Plant Circular RNA Database

Detail information of Os11g0204600_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os11g0204600_circ_g.3
					
						ID in PlantcircBase
						osa_circ_008787
					
						Alias
						Os_ciR1636
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 5278155-5279116  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, PcircRNA_finder, circRNA_finder, find_circ
					
						Parent gene
						
							Os11g0204600						
					
						Parent gene annotation
						
							Similar to Glucose-1-phosphate adenylyltransferase. (Os11t020460
0-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os11g0202300_circ_ag.1 Os11g0202300_circ_ag.2 Os11g0202300_circ_ag.3 Os11g0202450_circ_ag.1 Os11g0202600_circ_g.1 Os11g0202600_circ_g.2 Os11g0202600_circ_g.3 Os11g0202600_circ_g.4 Os11g0205500_circ_igg.1 Os11g0204600_circ_g.1 Os11g0204600_circ_g.2 Os11g0204600_circ_g.4 Os11g0205500_circ_g.1 						
					
						Support reads
						7/2
					
						Tissues
						root/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  
						
							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
						Os11t0204600-01:4

General Information
CircRNA Name	Os11g0204600_circ_g.3
ID in PlantcircBase	osa_circ_008787
Alias	Os_ciR1636
Organism	Oryza sativa
Position	chr11: 5278155-5279116 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, CIRI, PcircRNA_finder, circRNA_finder, find_circ
Parent gene	Os11g0204600
Parent gene annotation	Similar to Glucose-1-phosphate adenylyltransferase. (Os11t020460 0-01)
Parent gene strand	+
Alternative splicing	Os11g0202300_circ_ag.1 Os11g0202300_circ_ag.2 Os11g0202300_circ_ag.3 Os11g0202450_circ_ag.1 Os11g0202600_circ_g.1 Os11g0202600_circ_g.2 Os11g0202600_circ_g.3 Os11g0202600_circ_g.4 Os11g0205500_circ_igg.1 Os11g0204600_circ_g.1 Os11g0204600_circ_g.2 Os11g0204600_circ_g.4 Os11g0205500_circ_g.1
Support reads	7/2
Tissues	root/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	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	Os11t0204600-01:4

			
						 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  
						
							CCGCTTTTTTTGTTTATAGGCATATGTCTTCGCTGACTACTAGGAAGACATTGGAACGATCAGA
TTGTTCTTTGATGCAAACATGGCACTCTGTGAGGAGgtattagctgctacacaaatgccagggg
aggctgctggttggttccgggatacagcagatgcagttgaaaattttttctgggcacttgaggt
aaccacta

						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: 297
Transcript exons: 5278155-5278244,5278345-5278414,5278505-5278560,5279036-
5279116
GTATTAGCTGCTACACAAATGCCAGGGGAGGCTGCTGGTTGGTTCCGGGATACAGCAGATGCAG
TTGAAAATTTTTTCTGGGCACTTGAGGACTATATAGCACATTTTAAGCTTGTCAGGGGATCAGC
TTTATCGTATGGATTACATGAAGCTCATGCAGAAACATTTTGACAACAGTGCTGACATTACTTC
ATCATGTGCTCCTGTTGGAAAGAGGCATATGTCTTCGCTGACTACTAGGAAGACATTGGAACGA
TCAGATTGTTCTTTGATGCAAACATGGCACTCTGTGAGGAG
						
						Genomic sequence
						
							GTATTAGCTGCTACACAAATGCCAGGGGAGGCTGCTGGTTGGTTCCGGGATACAGCAGATGCAG
TTGAAAATTTTTTCTGGGCACTTGAGGTAACCACTATTTAGAAGCACACAATGCATATGCGGCT
CATACTTTCATTTGGATTGCTAAAGAAATATTCACTATGTTGTATGCGATGTATATATTCAGGA
CTATATAGCACATTTTAAGCTTGTCAGGGGATCAGCTTTATCGTATGGATTACATGAAGCTCAT
GCAGGTTTGTTCTGCTCTCATTCTTCTGTACTTTTACACATGCTTTTCTTTTGCACTGGCAGAC
CCTCCAACATATGCCATTCACCATTCGCAGAAACATTTTGACAACAGTGCTGACATTACTTCAT
CATGTGCTCCTGTTGGAAAGAGGTGTATTGATTGTACAATATTTCAAAAGTTAGCTAATTTTAT
CAGCATTTGTGTCAGAATGCAGTGCATCCTGATTTGCTTTTCTTTGTTATGGAAGCCAAGCGTC
TGACTTGGAAGCAATGGTTAGAAGTAACCTTGTGCCAGGCTCAGATATATGTTTGAACTTCCAG
GACATGAAACAACTTGTAGTATCTGAAGTATAAGCCATTGATCATTGTAGAAAGTGGATATCAG
CTTTCTCAATTTTTCCATAGACGACCCGACTAAATTTCCCTACAAGTAAATTTTTTAAGCTTGT
GCGCTATGTGACTCATTTTCACTGTTTGGGAAATCATGCCTTATGTTCCAATTTGGTAATAGTC
ATGTCCACTTTCAGTCTGTATTGCCTACTTGCATCAAATTCAGTATATACAATCATGAATCATG
TCCACCTTGTGGTGTGAACTGAACGTCCATCCGCTTTTTTTGTTTATAGGCATATGTCTTCGCT
GACTACTAGGAAGACATTGGAACGATCAGATTGTTCTTTGATGCAAACATGGCACTCTGTGAGG
AG

