Plant Circular RNA Database

Detail information of Os04g0679800_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os04g0679800_circ_g.4
					
						ID in PlantcircBase
						osa_circ_025959
					
						Alias
						Os_ciR1817
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 34715338-34716007  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os04g0679800						
					
						Parent gene annotation
						
							Similar to RNA-binding protein-like protein. (Os04t0679800-01);S
imilar to Zinc finger, RING-type. (Os04t0679800-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						7/1
					
						Tissues
						root/shoot, 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  
						
							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
						Os04t0679800-01:3
Os04t0679800-02:2

General Information
CircRNA Name	Os04g0679800_circ_g.4
ID in PlantcircBase	osa_circ_025959
Alias	Os_ciR1817
Organism	Oryza sativa
Position	chr4: 34715338-34716007 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os04g0679800
Parent gene annotation	Similar to RNA-binding protein-like protein. (Os04t0679800-01);S imilar to Zinc finger, RING-type. (Os04t0679800-02)
Parent gene strand	+
Alternative splicing	NA
Support reads	7/1
Tissues	root/shoot, 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	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	Os04t0679800-01:3 Os04t0679800-02:2

			
						 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  
						
							TCGAGAGAGAGGAAGAGTGCGGGATTTGCATGGAGATGAATAACAAGGTTGTCTTGCCCAACTG
CAGCCATGCTATGTGCATGAAGTGTTACCGTCAATGggcctcggatttctcgagggattatgac
ggggcttgcctccagatgcggatgtcgtacagccccgccgcgcagttcttcctcttcctggtgc
agtggacg

									
								

					

						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: 209
Transcript exons: 34715338-34715464,34715926-34716007
GGCCTCGGATTTCTCGAGGGATTATGACGGGGCTTGCCTCCAGATGCGGATGTCGTACAGCCCC
GCCGCGCAGTTCTTCCTCTTCCTGGTGCAGTGGACGGATTGTAGCCTTGCCGGTGCTCTTGGCG
CGGGATTTGCATGGAGATGAATAACAAGGTTGTCTTGCCCAACTGCAGCCATGCTATGTGCATG
AAGTGTTACCGTCAATG
Transcript length: 455
Transcript exons: 34715338-34715488,34715596-34715662,34715771-34716007
GGCCTCGGATTTCTCGAGGGATTATGACGGGGCTTGCCTCCAGATGCGGATGTCGTACAGCCCC
GCCGCGCAGTTCTTCCTCTTCCTGGTGCAGTGGACGGATTGTAGCCTTGCCGGTGCTCTTGGCC
TCCTCAGGATTCTCATTTATAAGGTTTATGTAGATGGAACGACCACCTTGTCAACTCATGAAAG
GAAAGCGAGCATTAGGGAATTCTATGCTGTTATATTTCCCTCACTCATGCAACTCCACAAGGGT
ATCAGCGATGTCGATGACCGGAGGCAGAAGCAATCTGTACTGAGAGATACAGAAGAAGAGATGA
GGATGAGAGCAAGAGGCATGTTTCTGAGATTGATGTCGAGAGAGAGGAAGAGTGCGGGATTTGC
ATGGAGATGAATAACAAGGTTGTCTTGCCCAACTGCAGCCATGCTATGTGCATGAAGTGTTACC
GTCAATG
						
					

						Genomic sequence
						
							GGCCTCGGATTTCTCGAGGGATTATGACGGGGCTTGCCTCCAGATGCGGATGTCGTACAGCCCC
GCCGCGCAGTTCTTCCTCTTCCTGGTGCAGTGGACGGATTGTAGCCTTGCCGGTGCTCTTGGCC
TCCTCAGGATTCTCATTTATAAGGTTGCGTGTATGCGTGCGTGGTGCGAGTTCAGAATTCAAGT
TTGCATATTGTCAGTGACTTTTTTTTAATCTAACGATTTTTTTGTTCGGCTTCGTTTGTTCATC
AGGTTTATGTAGATGGAACGACCACCTTGTCAACTCATGAAAGGAAAGCGAGCATTAGGGAATT
CTATGGTAAATGCTCTAAAATGTTGAGCTGAGATTTTCTTTTTCTTTTTCTTGGTTCACAATTG
AGAGGTGTTTACTGTCTAAAGTGTTAACATTAGCCTGCATTGTTTTCAGCTGTTATATTTCCCT
CACTCATGCAACTCCACAAGGGTATCAGCGATGTCGATGACCGGAGGCAGAAGCAATCTGTACT
GAGAGATACAGAAGAAGAGATGAGGATGAGAGCAAGAGGCATGTTTCTGAGATTGATGTCGAGA
GAGAGGAAGAGTGCGGGATTTGCATGGAGATGAATAACAAGGTTGTCTTGCCCAACTGCAGCCA
TGCTATGTGCATGAAGTGTTACCGTCAATG
						
