Plant Circular RNA Database

Detail information of Os03g0197400_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os03g0197400_circ_g.2
					
						ID in PlantcircBase
						osa_circ_018371
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 5119909-5121819  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os03g0197400						
					
						Parent gene annotation
						
							Similar to COP9 signalosome complex subunit 4 (Signalosome subun
it 4) (Constitutive photomorphogenesis protein 8) (FUSCA protein
 4) (FUSCA4) (AtS4). (Os03t0197400-01);Similar to COP9 signaloso
me complex subunit 4 (Signalosome subunit 4) (Constitutive photo
morphogenesis protein 8) (FUSCA protein 4) (FUSCA4) (AtS4). (Os0
3t0197400-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0197400_circ_g.1 Os03g0197400_circ_g.3 Os03g0197400_circ_g.4 						
					
						Support reads
						1
					
						Tissues
						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
						Os03t0197400-01:7
Os03t0197400-02:7

General Information
CircRNA Name	Os03g0197400_circ_g.2
ID in PlantcircBase	osa_circ_018371
Alias	NA
Organism	Oryza sativa
Position	chr3: 5119909-5121819 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os03g0197400
Parent gene annotation	Similar to COP9 signalosome complex subunit 4 (Signalosome subun it 4) (Constitutive photomorphogenesis protein 8) (FUSCA protein 4) (FUSCA4) (AtS4). (Os03t0197400-01);Similar to COP9 signaloso me complex subunit 4 (Signalosome subunit 4) (Constitutive photo morphogenesis protein 8) (FUSCA protein 4) (FUSCA4) (AtS4). (Os0 3t0197400-02)
Parent gene strand	-
Alternative splicing	Os03g0197400_circ_g.1 Os03g0197400_circ_g.3 Os03g0197400_circ_g.4
Support reads	1
Tissues	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	Os03t0197400-01:7 Os03t0197400-02:7

			
						 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  
						
							TGTAGCAAGAACACGAGATCGTTGCGGACCAGCACCAGCCAATATTGTGCATGTCACAGCAGCA
CTAAGAGCTTGCTCCAAAGCATTTTCATCGATCTCTctgttggtcccactgctgcagctcttca
gtgtcatcctcaaaatgtatcacagcttcaacctgtaaaataagccaggcgagttaatctcata
acaacttg

									
								

					

						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: 125
Transcript exons: 5119909-5119955,5121742-5121819
CTGTTGGTCCCACTGCTGCAGCTCTTCAGTGTCATCCTCAAAATGTATGCGGACCAGCACCAGC
CAATATTGTGCATGTCACAGCAGCACTAAGAGCTTGCTCCAAAGCATTTTCATCGATCTCT
Transcript length: 478
Transcript exons: 5119909-5119968,5120127-5120186,5120514-5120556,5120632-
5120723,5120806-5120874,5120960-5121004,5121711-5121819
CTGTTGGTCCCACTGCTGCAGCTCTTCAGTGTCATCCTCAAAATGTATCACAGCTTCAACCTGA
TCAATTGAACCTCGCATCCTATCTTCATAAATCATTCGCGATGCTATCTTTTCAGCCTTCCTAG
GGTCAATGCCCAATAATGCTCCAAGCTCATCAAAGCTGATATTAGTGTAAAGTTTACTGGCACT
AAGGAGGTTATGCTCAATCATTGCCCGGTCAAGCACAGTAGACTTATCTGGTAACAGAGCTTTT
TGATGCGGTCTCAGCTCCTCTGCAAATGCTTCAATTTCTGGTTTCCTCAAAATCCTTTCAAGAA
AGACCTTCTGCAGTATTGGGTATATCTTCAACTTTGAGCATCTCTCATCCTTGTACAATGTAGC
AAGAACACGAGATCGTTGCGGACCAGCACCAGCCAATATTGTGCATGTCACAGCAGCACTAAGA
GCTTGCTCCAAAGCATTTTCATCGATCTCT
						