Sequences
Splice junction sequence	CCGCTTTTTTTGTTTATAGGCATATGTCTTCGCTGACTACTAGGAAGACATTGGAACGATCAGA TTGTTCTTTGATGCAAACATGGCACTCTGTGAGGAGgtattagctgctacacaaatgccagggg aggctgctggttggttccgggatacagcagatgcagttgaaaattttttctgggcacttgaggt aaccacta
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: 297 Transcript exons: 5278155-5278244,5278345-5278414,5278505-5278560,5279036- 5279116 GTATTAGCTGCTACACAAATGCCAGGGGAGGCTGCTGGTTGGTTCCGGGATACAGCAGATGCAG TTGAAAATTTTTTCTGGGCACTTGAGGACTATATAGCACATTTTAAGCTTGTCAGGGGATCAGC TTTATCGTATGGATTACATGAAGCTCATGCAGAAACATTTTGACAACAGTGCTGACATTACTTC ATCATGTGCTCCTGTTGGAAAGAGGCATATGTCTTCGCTGACTACTAGGAAGACATTGGAACGA TCAGATTGTTCTTTGATGCAAACATGGCACTCTGTGAGGAG
Genomic sequence	GTATTAGCTGCTACACAAATGCCAGGGGAGGCTGCTGGTTGGTTCCGGGATACAGCAGATGCAG TTGAAAATTTTTTCTGGGCACTTGAGGTAACCACTATTTAGAAGCACACAATGCATATGCGGCT CATACTTTCATTTGGATTGCTAAAGAAATATTCACTATGTTGTATGCGATGTATATATTCAGGA CTATATAGCACATTTTAAGCTTGTCAGGGGATCAGCTTTATCGTATGGATTACATGAAGCTCAT GCAGGTTTGTTCTGCTCTCATTCTTCTGTACTTTTACACATGCTTTTCTTTTGCACTGGCAGAC CCTCCAACATATGCCATTCACCATTCGCAGAAACATTTTGACAACAGTGCTGACATTACTTCAT CATGTGCTCCTGTTGGAAAGAGGTGTATTGATTGTACAATATTTCAAAAGTTAGCTAATTTTAT CAGCATTTGTGTCAGAATGCAGTGCATCCTGATTTGCTTTTCTTTGTTATGGAAGCCAAGCGTC TGACTTGGAAGCAATGGTTAGAAGTAACCTTGTGCCAGGCTCAGATATATGTTTGAACTTCCAG GACATGAAACAACTTGTAGTATCTGAAGTATAAGCCATTGATCATTGTAGAAAGTGGATATCAG CTTTCTCAATTTTTCCATAGACGACCCGACTAAATTTCCCTACAAGTAAATTTTTTAAGCTTGT GCGCTATGTGACTCATTTTCACTGTTTGGGAAATCATGCCTTATGTTCCAATTTGGTAATAGTC ATGTCCACTTTCAGTCTGTATTGCCTACTTGCATCAAATTCAGTATATACAATCATGAATCATG TCCACCTTGTGGTGTGAACTGAACGTCCATCCGCTTTTTTTGTTTATAGGCATATGTCTTCGCT GACTACTAGGAAGACATTGGAACGATCAGATTGTTCTTTGATGCAAACATGGCACTCTGTGAGG AG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.316084849

Conservation Information
Conserved circRNAs	NA
PMCS	0.316084849

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5279100-5278512(+)
5278392-5278158(+)
						
						Potential amino acid sequence
						
							MALCEEVLAATQMPGEAAGWFRDTADAVENFFWALEDYIAHFKLVRGSALSYGLHEAHAETF*(
+)
MDYMKLMQKHFDNSADITSSCAPVGKRHMSSLTTRKTLERSDCSLMQTWHSVRRY*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5279100-5278512(+) 5278392-5278158(+)
Potential amino acid sequence	MALCEEVLAATQMPGEAAGWFRDTADAVENFFWALEDYIAHFKLVRGSALSYGLHEAHAETF( +) MDYMKLMQKHFDNSADITSSCAPVGKRHMSSLTTRKTLERSDCSLMQTWHSVRRY(+)
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 Os11g0204600_circ_g.3

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