Plant Circular RNA Database

Detail information of Os10g0125600_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os10g0125600_circ_g.1
					
						ID in PlantcircBase
						osa_circ_006144
					
						Alias
						Os10circ00663
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr10: 1644020-1644566  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, find_circ
					
						Parent gene
						
							Os10g0125600						
					
						Parent gene annotation
						
							Hypothetical gene. (Os10t0125600-01);Hypothetical protein. (Os10
t0125600-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						3/3
					
						Tissues
						leaf and panicle/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
						Os10t0125700-00:1
Os10t0125600-02:3
Os10t0125600-01:3
Os10t0125700-00:1

General Information
CircRNA Name	Os10g0125600_circ_g.1
ID in PlantcircBase	osa_circ_006144
Alias	Os10circ00663
Organism	Oryza sativa
Position	chr10: 1644020-1644566 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, find_circ
Parent gene	Os10g0125600
Parent gene annotation	Hypothetical gene. (Os10t0125600-01);Hypothetical protein. (Os10 t0125600-02)
Parent gene strand	-
Alternative splicing	NA
Support reads	3/3
Tissues	leaf and panicle/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	Os10t0125700-00:1 Os10t0125600-02:3 Os10t0125600-01:3 Os10t0125700-00:1

			
						 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  
						
							CAGGATGTCAAACATGTTCGTGTCCTCCGCCTTTTCCAAACAACGCTTGAATTTCTACCATCCA
AACTTATCCACCTTCGTTACTTAAGAATCCAAGCATctgtggtcggcacttggtgttataaact
gcagtggtcaggatgatagaatccaagatatagggctgaaatacattaacggattggtaaataa
tgggattt

						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: 360
Transcript exons: 1644020-1644082,1644182-1644312,1644401-1644566
CTGTGGTCGGCACTTGGTGTTATAAACTGCAGTGGTCAGGATGATAGAATCCAAGATATAGGGT
ATGTCATGCATGGTTTGCTTCATGAACTAGCACGGATTGTCTCATCACGTGAATGCCTCAGCAT
TGACTGCTCCAATCCTAGGTTTGCATATACCCCACCATCCATCCGACACTTATCCATCAGGACT
AGCTGCACACTGTGATGTTTATTGGGGAATATGATGAAAGGTTCTCTGAAGCTTTTAAAGAAAT
ACTTCAGGATGTCAAACATGTTCGTGTCCTCCGCCTTTTCCAAACAACGCTTGAATTTCTACCA
TCCAAACTTATCCACCTTCGTTACTTAAGAATCCAAGCAT
						
						Genomic sequence
						
							CTGTGGTCGGCACTTGGTGTTATAAACTGCAGTGGTCAGGATGATAGAATCCAAGATATAGGGC
TGAAATACATTAACGGATTGGTAAATAATGGGATTTTTCAGAAAGTTGATGGGGTAAAATTCTC
ACATAAAAAGGGGAGAGAAGTAAAGCACACATACTATGTCATGCATGGTTTGCTTCATGAACTA
GCACGGATTGTCTCATCACGTGAATGCCTCAGCATTGACTGCTCCAATCCTAGGTTTGCATATA
CCCCACCATCCATCCGACACTTATCCATCAGGACTAGCTGTACAAGTGATACTGTAGGCTTAGA
CCATTACCAGAATTTTAAGGAAGAAATTAGAAACCTGAAGGAGCAAATAAGTGTTGCAAACCTG
CACACTGTGATGTTTATTGGGGAATATGATGAAAGGTTCTCTGAAGCTTTTAAAGAAATACTTC
AGGATGTCAAACATGTTCGTGTCCTCCGCCTTTTCCAAACAACGCTTGAATTTCTACCATCCAA
ACTTATCCACCTTCGTTACTTAAGAATCCAAGCAT

Sequences
Splice junction sequence	CAGGATGTCAAACATGTTCGTGTCCTCCGCCTTTTCCAAACAACGCTTGAATTTCTACCATCCA AACTTATCCACCTTCGTTACTTAAGAATCCAAGCATctgtggtcggcacttggtgttataaact gcagtggtcaggatgatagaatccaagatatagggctgaaatacattaacggattggtaaataa tgggattt
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: 360 Transcript exons: 1644020-1644082,1644182-1644312,1644401-1644566 CTGTGGTCGGCACTTGGTGTTATAAACTGCAGTGGTCAGGATGATAGAATCCAAGATATAGGGT ATGTCATGCATGGTTTGCTTCATGAACTAGCACGGATTGTCTCATCACGTGAATGCCTCAGCAT TGACTGCTCCAATCCTAGGTTTGCATATACCCCACCATCCATCCGACACTTATCCATCAGGACT AGCTGCACACTGTGATGTTTATTGGGGAATATGATGAAAGGTTCTCTGAAGCTTTTAAAGAAAT ACTTCAGGATGTCAAACATGTTCGTGTCCTCCGCCTTTTCCAAACAACGCTTGAATTTCTACCA TCCAAACTTATCCACCTTCGTTACTTAAGAATCCAAGCAT
Genomic sequence	CTGTGGTCGGCACTTGGTGTTATAAACTGCAGTGGTCAGGATGATAGAATCCAAGATATAGGGC TGAAATACATTAACGGATTGGTAAATAATGGGATTTTTCAGAAAGTTGATGGGGTAAAATTCTC ACATAAAAAGGGGAGAGAAGTAAAGCACACATACTATGTCATGCATGGTTTGCTTCATGAACTA GCACGGATTGTCTCATCACGTGAATGCCTCAGCATTGACTGCTCCAATCCTAGGTTTGCATATA CCCCACCATCCATCCGACACTTATCCATCAGGACTAGCTGTACAAGTGATACTGTAGGCTTAGA CCATTACCAGAATTTTAAGGAAGAAATTAGAAACCTGAAGGAGCAAATAAGTGTTGCAAACCTG CACACTGTGATGTTTATTGGGGAATATGATGAAAGGTTCTCTGAAGCTTTTAAAGAAATACTTC AGGATGTCAAACATGTTCGTGTCCTCCGCCTTTTCCAAACAACGCTTGAATTTCTACCATCCAA ACTTATCCACCTTCGTTACTTAAGAATCCAAGCAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.108013406

Conservation Information
Conserved circRNAs	NA
PMCS	0.108013406

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1644414-1644060(+)
1644207-1644536(-)
						
						Potential amino acid sequence
						
							MFIGEYDERFSEAFKEILQDVKHVRVLRLFQTTLEFLPSKLIHLRYLRIQASVVGTWCYKLQWS
G*(+)
MKQTMHDIPYILDSIILTTAVYNTKCRPQMLGFLSNEGG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1644414-1644060(+) 1644207-1644536(-)
Potential amino acid sequence	MFIGEYDERFSEAFKEILQDVKHVRVLRLFQTTLEFLPSKLIHLRYLRIQASVVGTWCYKLQWS G(+) MKQTMHDIPYILDSIILTTAVYNTKCRPQMLGFLSNEGG(-)
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 Os10g0125600_circ_g.1

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