Plant Circular RNA Database

Detail information of Os01g0830700_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0830700_circ_g.3
					
						ID in PlantcircBase
						osa_circ_004692
					
						Alias
						Os_ciR1846, 
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 35539899-35540363  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ, CIRI-long
					
						Parent gene
						
							Os01g0830700						
					
						Parent gene annotation
						
							Protein of unknown function DUF231, plant domain containing prot
ein. (Os01t0830700-01);Protein of unknown function DUF231, plant
 domain containing protein. (Os01t0830700-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0830700_circ_g.1 Os01g0830700_circ_g.2 						
					
						Support reads
						6/18/21
					
						Tissues
						root/root/shoot, root, anther, pistil, root, leaf
					
						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
						Os01t0830700-01:2
Os01t0830700-02:2

General Information
CircRNA Name	Os01g0830700_circ_g.3
ID in PlantcircBase	osa_circ_004692
Alias	Os_ciR1846,
Organism	Oryza sativa
Position	chr1: 35539899-35540363 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ, CIRI-long
Parent gene	Os01g0830700
Parent gene annotation	Protein of unknown function DUF231, plant domain containing prot ein. (Os01t0830700-01);Protein of unknown function DUF231, plant domain containing protein. (Os01t0830700-02)
Parent gene strand	+
Alternative splicing	Os01g0830700_circ_g.1 Os01g0830700_circ_g.2
Support reads	6/18/21
Tissues	root/root/shoot, root, anther, pistil, root, leaf
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	Os01t0830700-01:2 Os01t0830700-02:2

			
						 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  
						
							ATCGGAAGGTGCTGACGACGTGGGCGAGCTGGGTGAACGACAACATCGACCCGGCGCGCACGTC
CGTCTTCTTCATGAGCATCTCCCCTCTTCACATCAGgagtacaacgcgacggtggagttctact
gggcgccgttcctggtggagtccaactccgacgaccccaagatccacagcatccagcaccggat
catcaagg

									
								

					

						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: 188
Transcript exons: 35539899-35540005,35540283-35540363
GAGTACAACGCGACGGTGGAGTTCTACTGGGCGCCGTTCCTGGTGGAGTCCAACTCCGACGACC
CCAAGATCCACAGCATCCAGCACCGGATCATCAAGGCGGACGCGTGGGCGAGCTGGGTGAACGA
CAACATCGACCCGGCGCGCACGTCCGTCTTCTTCATGAGCATCTCCCCTCTTCACATCAG
Transcript length: 320
Transcript exons: 35539899-35540079,35540225-35540363
GAGTACAACGCGACGGTGGAGTTCTACTGGGCGCCGTTCCTGGTGGAGTCCAACTCCGACGACC
CCAAGATCCACAGCATCCAGCACCGGATCATCAAGGCGGACGCGATCGCGGCGCACGCACAGAA
CTGGCGCGGCGTCGACTACCTCGTCTTCAACACCTACATCTGGTGGATGAACAGCTGGGAGGAG
CATGACGAGGTCGTGAGGATCGAGGCGTATCGGAAGGTGCTGACGACGTGGGCGAGCTGGGTGA
ACGACAACATCGACCCGGCGCGCACGTCCGTCTTCTTCATGAGCATCTCCCCTCTTCACATCAG
Transcript length: 356
Transcript exons: 35539899-35540098,35540208-35540363
GAGTACAACGCGACGGTGGAGTTCTACTGGGCGCCGTTCCTGGTGGAGTCCAACTCCGACGACC
CCAAGATCCACAGCATCCAGCACCGGATCATCAAGGCGGACGCGATCGCGGCGCACGCACAGAA
CTGGCGCGGCGTCGACTACCTCGTCTTCAACACCTACATCTGGTGGATGAACACCCTCAACATG
AAGATCATGAGACCGGGCGGGCAGAGCTGGGAGGAGCATGACGAGGTCGTGAGGATCGAGGCGT
ATCGGAAGGTGCTGACGACGTGGGCGAGCTGGGTGAACGACAACATCGACCCGGCGCGCACGTC
CGTCTTCTTCATGAGCATCTCCCCTCTTCACATCAG
						
					

						Genomic sequence
						
							GAGTACAACGCGACGGTGGAGTTCTACTGGGCGCCGTTCCTGGTGGAGTCCAACTCCGACGACC
CCAAGATCCACAGCATCCAGCACCGGATCATCAAGGCGGACGCGATCGCGGCGCACGCACAGAA
CTGGCGCGGCGTCGACTACCTCGTCTTCAACACCTACATCTGGTGGATGAACACCCTCAACATG
AAGATCATGTACGCTAAATTTACGTTGCACGATATATCGATCGATCACAACGCCGTGCCGTGCA
ACCAACGGCGATCGATCGTGGGATGACAGTGACTGATAGGGGTGATCTTGCAGGAGACCGGGCG
GGCAGAGCTGGGAGGAGCATGACGAGGTCGTGAGGATCGAGGCGTATCGGAAGGTGCTGACGAC
GTGGGCGAGCTGGGTGAACGACAACATCGACCCGGCGCGCACGTCCGTCTTCTTCATGAGCATC
TCCCCTCTTCACATCAG
						
