Plant Circular RNA Database

Detail information of Os03g0198300_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os03g0198300_circ_g.3
					
						ID in PlantcircBase
						osa_circ_018381
					
						Alias
						Os03circ05988
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 5163438-5164908  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, SMALT, Segemehl
					
						Parent gene
						
							Os03g0198300						
					
						Parent gene annotation
						
							Heat shock protein DnaJ, N-terminal domain containing protein. (
Os03t0198300-01);Heat shock protein DnaJ, N-terminal domain cont
aining protein. (Os03t0198300-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0198300_circ_g.1 Os03g0198300_circ_g.2 Os03g0198300_circ_g.4 						
					
						Support reads
						9/1
					
						Tissues
						leaf and panicle/shoot, 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  
						
							GT-AG							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
						Os03t0198300-02:5
Os03t0198300-01:5

General Information
CircRNA Name	Os03g0198300_circ_g.3
ID in PlantcircBase	osa_circ_018381
Alias	Os03circ05988
Organism	Oryza sativa
Position	chr3: 5163438-5164908 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, SMALT, Segemehl
Parent gene	Os03g0198300
Parent gene annotation	Heat shock protein DnaJ, N-terminal domain containing protein. ( Os03t0198300-01);Heat shock protein DnaJ, N-terminal domain cont aining protein. (Os03t0198300-02)
Parent gene strand	+
Alternative splicing	Os03g0198300_circ_g.1 Os03g0198300_circ_g.2 Os03g0198300_circ_g.4
Support reads	9/1
Tissues	leaf and panicle/shoot, 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	GT-AG 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	Os03t0198300-02:5 Os03t0198300-01:5

			
						 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  
						
							TTTCTTGCCCATTTCAATGTAGATTTCTGAATCCAAAATCTGGGAATGGTCAAAGGGAAAAGAA
GGAAATATTAGGTCATTGCTTTCTACACTACAATATgaacaaaacataacaccaataatgcaaa
gaacaatgtattaggagctagccccagctctaaaagttctcggtcaccttcaggagagaaaagt
cgtggcag

									
								

					

						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: 641
Transcript exons: 5163438-5163745,5163898-5164006,5164373-5164458,5164675-
5164734,5164831-5164908
GAACAAAACATAACACCAATAATGCAAAGAACAATGTATTAGGAGCTAGCCCCAGCTCTAAAAG
TTCTCGGTCACCTTCAGGAGAGAAAAGTCGTGGCAGCAGAGTGAAAGGAAAAGTAAAGGACTTC
ATGAAAATATTTAGTCCTGAGAGTTCACCGAAGAGCAAACGAGATCGGACATCCAGTGGGAAAA
ACGGAAGCAAAAGTGGTCCTGAAGATAAATTTAGCATATCCAATTCGGAGGTCGATGACAATGT
CAGAACAGCCAATATGAACAAGCAGAATGTGTTCCCTCCTGTACCCTCTCCAATCAGCGAAGCA
CAAGACAGGACGGAGATACCGGTTTTTACAGTGGATAATGAAATGGATTCAAAGGCAGATTTTG
GAAGAAAAGAAGTTACACCTCCCTCTTTTGATGAGTCAAGCGATGCCCAAACAAAATATAAGGT
AGATGAGATAACAGATCTTGCGGAAGGTCCAGTGGAAGATCTTGAAGAATGTGTGGTTGAGGAT
GTCTCTGAAGATTTTATTCTTCGTAATAATGAGGAAAAAGAGCAAATAAAGATTTCTGAATCCA
AAATCTGGGAATGGTCAAAGGGAAAAGAAGGAAATATTAGGTCATTGCTTTCTACACTACAATA
T
						
					

