Plant Circular RNA Database

Detail information of Os03g0711300_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os03g0711300_circ_g.4
					
						ID in PlantcircBase
						osa_circ_021238
					
						Alias
						Os_ciR3848
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 28713714-28715411  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os03g0711300						
					
						Parent gene annotation
						
							Serine/threonine protein kinase domain containing protein. (Os03
t0711300-01);Similar to Protein kinase. (Os03t0711300-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0711300_circ_g.1 Os03g0711300_circ_g.2 Os03g0711300_circ_g.3 						
					
						Support reads
						2/1
					
						Tissues
						root/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
						Os03t0711300-02:4
Os03t0711300-01:4

General Information
CircRNA Name	Os03g0711300_circ_g.4
ID in PlantcircBase	osa_circ_021238
Alias	Os_ciR3848
Organism	Oryza sativa
Position	chr3: 28713714-28715411 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os03g0711300
Parent gene annotation	Serine/threonine protein kinase domain containing protein. (Os03 t0711300-01);Similar to Protein kinase. (Os03t0711300-02)
Parent gene strand	-
Alternative splicing	Os03g0711300_circ_g.1 Os03g0711300_circ_g.2 Os03g0711300_circ_g.3
Support reads	2/1
Tissues	root/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	Os03t0711300-02:4 Os03t0711300-01:4

			
						 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  
						
							TCGACTTACAGACACCCTAGGCTTCCTTAAAAAGCCAAAACAACTACAGCAGCCCATGTCGGTC
AGGTCAGCCATTCAGACCAAGTAGGCACCAGGAACCttcccgaagaacatctgtcatggcagtt
tctgatcgcacaacacgtactttcatcatgtaagatttattcaaaacctacaatagaagggcaa
aggctaca

									
								

					

						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: 610
Transcript exons: 28713714-28713788,28714006-28714050,28714126-28714200,28
714997-28715411
TTCCCGAAGAACATCTGTCATGGCAGTTTCTGATCGCACAACACGTACTTTCATCATGTAAGAT
TTATTCAAAACCTTCACTGCGTAAAGCTTTCCATCTTTCATGCTTCGGTATAAGACCACTTTGC
CATAGCTTCCAGAACCAATCTTCCCCAGGTGGACATATTGGTTGACCATCTTGCTGCCATTTTC
ATCCTCTGAGCGAAATACTTTTTTAGTCTCCTTAACTAGGCTTTCTCTACATGCAAAGCCATTC
TGAGCCCTTGACAGTATAATATCTTCAGATCTCTTCCTTGGCTGCCCATCATCACTTCCATAAA
GATGATCAGGATCATCTCCATCATAGAAGCTTCTGTCAGGGTCATCGCCATTGTAGAAGCTTCT
ATCGAGATCATCCCTGTCGTAGAAGCTTCTATCAGGATCATCCCCGGTGTAGAAGCTTCCATCA
GGATCCTCCGCAGATTTATGGTTCAACAAGTCTTCAGATAGGATGCCATCAGCGTCGCGAGGTC
GACTTACAGACACCCTAGGCTTCCTTAAAAAGCCAAAACAACTACAGCAGCCCATGTCGGTCAG
GTCAGCCATTCAGACCAAGTAGGCACCAGGAACC
						
					

