAGACA PCR primers used in full-length (FL) sequence validation.

			
						 Sequences
					
						Splice junction sequence  
						
							TATATATATATATATACCTTTATAAAGCTTGCATTGATATAATCATTGCTTGAAGTCTGACTGG
TGGTTGATCGTTTTAGCCTTACCCTGGTAGTATCAActtaagactgtcgaattgtgtgagcata
acaataacaggacattgatattcatagaccatttcccagaaatcatcaaatgtcttggctagtg
gaccttga

						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: 221
Transcript exons: 3795289-3795426,3795522-3795604
CTTAAGACTGTCGAATTGTGTGAGCATAACAATAACAGGACATTGATATTCATAGACCATTTCC
CAGAAATCATCAAATGTCTTGGCTAGTGGACCTTGAGTGGAAATAAATTTTGCAACTCTGTTGT
CCTCAGTGACCTTTATAAAGCTTGCATTGATATAATCATTGCTTGAAGTCTGACTGGTGGTTGA
TCGTTTTAGCCTTACCCTGGTAGTATCAA
Transcript length: 316
Transcript exons: 3795289-3795604
CTTAAGACTGTCGAATTGTGTGAGCATAACAATAACAGGACATTGATATTCATAGACCATTTCC
CAGAAATCATCAAATGTCTTGGCTAGTGGACCTTGAGTGGAAATAAATTTTGCAACTCTGTTGT
CCTCAGTGACCTTTATAAAGCTTGCATTGATATAATCATTGCTTGAAGTCTGACTGGTGGTTGA
TCGTTTTAGCCTTACCCTGGTAGTATCAA
						
						Genomic sequence
						
							CTTAAGACTGTCGAATTGTGTGAGCATAACAATAACAGGACATTGATATTCATAGACCATTTCC
CAGAAATCATCAAATGTCTTGGCTAGTGGACCTTGAGTGGAAATAAATTTTGCAACTCTGTTGT
CCTCAGTGACCTGCAATTTTCATAAACCACATGTACAGATGCTCAATTGTCCCAGGCACTATTC
AGAAAGTGAAAAAGAATTGCAGTATATATATATATATATACCTTTATAAAGCTTGCATTGATAT
AATCATTGCTTGAAGTCTGACTGGTGGTTGATCGTTTTAGCCTTACCCTGGTAGTATCAA

Sequences
Splice junction sequence	TATATATATATATATACCTTTATAAAGCTTGCATTGATATAATCATTGCTTGAAGTCTGACTGG TGGTTGATCGTTTTAGCCTTACCCTGGTAGTATCAActtaagactgtcgaattgtgtgagcata acaataacaggacattgatattcatagaccatttcccagaaatcatcaaatgtcttggctagtg gaccttga
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: 221 Transcript exons: 3795289-3795426,3795522-3795604 CTTAAGACTGTCGAATTGTGTGAGCATAACAATAACAGGACATTGATATTCATAGACCATTTCC CAGAAATCATCAAATGTCTTGGCTAGTGGACCTTGAGTGGAAATAAATTTTGCAACTCTGTTGT CCTCAGTGACCTTTATAAAGCTTGCATTGATATAATCATTGCTTGAAGTCTGACTGGTGGTTGA TCGTTTTAGCCTTACCCTGGTAGTATCAA Transcript length: 316 Transcript exons: 3795289-3795604 CTTAAGACTGTCGAATTGTGTGAGCATAACAATAACAGGACATTGATATTCATAGACCATTTCC CAGAAATCATCAAATGTCTTGGCTAGTGGACCTTGAGTGGAAATAAATTTTGCAACTCTGTTGT CCTCAGTGACCTTTATAAAGCTTGCATTGATATAATCATTGCTTGAAGTCTGACTGGTGGTTGA TCGTTTTAGCCTTACCCTGGTAGTATCAA
Genomic sequence	CTTAAGACTGTCGAATTGTGTGAGCATAACAATAACAGGACATTGATATTCATAGACCATTTCC CAGAAATCATCAAATGTCTTGGCTAGTGGACCTTGAGTGGAAATAAATTTTGCAACTCTGTTGT CCTCAGTGACCTGCAATTTTCATAAACCACATGTACAGATGCTCAATTGTCCCAGGCACTATTC AGAAAGTGAAAAAGAATTGCAGTATATATATATATATATACCTTTATAAAGCTTGCATTGATAT AATCATTGCTTGAAGTCTGACTGGTGGTTGATCGTTTTAGCCTTACCCTGGTAGTATCAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_003319* 						
					
						PMCS
						0.434586419

Conservation Information
Conserved circRNAs	osi_circ_003319*
PMCS	0.434586419

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3795364-3795603(-)
3795350-3795589(-)
						
						Potential amino acid sequence
						
							MISGKWSMNINVLLLLCSHNSTVLS*(-)
MVYEYQCPVIVMLTQFDSLKLILPG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3795364-3795603(-) 3795350-3795589(-)
Potential amino acid sequence	MISGKWSMNINVLLLLCSHNSTVLS(-) MVYEYQCPVIVMLTQFDSLKLILPG(-)
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 Os12g0174800_circ_g.2

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