Plant Circular RNA Database

Detail information of Os03g0231800_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os03g0231800_circ_g.1
					
						ID in PlantcircBase
						osa_circ_018730
					
						Alias
						Os_ciR3885
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 6958237-6959434  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os03g0231850						
					
						Parent gene annotation
						
							Hypothetical protein. (Os03t0231850-00)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0231700_circ_g.3 Os03g0231750_circ_ag.1 Os03g0231750_circ_ag.2 Os03g0231750_circ_ag.3 Os03g0231700_circ_g.4 Os03g0231800_circ_g.2 Os03g0231800_circ_g.3 Os03g0231800_circ_g.4 						
					
						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
						Os03t0231800-02:4
Os03t0231800-03:4
Os03t0231800-02:4
Os03t0231850-00:4
Os03t0231800-03:4

General Information
CircRNA Name	Os03g0231800_circ_g.1
ID in PlantcircBase	osa_circ_018730
Alias	Os_ciR3885
Organism	Oryza sativa
Position	chr3: 6958237-6959434 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ui-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os03g0231850
Parent gene annotation	Hypothetical protein. (Os03t0231850-00)
Parent gene strand	+
Alternative splicing	Os03g0231700_circ_g.3 Os03g0231750_circ_ag.1 Os03g0231750_circ_ag.2 Os03g0231750_circ_ag.3 Os03g0231700_circ_g.4 Os03g0231800_circ_g.2 Os03g0231800_circ_g.3 Os03g0231800_circ_g.4
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	Os03t0231800-02:4 Os03t0231800-03:4 Os03t0231800-02:4 Os03t0231850-00:4 Os03t0231800-03:4

			
						 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  
						
							TGCTTTTAATTCTTCACCTGACTTGGTCTTGTATTTAACACCCTTAACTGTACCATCTTCTTCA
ACCAATGATGTAACAGTTCCTTGCTCCAATTGAACAggaaatcagtcttacgccgatccacatg
cgtttaggtgaagggaggggaagcattaggcgaccgacaccatagatagcgacagcaaagaaat
gtgccact

									
								

					

						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: 943
Transcript exons: 6958237-6958515,6958601-6958876,6958968-6959186,6959266-
6959434
GGAAATCAGTCTTACGCCGATCCACATGCGTTTAGGTGAAGGGAGGGGAAGCATTAGGCGACCG
ACACCATAGATAGCGACAGCAAAGAAATGTGCCACTAAACTCAATGGTCGAGGATTCAGACCAG
ACAGAAGAGCAATAGGCCCATTTGAAAAGACACCTCCAAGGCTCAAGTAATCAAAGCAGGCTTG
GCGCATCTCATTCCTAGCCTGATCAGGTGAGGCACTGAAAACCTTGTATAGAGCACCAGCTAAT
GTGTTTATGGTAGAAGCAACCGGCTTCCGCAGTGTATAGAATGATTCAAGGTATTTGCAAAGAG
CAGATGCATCATGCAGATTGCGGAGAGGCTTGAGAAGATTACGTAGCACAACAATGTCAGATAA
TGCAACAGTCATTCCGCCACCAGTCAAAGGATGCCGCATGTTGAATGCATCACCCATCAAAAGT
GCACCAGGGGTTGGATGTGGAGCAGCCGGCATGCTCCTGTTTGGCATTGTTCTTATGCTTCCCT
TATCAATGGCTGCTATGAATGAATCATAGATTTCTGGAGGAATCTGAGGTGCAACCACTGTTTT
GAGATATTTTGCCATTTCACCGTTTGCTATGGAAGGCACCTTCTGACCAGGGACATCAACCAAA
CAGCGAACTTCAGTGCTGCTTATTGGGTAAAATAGGATAGGTGAAGGATTGGCCAGGACAACAT
GGCCATGGTTTGCATGAGGAAGTTGACAATTCTCCAGGACCAGCCCAACAAAACAAGATGGTAC
ATCAACCTTTGGAGAGCAAAGGGCGCGGCGAAGGTTTGAGAAACAGCCATCGCATACAATTGTC
AGAGGTGCATATGCTTTTAATTCTTCACCTGACTTGGTCTTGTATTTAACACCCTTAACTGTAC
CATCTTCTTCAACCAATGATGTAACAGTTCCTTGCTCCAATTGAACA
						
					