						Genomic sequence
						
							TTCCCGAAGAACATCTGTCATGGCAGTTTCTGATCGCACAACACGTACTTTCATCATGTAAGAT
TTATTCAAAACCTACAATAGAAGGGCAAAGGCTACAGTTCCATCAGTTAGATGCAGACACTGTG
CACGCAACATAAATTTAACCTTGTAACCATAAGAATAATGGTGCTGAACGAGTAAAACCAACTA
CTCAGACTAGCAGCTAGTTATTAATGAGTTCAGATGCAAGAAATAAAAATTAGTAACTAACATA
AAGAAATCAGCACATAAGGACAGCGAAAAACCCTACCTTCACTGCGTAAAGCTTTCCATCTTTC
ATGCTTCGGTATAAGACCTTTAAGCCAAAAAAAAAAAGATTTAGACATTTACCGTGGGAAGTCA
CTTCATAACATAATGTGAGCTATCTTACCACTTTGCCATAGCTTCCAGAACCAATCTTCCCCAG
GTGGACATATTGGTTGACCATCTTGCTGCCATTTTCATCCTAAATGTGCCGAAAGGAAAAAAGT
TATTGTACTGTTTAATGCAAAAAGGTAATAGATCGCATACAGCTTTATGGATTTGCAAAGGTCA
CGACAACACTGATTGAAACAGTAGATCATCTGAGCATGGCGCCTTAAACAATTAAAGTTTACAT
CTTATACGTATAATGCAAAAGATGTTTTAACCGATCATTTATAACACAGTTATAATTTTCTATA
ATAAGTTAAACAATGTTACTCTACTAAATAATATAACGACAAGGATAGATTAATTACCAATCAT
TCCAAAATCGTATACTACATAGCAACAACCAAATAATCTAGACTTTCCATGATTGGTTAGTGGG
CTTCAGGTTGTCACTTTCCTAGCAGGAGGTCCCACATTCTAATCCTAGCAGACGCACAAAATTA
GGACAAATGGCAGTTATTCTACAAGGATGGATTAATTATTAATTGTTCCAAAAGGAAAGTGGCA
TAATGTGCGGCATTAGCATTGATGTTGTCGTAGAAGATGCCACGTTCAAAACCTAGCAGAGGCG
CCAAAATTTGCATTCCTGCATGATGGAGATTCAATCACTCGAACAAGACTGAACTACGACATTT
ACCTATTTCGCAGTCTAACCGCTGAGCTAACCTTGTCTTTAATACAATGGTCCATGTGTGACAG
TTTCTCATGCACGGGCTAGCTTGTAAAAGAAGTCTGCACTAGATAAGACTATACCTCTATATAT
GGGCATGAAAAATGGAAATGAAAATAGAATAACAGTGGTAAAGAATTCAAATCTAAGAGGATAG
TACCTCTGAGCGAAATACTTTTTTAGTCTCCTTAACTAGGCTTTCTCTACATGCAAAGCCATTC
TGAGCCCTTGACAGTATAATATCTTCAGATCTCTTCCTTGGCTGCCCATCATCACTTCCATAAA
GATGATCAGGATCATCTCCATCATAGAAGCTTCTGTCAGGGTCATCGCCATTGTAGAAGCTTCT
ATCGAGATCATCCCTGTCGTAGAAGCTTCTATCAGGATCATCCCCGGTGTAGAAGCTTCCATCA
GGATCCTCCGCAGATTTATGGTTCAACAAGTCTTCAGATAGGATGCCATCAGCGTCGCGAGGTC
GACTTACAGACACCCTAGGCTTCCTTAAAAAGCCAAAACAACTACAGCAGCCCATGTCGGTCAG
GTCAGCCATTCAGACCAAGTAGGCACCAGGAACC
						
					

			
		