						Genomic sequence
						
							GAACAAAACATAACACCAATAATGCAAAGAACAATGTATTAGGAGCTAGCCCCAGCTCTAAAAG
TTCTCGGTCACCTTCAGGAGAGAAAAGTCGTGGCAGCAGAGTGAAAGGAAAAGTAAAGGACTTC
ATGAAAATATTTAGTCCTGAGAGTTCACCGAAGAGCAAACGAGATCGGACATCCAGTGGGAAAA
ACGGAAGCAAAAGTGGTCCTGAAGATAAATTTAGCATATCCAATTCGGAGGTCGATGACAATGT
CAGAACAGCCAATATGAACAAGCAGAATGTGTTCCCTCCTGTACCCTCTCCAGTAAGTTGATCT
TAGACCAGGATAATTCTCTGAATACTGATCAATTTCTTAGAAGTCTGTTTTTCTTTTGTGAGTA
CTGTCTTCAACAAGATAGGTGGTTTTATATTAGAAAGAAGAGTACACCTGTTGGATTAATCTTT
GACTTGTTCCAGATCAGCGAAGCACAAGACAGGACGGAGATACCGGTTTTTACAGTGGATAATG
AAATGGATTCAAAGGCAGATTTTGGAAGAAAAGAAGTTACACCTCCCTCTTTTGATGGTAAGAT
ATGCATACCTTTGAATGAATTAAGATATTTTCTTTTCCTTTCTTCAGACAACTGCAGCAGTAAA
ACCATTGCCATGTTTTGCTAGTCTTAAAATCTCACGCATGTCATTCTTAACCTCTTGATGCTCG
TGTTAATCATTCAGTGACTTTCTGCTAGTTATATTTGCAACAGTCACATTGAAATTATGGGACT
ACGGTAGAATTGTTTATTCATGTTCTGCTAGTTTTTTTCTCTGGAAGTTCCTTTTTAAGAGCAT
GTTTTTGTATGCTTGGTGTCATCATTTGTTTTCTGAAACTAGTGTTGCTTGTGTAATATTCAAG
AATAACATATACAATATTTCTTCTTGTTCTGCTTACTAGAGTCAAGCGATGCCCAAACAAAATA
TAAGGTAGATGAGATAACAGATCTTGCGGAAGGTCCAGTGGAAGATCTTGAAGAATGTGTGGTA
TGTCATACTTGTGAAGTCATTATATGCTTCTAGGTCTAAGCAAATTCGAAAATTGTCTGCCCAT
TAAACAGATCATTGTAACCCAGTTAATTTGTCGACCAAAGCTGAAAGCTGCTTCCATTATTTGT
CATTTGGCCTTTGTTTCTTGTTTGTATACATTATCTGCCTAACCTTATAATTGCATATATCCGT
TTGTTTTGTTTTATAAACTAGGTTGAGGATGTCTCTGAAGATTTTATTCTTCGTAATAATGAGG
AAAAAGAGCAAATAAAGGTAGTGCACACAACATGAATTGGTGTGGCAACTTGTCACTCCTTTCC
CATTACCTTTCTTTTCCAATTCTGAACTTTCTTGCCCATTTCAATGTAGATTTCTGAATCCAAA
ATCTGGGAATGGTCAAAGGGAAAAGAAGGAAATATTAGGTCATTGCTTTCTACACTACAATAT
						
					

			
		

Sequences
Splice junction sequence	TTTCTTGCCCATTTCAATGTAGATTTCTGAATCCAAAATCTGGGAATGGTCAAAGGGAAAAGAA GGAAATATTAGGTCATTGCTTTCTACACTACAATATgaacaaaacataacaccaataatgcaaa gaacaatgtattaggagctagccccagctctaaaagttctcggtcaccttcaggagagaaaagt cgtggcag
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: 641 Transcript exons: 5163438-5163745,5163898-5164006,5164373-5164458,5164675- 5164734,5164831-5164908 GAACAAAACATAACACCAATAATGCAAAGAACAATGTATTAGGAGCTAGCCCCAGCTCTAAAAG TTCTCGGTCACCTTCAGGAGAGAAAAGTCGTGGCAGCAGAGTGAAAGGAAAAGTAAAGGACTTC ATGAAAATATTTAGTCCTGAGAGTTCACCGAAGAGCAAACGAGATCGGACATCCAGTGGGAAAA ACGGAAGCAAAAGTGGTCCTGAAGATAAATTTAGCATATCCAATTCGGAGGTCGATGACAATGT CAGAACAGCCAATATGAACAAGCAGAATGTGTTCCCTCCTGTACCCTCTCCAATCAGCGAAGCA CAAGACAGGACGGAGATACCGGTTTTTACAGTGGATAATGAAATGGATTCAAAGGCAGATTTTG GAAGAAAAGAAGTTACACCTCCCTCTTTTGATGAGTCAAGCGATGCCCAAACAAAATATAAGGT AGATGAGATAACAGATCTTGCGGAAGGTCCAGTGGAAGATCTTGAAGAATGTGTGGTTGAGGAT GTCTCTGAAGATTTTATTCTTCGTAATAATGAGGAAAAAGAGCAAATAAAGATTTCTGAATCCA AAATCTGGGAATGGTCAAAGGGAAAAGAAGGAAATATTAGGTCATTGCTTTCTACACTACAATA T
Genomic sequence	GAACAAAACATAACACCAATAATGCAAAGAACAATGTATTAGGAGCTAGCCCCAGCTCTAAAAG TTCTCGGTCACCTTCAGGAGAGAAAAGTCGTGGCAGCAGAGTGAAAGGAAAAGTAAAGGACTTC ATGAAAATATTTAGTCCTGAGAGTTCACCGAAGAGCAAACGAGATCGGACATCCAGTGGGAAAA ACGGAAGCAAAAGTGGTCCTGAAGATAAATTTAGCATATCCAATTCGGAGGTCGATGACAATGT CAGAACAGCCAATATGAACAAGCAGAATGTGTTCCCTCCTGTACCCTCTCCAGTAAGTTGATCT TAGACCAGGATAATTCTCTGAATACTGATCAATTTCTTAGAAGTCTGTTTTTCTTTTGTGAGTA CTGTCTTCAACAAGATAGGTGGTTTTATATTAGAAAGAAGAGTACACCTGTTGGATTAATCTTT GACTTGTTCCAGATCAGCGAAGCACAAGACAGGACGGAGATACCGGTTTTTACAGTGGATAATG AAATGGATTCAAAGGCAGATTTTGGAAGAAAAGAAGTTACACCTCCCTCTTTTGATGGTAAGAT ATGCATACCTTTGAATGAATTAAGATATTTTCTTTTCCTTTCTTCAGACAACTGCAGCAGTAAA ACCATTGCCATGTTTTGCTAGTCTTAAAATCTCACGCATGTCATTCTTAACCTCTTGATGCTCG TGTTAATCATTCAGTGACTTTCTGCTAGTTATATTTGCAACAGTCACATTGAAATTATGGGACT ACGGTAGAATTGTTTATTCATGTTCTGCTAGTTTTTTTCTCTGGAAGTTCCTTTTTAAGAGCAT GTTTTTGTATGCTTGGTGTCATCATTTGTTTTCTGAAACTAGTGTTGCTTGTGTAATATTCAAG AATAACATATACAATATTTCTTCTTGTTCTGCTTACTAGAGTCAAGCGATGCCCAAACAAAATA TAAGGTAGATGAGATAACAGATCTTGCGGAAGGTCCAGTGGAAGATCTTGAAGAATGTGTGGTA TGTCATACTTGTGAAGTCATTATATGCTTCTAGGTCTAAGCAAATTCGAAAATTGTCTGCCCAT TAAACAGATCATTGTAACCCAGTTAATTTGTCGACCAAAGCTGAAAGCTGCTTCCATTATTTGT CATTTGGCCTTTGTTTCTTGTTTGTATACATTATCTGCCTAACCTTATAATTGCATATATCCGT TTGTTTTGTTTTATAAACTAGGTTGAGGATGTCTCTGAAGATTTTATTCTTCGTAATAATGAGG AAAAAGAGCAAATAAAGGTAGTGCACACAACATGAATTGGTGTGGCAACTTGTCACTCCTTTCC CATTACCTTTCTTTTCCAATTCTGAACTTTCTTGCCCATTTCAATGTAGATTTCTGAATCCAAA ATCTGGGAATGGTCAAAGGGAAAAGAAGGAAATATTAGGTCATTGCTTTCTACACTACAATAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_004613* osi_circ_014017 						
					