						Genomic sequence
						
							GGAAATCAGTCTTACGCCGATCCACATGCGTTTAGGTGAAGGGAGGGGAAGCATTAGGCGACCG
ACACCATAGATAGCGACAGCAAAGAAATGTGCCACTAAACTCAATGGTCGAGGATTCAGACCAG
ACAGAAGAGCAATAGGCCCATTTGAAAAGACACCTCCAAGGCTCAAGTAATCAAAGCAGGCTTG
GCGCATCTCATTCCTAGCCTGATCAGGTGAGGCACTGAAAACCTTGTATAGAGCACCAGCTAAT
GTGTTTATGGTAGAAGCAACCGGCTGTGAACATGAAAGCGCCATACATTAGACAGCATACATTT
TGAAAGGTGGGTGGTAAATTGTGAAATGAAGAGTGAAGACTAACCTTCCGCAGTGTATAGAATG
ATTCAAGGTATTTGCAAAGAGCAGATGCATCATGCAGATTGCGGAGAGGCTTGAGAAGATTACG
TAGCACAACAATGTCAGATAATGCAACAGTCATTCCGCCACCAGTCAAAGGATGCCGCATGTTG
AATGCATCACCCATCAAAAGTGCACCAGGGGTTGGATGTGGAGCAGCCGGCATGCTCCTGTTTG
GCATTGTTCTTATGCTTCCCTTATCAATGGCTGCTATGAATGAATCATAGATTTCTGGAGGAAT
CTGTCAACAGAACATTTCCATTGACATTTAGTTGCTATGAGTAGGCAAGCAAAAACTCGGGACA
AGACTGACTGAAATAGCAAAATAATACCTGAGGTGCAACCACTGTTTTGAGATATTTTGCCATT
TCACCGTTTGCTATGGAAGGCACCTTCTGACCAGGGACATCAACCAAACAGCGAACTTCAGTGC
TGCTTATTGGGTAAAATAGGATAGGTGAAGGATTGGCCAGGACAACATGGCCATGGTTTGCATG
AGGAAGTTGACAATTCTCCAGGACCAGCCCAACAAAACAAGATGGTACATCAACCTAACCACAT
ATTTCCATCAGTATTAGATCTTCTACATGCATGAACAAAAAAGGATAGTGCAAAATCTAAAAAC
TGTACCTTTGGAGAGCAAAGGGCGCGGCGAAGGTTTGAGAAACAGCCATCGCATACAATTGTCA
GAGGTGCATATGCTTTTAATTCTTCACCTGACTTGGTCTTGTATTTAACACCCTTAACTGTACC
ATCTTCTTCAACCAATGATGTAACAGTTCCTTGCTCCAATTGAACA
						
					

			
		