Sequences
Splice junction sequence	TCGACTTACAGACACCCTAGGCTTCCTTAAAAAGCCAAAACAACTACAGCAGCCCATGTCGGTC AGGTCAGCCATTCAGACCAAGTAGGCACCAGGAACCttcccgaagaacatctgtcatggcagtt tctgatcgcacaacacgtactttcatcatgtaagatttattcaaaacctacaatagaagggcaa aggctaca
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: 610 Transcript exons: 28713714-28713788,28714006-28714050,28714126-28714200,28 714997-28715411 TTCCCGAAGAACATCTGTCATGGCAGTTTCTGATCGCACAACACGTACTTTCATCATGTAAGAT TTATTCAAAACCTTCACTGCGTAAAGCTTTCCATCTTTCATGCTTCGGTATAAGACCACTTTGC CATAGCTTCCAGAACCAATCTTCCCCAGGTGGACATATTGGTTGACCATCTTGCTGCCATTTTC ATCCTCTGAGCGAAATACTTTTTTAGTCTCCTTAACTAGGCTTTCTCTACATGCAAAGCCATTC TGAGCCCTTGACAGTATAATATCTTCAGATCTCTTCCTTGGCTGCCCATCATCACTTCCATAAA GATGATCAGGATCATCTCCATCATAGAAGCTTCTGTCAGGGTCATCGCCATTGTAGAAGCTTCT ATCGAGATCATCCCTGTCGTAGAAGCTTCTATCAGGATCATCCCCGGTGTAGAAGCTTCCATCA GGATCCTCCGCAGATTTATGGTTCAACAAGTCTTCAGATAGGATGCCATCAGCGTCGCGAGGTC GACTTACAGACACCCTAGGCTTCCTTAAAAAGCCAAAACAACTACAGCAGCCCATGTCGGTCAG GTCAGCCATTCAGACCAAGTAGGCACCAGGAACC
Genomic sequence	TTCCCGAAGAACATCTGTCATGGCAGTTTCTGATCGCACAACACGTACTTTCATCATGTAAGAT TTATTCAAAACCTACAATAGAAGGGCAAAGGCTACAGTTCCATCAGTTAGATGCAGACACTGTG CACGCAACATAAATTTAACCTTGTAACCATAAGAATAATGGTGCTGAACGAGTAAAACCAACTA CTCAGACTAGCAGCTAGTTATTAATGAGTTCAGATGCAAGAAATAAAAATTAGTAACTAACATA AAGAAATCAGCACATAAGGACAGCGAAAAACCCTACCTTCACTGCGTAAAGCTTTCCATCTTTC ATGCTTCGGTATAAGACCTTTAAGCCAAAAAAAAAAAGATTTAGACATTTACCGTGGGAAGTCA CTTCATAACATAATGTGAGCTATCTTACCACTTTGCCATAGCTTCCAGAACCAATCTTCCCCAG GTGGACATATTGGTTGACCATCTTGCTGCCATTTTCATCCTAAATGTGCCGAAAGGAAAAAAGT TATTGTACTGTTTAATGCAAAAAGGTAATAGATCGCATACAGCTTTATGGATTTGCAAAGGTCA CGACAACACTGATTGAAACAGTAGATCATCTGAGCATGGCGCCTTAAACAATTAAAGTTTACAT CTTATACGTATAATGCAAAAGATGTTTTAACCGATCATTTATAACACAGTTATAATTTTCTATA ATAAGTTAAACAATGTTACTCTACTAAATAATATAACGACAAGGATAGATTAATTACCAATCAT TCCAAAATCGTATACTACATAGCAACAACCAAATAATCTAGACTTTCCATGATTGGTTAGTGGG CTTCAGGTTGTCACTTTCCTAGCAGGAGGTCCCACATTCTAATCCTAGCAGACGCACAAAATTA GGACAAATGGCAGTTATTCTACAAGGATGGATTAATTATTAATTGTTCCAAAAGGAAAGTGGCA TAATGTGCGGCATTAGCATTGATGTTGTCGTAGAAGATGCCACGTTCAAAACCTAGCAGAGGCG CCAAAATTTGCATTCCTGCATGATGGAGATTCAATCACTCGAACAAGACTGAACTACGACATTT ACCTATTTCGCAGTCTAACCGCTGAGCTAACCTTGTCTTTAATACAATGGTCCATGTGTGACAG TTTCTCATGCACGGGCTAGCTTGTAAAAGAAGTCTGCACTAGATAAGACTATACCTCTATATAT GGGCATGAAAAATGGAAATGAAAATAGAATAACAGTGGTAAAGAATTCAAATCTAAGAGGATAG TACCTCTGAGCGAAATACTTTTTTAGTCTCCTTAACTAGGCTTTCTCTACATGCAAAGCCATTC TGAGCCCTTGACAGTATAATATCTTCAGATCTCTTCCTTGGCTGCCCATCATCACTTCCATAAA GATGATCAGGATCATCTCCATCATAGAAGCTTCTGTCAGGGTCATCGCCATTGTAGAAGCTTCT ATCGAGATCATCCCTGTCGTAGAAGCTTCTATCAGGATCATCCCCGGTGTAGAAGCTTCCATCA GGATCCTCCGCAGATTTATGGTTCAACAAGTCTTCAGATAGGATGCCATCAGCGTCGCGAGGTC GACTTACAGACACCCTAGGCTTCCTTAAAAAGCCAAAACAACTACAGCAGCCCATGTCGGTCAG GTCAGCCATTCAGACCAAGTAGGCACCAGGAACC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005057* osi_circ_013499 						
					
						PMCS
						0.240756243

Conservation Information
Conserved circRNAs	osi_circ_005057* osi_circ_013499
PMCS	0.240756243

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							28715388-28715381(-)
						
						Potential amino acid sequence
						
							MADLTDMGCCSCFGFLRKPRVSVSRPRDADGILSEDLLNHKSAEDPDGSFYTGDDPDRSFYDRD
DLDRSFYNGDDPDRSFYDGDDPDHLYGSDDGQPRKRSEDIILSRAQNGFACRESLVKETKKVFR
SEDENGSKMVNQYVHLGKIGSGSYGKVVLYRSMKDGKLYAVKVLNKSYMMKVRVVRSETAMTDV
LREGSWCLLGLNG*(-)
						
						Sponge-miRNAs
						
							osa-miR5538 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	28715388-28715381(-)
Potential amino acid sequence	MADLTDMGCCSCFGFLRKPRVSVSRPRDADGILSEDLLNHKSAEDPDGSFYTGDDPDRSFYDRD DLDRSFYNGDDPDRSFYDGDDPDHLYGSDDGQPRKRSEDIILSRAQNGFACRESLVKETKKVFR SEDENGSKMVNQYVHLGKIGSGSYGKVVLYRSMKDGKLYAVKVLNKSYMMKVRVVRSETAMTDV LREGSWCLLGLNG*(-)
Sponge-miRNAs	osa-miR5538
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os03g0711300_circ_g.4

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