					

			
		

Sequences
Splice junction sequence	TCGAGAGAGAGGAAGAGTGCGGGATTTGCATGGAGATGAATAACAAGGTTGTCTTGCCCAACTG CAGCCATGCTATGTGCATGAAGTGTTACCGTCAATGggcctcggatttctcgagggattatgac ggggcttgcctccagatgcggatgtcgtacagccccgccgcgcagttcttcctcttcctggtgc agtggacg
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: 209 Transcript exons: 34715338-34715464,34715926-34716007 GGCCTCGGATTTCTCGAGGGATTATGACGGGGCTTGCCTCCAGATGCGGATGTCGTACAGCCCC GCCGCGCAGTTCTTCCTCTTCCTGGTGCAGTGGACGGATTGTAGCCTTGCCGGTGCTCTTGGCG CGGGATTTGCATGGAGATGAATAACAAGGTTGTCTTGCCCAACTGCAGCCATGCTATGTGCATG AAGTGTTACCGTCAATG Transcript length: 455 Transcript exons: 34715338-34715488,34715596-34715662,34715771-34716007 GGCCTCGGATTTCTCGAGGGATTATGACGGGGCTTGCCTCCAGATGCGGATGTCGTACAGCCCC GCCGCGCAGTTCTTCCTCTTCCTGGTGCAGTGGACGGATTGTAGCCTTGCCGGTGCTCTTGGCC TCCTCAGGATTCTCATTTATAAGGTTTATGTAGATGGAACGACCACCTTGTCAACTCATGAAAG GAAAGCGAGCATTAGGGAATTCTATGCTGTTATATTTCCCTCACTCATGCAACTCCACAAGGGT ATCAGCGATGTCGATGACCGGAGGCAGAAGCAATCTGTACTGAGAGATACAGAAGAAGAGATGA GGATGAGAGCAAGAGGCATGTTTCTGAGATTGATGTCGAGAGAGAGGAAGAGTGCGGGATTTGC ATGGAGATGAATAACAAGGTTGTCTTGCCCAACTGCAGCCATGCTATGTGCATGAAGTGTTACC GTCAATG
Genomic sequence	GGCCTCGGATTTCTCGAGGGATTATGACGGGGCTTGCCTCCAGATGCGGATGTCGTACAGCCCC GCCGCGCAGTTCTTCCTCTTCCTGGTGCAGTGGACGGATTGTAGCCTTGCCGGTGCTCTTGGCC TCCTCAGGATTCTCATTTATAAGGTTGCGTGTATGCGTGCGTGGTGCGAGTTCAGAATTCAAGT TTGCATATTGTCAGTGACTTTTTTTTAATCTAACGATTTTTTTGTTCGGCTTCGTTTGTTCATC AGGTTTATGTAGATGGAACGACCACCTTGTCAACTCATGAAAGGAAAGCGAGCATTAGGGAATT CTATGGTAAATGCTCTAAAATGTTGAGCTGAGATTTTCTTTTTCTTTTTCTTGGTTCACAATTG AGAGGTGTTTACTGTCTAAAGTGTTAACATTAGCCTGCATTGTTTTCAGCTGTTATATTTCCCT CACTCATGCAACTCCACAAGGGTATCAGCGATGTCGATGACCGGAGGCAGAAGCAATCTGTACT GAGAGATACAGAAGAAGAGATGAGGATGAGAGCAAGAGGCATGTTTCTGAGATTGATGTCGAGA GAGAGGAAGAGTGCGGGATTTGCATGGAGATGAATAACAAGGTTGTCTTGCCCAACTGCAGCCA TGCTATGTGCATGAAGTGTTACCGTCAATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_015011 						
					
						PMCS
						0.397982264

Conservation Information
Conserved circRNAs	osi_circ_015011
PMCS	0.397982264

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							34715938-34715943(+)
						
						Potential amino acid sequence
						
							MEMNNKVVLPNCSHAMCMKCYRQWASDFSRDYDGACLQMRMSYSPAAQFFLFLVQWTDCSLAGA
LGLLRILIYKVYVDGTTTLSTHERKASIREFYAVIFPSLMQLHKGISDVDDRRQKQSVLRDTEE
EMRMRARGMFLRLMSRERKSAGFAWR*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	34715938-34715943(+)
Potential amino acid sequence	MEMNNKVVLPNCSHAMCMKCYRQWASDFSRDYDGACLQMRMSYSPAAQFFLFLVQWTDCSLAGA LGLLRILIYKVYVDGTTTLSTHERKASIREFYAVIFPSLMQLHKGISDVDDRRQKQSVLRDTEE EMRMRARGMFLRLMSRERKSAGFAWR*(+)
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 Os04g0679800_circ_g.4

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