						PMCS
						0.317207081

Conservation Information
Conserved circRNAs	osi_circ_004613* osi_circ_014017
PMCS	0.317207081

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5163567-5163476(+)
5163450-5164897(-)
5163668-5164897(-)
						
						Potential amino acid sequence
						
							MKIFSPESSPKSKRDRTSSGKNGSKSGPEDKFSISNSEVDDNVRTANMNKQNVFPPVPSPISEA
QDRTEIPVFTVDNEMDSKADFGRKEVTPPSFDESSDAQTKYKVDEITDLAEGPVEDLEECVVED
VSEDFILRNNEEKEQIKISESKIWEWSKGKEGNIRSLLSTLQYEQNITPIMQRTMY*(+)
MFCSYCSVESNDLIFPSFPFDHSQILDSEIFICSFSSLLRRIKSSETSSTTHSSRSSTGPSARS
VISSTLYFVWASLDSSKEGGVTSFLPKSAFESISLSTVKTGISVLSCASLIGEGTGGNTFCLFI
LAVLTLSSTSELDMLNLSSGPLLLPFFPLDVRSRLLFGELSGLNIFMKSFTFPFTLLPRLFSPE
GDRELLELGLAPNTLFFALLVLCFVHIVV*(-)
MLNLSSGPLLLPFFPLDVRSRLLFGELSGLNIFMKSFTFPFTLLPRLFSPEGDRELLELGLAPN
TLFFALLVLCFVHIVV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5163567-5163476(+) 5163450-5164897(-) 5163668-5164897(-)
Potential amino acid sequence	MKIFSPESSPKSKRDRTSSGKNGSKSGPEDKFSISNSEVDDNVRTANMNKQNVFPPVPSPISEA QDRTEIPVFTVDNEMDSKADFGRKEVTPPSFDESSDAQTKYKVDEITDLAEGPVEDLEECVVED VSEDFILRNNEEKEQIKISESKIWEWSKGKEGNIRSLLSTLQYEQNITPIMQRTMY(+) MFCSYCSVESNDLIFPSFPFDHSQILDSEIFICSFSSLLRRIKSSETSSTTHSSRSSTGPSARS VISSTLYFVWASLDSSKEGGVTSFLPKSAFESISLSTVKTGISVLSCASLIGEGTGGNTFCLFI LAVLTLSSTSELDMLNLSSGPLLLPFFPLDVRSRLLFGELSGLNIFMKSFTFPFTLLPRLFSPE GDRELLELGLAPNTLFFALLVLCFVHIVV(-) MLNLSSGPLLLPFFPLDVRSRLLFGELSGLNIFMKSFTFPFTLLPRLFSPEGDRELLELGLAPN TLFFALLVLCFVHIVV*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os03g0198300_circ_g.3

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