					

						Genomic sequence
						
							CTGTTGGTCCCACTGCTGCAGCTCTTCAGTGTCATCCTCAAAATGTATCACAGCTTCAACCTGT
AAAATAAGCCAGGCGAGTTAATCTCATAACAACTTGAATTAAACCACAAACGGTAAAACATGGT
TACAGTGTAAGTCTATTTCAGATGTCTGCTCGAAATGGTGGAATAGTATGAATATCAACATAAG
GATTAAGGAAGTCATATGAATAAAACCTGATCAATTGAACCTCGCATCCTATCTTCATAAATCA
TTCGCGATGCTATCTTTTCAGCCTGCCAGCATCAAAATCAGTTGCAGTAAGACTCCAATTTGAA
TACTTTCATATTTAAAATCAAACATAAATAAAGAATTTATAGAGAAAATGCCAGTTCTTCCTGG
TACCAGTTACAGGCCAGATGATTTGAACTATCCTATTTGATTTTAAATTGTGAAATTCGGTGGT
TCTTCCCAGTTTGACTAGTTTCCAGCAAGTACCACTCAGAACCCATATATTCCAAATTCTTTTC
TTTTTCTTAGTCATATGGACTTTGTGTGAATCTGTCTCTATAAACATGAAATGATGTATCATAT
CAACAGGAAAAATTAACCAAAATACTAACCTTCCTAGGGTCAATGCCCAATAATGCTCCAAGCT
CATCAAAGCTACAGAAATAAATCAATAGTTGATCAGAATGATAAATCACAATGACCCAGGAAAA
TTTCAATGCAAAAACTAACCTGATATTAGTGTAAAGTTTACTGGCACTAAGGAGGTTATGCTCA
ATCATTGCCCGGTCAAGCACAGTAGACTTATCTGGTAACAGAGCTTTCTGTTGAACAGAAGAAA
AATCCAGTCAATAAAATTACAAGCTACTACTACAAGTTATCTTGGAAGAGAGTATGTTCACTAA
CTTGATGCGGTCTCAGCTCCTCTGCAAATGCTTCAATTTCTGGTTTCCTCAAAATCCTTTCAAG
AAAGACCTACACATTTGAAGTAGAAGGCCTGTCAATAAAGGGAGCTTATGCTCCAAATATAAAT
GCCAGGGGAGTATATCAAGATAGGCACCTTCTGCAGTATTGGGTATATCTTCAACTTTGAGCAT
CTCTCATCCTAAAGGGAAAAGACAGTATAAAATCATGCCACGAGTCATAATTTAAGCACCGCTA
TAATGAGAAAAATCAGATGCAAAACAATTGTATTTTCATGCTACTACAATGTTGATACAAGGTG
TTGGTTCATTTGATGACCATGATTACAGATTGGTCAACATCAAACAGTATGAAACTATAAACTA
CCCACTGAAACTGGATGCTAGCATATTTATTAGTTTAGCAGAACTATAAAAAAAATCCTAAATA
ACTATTTGGAAGGATCTTGATATTAGTAATTCAATATCAAATGGGTTAAGTTTTTGTATAATGA
TGCCACATTCCAATGAGTTCGGAGACAATTCCTCTGTTTCAATATACATACTTTTTTCCCCGGA
AAACATAAATTTTGGAGTGTACCAAGAATGATGTACAGTAAATGGGAATACAAATCACTGCGTA
AGGGAGAGAAGCCACAGCATGTATATCATAGTAAGCTAAAGCCACAACCTATGGTGCTCCATAA
CAGAAACCAATCAATATCGATACAGAGCTCTGCAGAGCATCTGATAATTCAGATTTGTCCATTT
GATAAACATGGCACAGGGAAAGGGCAAAGATGATTACGATAGTATGATACATAAAAAGTTATTG
CAGACAATAAATGACATGTAGATATAACAAGCACTGCAAACCAGAATGTTATGATAAACCAACA
AAGCAAATACCTTGTACAATGTAGCAAGAACACGAGATCGTTGCGGACCAGCACCAGCCAATAT
TGTGCATGTCACAGCAGCACTAAGAGCTTGCTCCAAAGCATTTTCATCGATCTCT
						