Sequences
Splice junction sequence	TGCTTTTAATTCTTCACCTGACTTGGTCTTGTATTTAACACCCTTAACTGTACCATCTTCTTCA ACCAATGATGTAACAGTTCCTTGCTCCAATTGAACAggaaatcagtcttacgccgatccacatg cgtttaggtgaagggaggggaagcattaggcgaccgacaccatagatagcgacagcaaagaaat gtgccact
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: 943 Transcript exons: 6958237-6958515,6958601-6958876,6958968-6959186,6959266- 6959434 GGAAATCAGTCTTACGCCGATCCACATGCGTTTAGGTGAAGGGAGGGGAAGCATTAGGCGACCG ACACCATAGATAGCGACAGCAAAGAAATGTGCCACTAAACTCAATGGTCGAGGATTCAGACCAG ACAGAAGAGCAATAGGCCCATTTGAAAAGACACCTCCAAGGCTCAAGTAATCAAAGCAGGCTTG GCGCATCTCATTCCTAGCCTGATCAGGTGAGGCACTGAAAACCTTGTATAGAGCACCAGCTAAT GTGTTTATGGTAGAAGCAACCGGCTTCCGCAGTGTATAGAATGATTCAAGGTATTTGCAAAGAG CAGATGCATCATGCAGATTGCGGAGAGGCTTGAGAAGATTACGTAGCACAACAATGTCAGATAA TGCAACAGTCATTCCGCCACCAGTCAAAGGATGCCGCATGTTGAATGCATCACCCATCAAAAGT GCACCAGGGGTTGGATGTGGAGCAGCCGGCATGCTCCTGTTTGGCATTGTTCTTATGCTTCCCT TATCAATGGCTGCTATGAATGAATCATAGATTTCTGGAGGAATCTGAGGTGCAACCACTGTTTT GAGATATTTTGCCATTTCACCGTTTGCTATGGAAGGCACCTTCTGACCAGGGACATCAACCAAA CAGCGAACTTCAGTGCTGCTTATTGGGTAAAATAGGATAGGTGAAGGATTGGCCAGGACAACAT GGCCATGGTTTGCATGAGGAAGTTGACAATTCTCCAGGACCAGCCCAACAAAACAAGATGGTAC ATCAACCTTTGGAGAGCAAAGGGCGCGGCGAAGGTTTGAGAAACAGCCATCGCATACAATTGTC AGAGGTGCATATGCTTTTAATTCTTCACCTGACTTGGTCTTGTATTTAACACCCTTAACTGTAC CATCTTCTTCAACCAATGATGTAACAGTTCCTTGCTCCAATTGAACA
Genomic sequence	GGAAATCAGTCTTACGCCGATCCACATGCGTTTAGGTGAAGGGAGGGGAAGCATTAGGCGACCG ACACCATAGATAGCGACAGCAAAGAAATGTGCCACTAAACTCAATGGTCGAGGATTCAGACCAG ACAGAAGAGCAATAGGCCCATTTGAAAAGACACCTCCAAGGCTCAAGTAATCAAAGCAGGCTTG GCGCATCTCATTCCTAGCCTGATCAGGTGAGGCACTGAAAACCTTGTATAGAGCACCAGCTAAT GTGTTTATGGTAGAAGCAACCGGCTGTGAACATGAAAGCGCCATACATTAGACAGCATACATTT TGAAAGGTGGGTGGTAAATTGTGAAATGAAGAGTGAAGACTAACCTTCCGCAGTGTATAGAATG ATTCAAGGTATTTGCAAAGAGCAGATGCATCATGCAGATTGCGGAGAGGCTTGAGAAGATTACG TAGCACAACAATGTCAGATAATGCAACAGTCATTCCGCCACCAGTCAAAGGATGCCGCATGTTG AATGCATCACCCATCAAAAGTGCACCAGGGGTTGGATGTGGAGCAGCCGGCATGCTCCTGTTTG GCATTGTTCTTATGCTTCCCTTATCAATGGCTGCTATGAATGAATCATAGATTTCTGGAGGAAT CTGTCAACAGAACATTTCCATTGACATTTAGTTGCTATGAGTAGGCAAGCAAAAACTCGGGACA AGACTGACTGAAATAGCAAAATAATACCTGAGGTGCAACCACTGTTTTGAGATATTTTGCCATT TCACCGTTTGCTATGGAAGGCACCTTCTGACCAGGGACATCAACCAAACAGCGAACTTCAGTGC TGCTTATTGGGTAAAATAGGATAGGTGAAGGATTGGCCAGGACAACATGGCCATGGTTTGCATG AGGAAGTTGACAATTCTCCAGGACCAGCCCAACAAAACAAGATGGTACATCAACCTAACCACAT ATTTCCATCAGTATTAGATCTTCTACATGCATGAACAAAAAAGGATAGTGCAAAATCTAAAAAC TGTACCTTTGGAGAGCAAAGGGCGCGGCGAAGGTTTGAGAAACAGCCATCGCATACAATTGTCA GAGGTGCATATGCTTTTAATTCTTCACCTGACTTGGTCTTGTATTTAACACCCTTAACTGTACC ATCTTCTTCAACCAATGATGTAACAGTTCCTTGCTCCAATTGAACA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.596894157

Conservation Information
Conserved circRNAs	NA
PMCS	0.596894157

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6959005-6959398(-)
						
						Potential amino acid sequence
						
							MAKYLKTVVAPQIPPEIYDSFIAAIDKGSIRTMPNRSMPAAPHPTPGALLMGDAFNMRHPLTGG
GMTVALSDIVVLRNLLKPLRNLHDASALCKYLESFYTLRKPVASTINTLAGALYKVFSASPDQA
RNEMRQACFDYLSLGGVFSNGPIALLSGLNPRPLSLVAHFFAVAIYGVGRLMLPLPSPKRMWIG
VRLISCSIGARNCYIIG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6959005-6959398(-)
Potential amino acid sequence	MAKYLKTVVAPQIPPEIYDSFIAAIDKGSIRTMPNRSMPAAPHPTPGALLMGDAFNMRHPLTGG GMTVALSDIVVLRNLLKPLRNLHDASALCKYLESFYTLRKPVASTINTLAGALYKVFSASPDQA RNEMRQACFDYLSLGGVFSNGPIALLSGLNPRPLSLVAHFFAVAIYGVGRLMLPLPSPKRMWIG VRLISCSIGARNCYIIG*(-)
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 Os03g0231800_circ_g.1

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