					

			
		

Sequences
Splice junction sequence	TGTAGCAAGAACACGAGATCGTTGCGGACCAGCACCAGCCAATATTGTGCATGTCACAGCAGCA CTAAGAGCTTGCTCCAAAGCATTTTCATCGATCTCTctgttggtcccactgctgcagctcttca gtgtcatcctcaaaatgtatcacagcttcaacctgtaaaataagccaggcgagttaatctcata acaacttg
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: 125 Transcript exons: 5119909-5119955,5121742-5121819 CTGTTGGTCCCACTGCTGCAGCTCTTCAGTGTCATCCTCAAAATGTATGCGGACCAGCACCAGC CAATATTGTGCATGTCACAGCAGCACTAAGAGCTTGCTCCAAAGCATTTTCATCGATCTCT Transcript length: 478 Transcript exons: 5119909-5119968,5120127-5120186,5120514-5120556,5120632- 5120723,5120806-5120874,5120960-5121004,5121711-5121819 CTGTTGGTCCCACTGCTGCAGCTCTTCAGTGTCATCCTCAAAATGTATCACAGCTTCAACCTGA TCAATTGAACCTCGCATCCTATCTTCATAAATCATTCGCGATGCTATCTTTTCAGCCTTCCTAG GGTCAATGCCCAATAATGCTCCAAGCTCATCAAAGCTGATATTAGTGTAAAGTTTACTGGCACT AAGGAGGTTATGCTCAATCATTGCCCGGTCAAGCACAGTAGACTTATCTGGTAACAGAGCTTTT TGATGCGGTCTCAGCTCCTCTGCAAATGCTTCAATTTCTGGTTTCCTCAAAATCCTTTCAAGAA AGACCTTCTGCAGTATTGGGTATATCTTCAACTTTGAGCATCTCTCATCCTTGTACAATGTAGC AAGAACACGAGATCGTTGCGGACCAGCACCAGCCAATATTGTGCATGTCACAGCAGCACTAAGA GCTTGCTCCAAAGCATTTTCATCGATCTCT
Genomic sequence	CTGTTGGTCCCACTGCTGCAGCTCTTCAGTGTCATCCTCAAAATGTATCACAGCTTCAACCTGT AAAATAAGCCAGGCGAGTTAATCTCATAACAACTTGAATTAAACCACAAACGGTAAAACATGGT TACAGTGTAAGTCTATTTCAGATGTCTGCTCGAAATGGTGGAATAGTATGAATATCAACATAAG GATTAAGGAAGTCATATGAATAAAACCTGATCAATTGAACCTCGCATCCTATCTTCATAAATCA TTCGCGATGCTATCTTTTCAGCCTGCCAGCATCAAAATCAGTTGCAGTAAGACTCCAATTTGAA TACTTTCATATTTAAAATCAAACATAAATAAAGAATTTATAGAGAAAATGCCAGTTCTTCCTGG TACCAGTTACAGGCCAGATGATTTGAACTATCCTATTTGATTTTAAATTGTGAAATTCGGTGGT TCTTCCCAGTTTGACTAGTTTCCAGCAAGTACCACTCAGAACCCATATATTCCAAATTCTTTTC TTTTTCTTAGTCATATGGACTTTGTGTGAATCTGTCTCTATAAACATGAAATGATGTATCATAT CAACAGGAAAAATTAACCAAAATACTAACCTTCCTAGGGTCAATGCCCAATAATGCTCCAAGCT CATCAAAGCTACAGAAATAAATCAATAGTTGATCAGAATGATAAATCACAATGACCCAGGAAAA TTTCAATGCAAAAACTAACCTGATATTAGTGTAAAGTTTACTGGCACTAAGGAGGTTATGCTCA ATCATTGCCCGGTCAAGCACAGTAGACTTATCTGGTAACAGAGCTTTCTGTTGAACAGAAGAAA AATCCAGTCAATAAAATTACAAGCTACTACTACAAGTTATCTTGGAAGAGAGTATGTTCACTAA CTTGATGCGGTCTCAGCTCCTCTGCAAATGCTTCAATTTCTGGTTTCCTCAAAATCCTTTCAAG AAAGACCTACACATTTGAAGTAGAAGGCCTGTCAATAAAGGGAGCTTATGCTCCAAATATAAAT GCCAGGGGAGTATATCAAGATAGGCACCTTCTGCAGTATTGGGTATATCTTCAACTTTGAGCAT CTCTCATCCTAAAGGGAAAAGACAGTATAAAATCATGCCACGAGTCATAATTTAAGCACCGCTA TAATGAGAAAAATCAGATGCAAAACAATTGTATTTTCATGCTACTACAATGTTGATACAAGGTG TTGGTTCATTTGATGACCATGATTACAGATTGGTCAACATCAAACAGTATGAAACTATAAACTA CCCACTGAAACTGGATGCTAGCATATTTATTAGTTTAGCAGAACTATAAAAAAAATCCTAAATA ACTATTTGGAAGGATCTTGATATTAGTAATTCAATATCAAATGGGTTAAGTTTTTGTATAATGA TGCCACATTCCAATGAGTTCGGAGACAATTCCTCTGTTTCAATATACATACTTTTTTCCCCGGA AAACATAAATTTTGGAGTGTACCAAGAATGATGTACAGTAAATGGGAATACAAATCACTGCGTA AGGGAGAGAAGCCACAGCATGTATATCATAGTAAGCTAAAGCCACAACCTATGGTGCTCCATAA CAGAAACCAATCAATATCGATACAGAGCTCTGCAGAGCATCTGATAATTCAGATTTGTCCATTT GATAAACATGGCACAGGGAAAGGGCAAAGATGATTACGATAGTATGATACATAAAAAGTTATTG CAGACAATAAATGACATGTAGATATAACAAGCACTGCAAACCAGAATGTTATGATAAACCAACA AAGCAAATACCTTGTACAATGTAGCAAGAACACGAGATCGTTGCGGACCAGCACCAGCCAATAT TGTGCATGTCACAGCAGCACTAAGAGCTTGCTCCAAAGCATTTTCATCGATCTCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.24966122

Conservation Information
Conserved circRNAs	NA
PMCS	0.24966122

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5120683-5121810(-)
5119945-5121810(-)
						
						Potential amino acid sequence
						
							MIEHNLLSASKLYTNISFDELGALLGIDPRKAEKIASRMIYEDRMRGSIDQVEAVIHFEDDTEE
LQQWDQQRDR*(-)
MTLKSCSSGTNREIDENALEQALSAAVTCTILAGAGPQRSRVLATLYKDERCSKLKIYPILQKV
FLERILRKPEIEAFAEELRPHQKALLPDKSTVLDRAMIEHNLLSASKLYTNISFDELGALLGID
PRKAEKIASRMIYEDRMRGSIDQVEAVIHFEDDTEELQQWDQQRDR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5120683-5121810(-) 5119945-5121810(-)
Potential amino acid sequence	MIEHNLLSASKLYTNISFDELGALLGIDPRKAEKIASRMIYEDRMRGSIDQVEAVIHFEDDTEE LQQWDQQRDR(-) MTLKSCSSGTNREIDENALEQALSAAVTCTILAGAGPQRSRVLATLYKDERCSKLKIYPILQKV FLERILRKPEIEAFAEELRPHQKALLPDKSTVLDRAMIEHNLLSASKLYTNISFDELGALLGID PRKAEKIASRMIYEDRMRGSIDQVEAVIHFEDDTEELQQWDQQRDR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os03g0197400_circ_g.2

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