					

			
		

Sequences
Splice junction sequence	ATCGGAAGGTGCTGACGACGTGGGCGAGCTGGGTGAACGACAACATCGACCCGGCGCGCACGTC CGTCTTCTTCATGAGCATCTCCCCTCTTCACATCAGgagtacaacgcgacggtggagttctact gggcgccgttcctggtggagtccaactccgacgaccccaagatccacagcatccagcaccggat catcaagg
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: 188 Transcript exons: 35539899-35540005,35540283-35540363 GAGTACAACGCGACGGTGGAGTTCTACTGGGCGCCGTTCCTGGTGGAGTCCAACTCCGACGACC CCAAGATCCACAGCATCCAGCACCGGATCATCAAGGCGGACGCGTGGGCGAGCTGGGTGAACGA CAACATCGACCCGGCGCGCACGTCCGTCTTCTTCATGAGCATCTCCCCTCTTCACATCAG Transcript length: 320 Transcript exons: 35539899-35540079,35540225-35540363 GAGTACAACGCGACGGTGGAGTTCTACTGGGCGCCGTTCCTGGTGGAGTCCAACTCCGACGACC CCAAGATCCACAGCATCCAGCACCGGATCATCAAGGCGGACGCGATCGCGGCGCACGCACAGAA CTGGCGCGGCGTCGACTACCTCGTCTTCAACACCTACATCTGGTGGATGAACAGCTGGGAGGAG CATGACGAGGTCGTGAGGATCGAGGCGTATCGGAAGGTGCTGACGACGTGGGCGAGCTGGGTGA ACGACAACATCGACCCGGCGCGCACGTCCGTCTTCTTCATGAGCATCTCCCCTCTTCACATCAG Transcript length: 356 Transcript exons: 35539899-35540098,35540208-35540363 GAGTACAACGCGACGGTGGAGTTCTACTGGGCGCCGTTCCTGGTGGAGTCCAACTCCGACGACC CCAAGATCCACAGCATCCAGCACCGGATCATCAAGGCGGACGCGATCGCGGCGCACGCACAGAA CTGGCGCGGCGTCGACTACCTCGTCTTCAACACCTACATCTGGTGGATGAACACCCTCAACATG AAGATCATGAGACCGGGCGGGCAGAGCTGGGAGGAGCATGACGAGGTCGTGAGGATCGAGGCGT ATCGGAAGGTGCTGACGACGTGGGCGAGCTGGGTGAACGACAACATCGACCCGGCGCGCACGTC CGTCTTCTTCATGAGCATCTCCCCTCTTCACATCAG
Genomic sequence	GAGTACAACGCGACGGTGGAGTTCTACTGGGCGCCGTTCCTGGTGGAGTCCAACTCCGACGACC CCAAGATCCACAGCATCCAGCACCGGATCATCAAGGCGGACGCGATCGCGGCGCACGCACAGAA CTGGCGCGGCGTCGACTACCTCGTCTTCAACACCTACATCTGGTGGATGAACACCCTCAACATG AAGATCATGTACGCTAAATTTACGTTGCACGATATATCGATCGATCACAACGCCGTGCCGTGCA ACCAACGGCGATCGATCGTGGGATGACAGTGACTGATAGGGGTGATCTTGCAGGAGACCGGGCG GGCAGAGCTGGGAGGAGCATGACGAGGTCGTGAGGATCGAGGCGTATCGGAAGGTGCTGACGAC GTGGGCGAGCTGGGTGAACGACAACATCGACCCGGCGCGCACGTCCGTCTTCTTCATGAGCATC TCCCCTCTTCACATCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002510* osi_circ_010891 						
					
						PMCS
						0.609875666

Conservation Information
Conserved circRNAs	osi_circ_002510* osi_circ_010891
PMCS	0.609875666

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							35540074-35540073(+)
35540240-35540357(-)
						
						Potential amino acid sequence
						
							MNTLNMKIMRPGGQSWEEHDEVVRIEAYRKVLTTWASWVNDNIDPARTSVFFMSISPLHIRSTT
RRWSSTGRRSWWSPTPTTPRSTASSTGSSRRTRSRRTHRTGAASTTSSSTPTSGG*(+)
MLLPALPARSHDLHVEGVHPPDVGVEDEVVDAAPVLCVRRDRVRLDDPVLDAVDLGVVGVGLHQ
ERRPVELHRRVVLLM*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	35540074-35540073(+) 35540240-35540357(-)
Potential amino acid sequence	MNTLNMKIMRPGGQSWEEHDEVVRIEAYRKVLTTWASWVNDNIDPARTSVFFMSISPLHIRSTT RRWSSTGRRSWWSPTPTTPRSTASSTGSSRRTRSRRTHRTGAASTTSSSTPTSGG(+) MLLPALPARSHDLHVEGVHPPDVGVEDEVVDAAPVLCVRRDRVRLDDPVLDAVDLGVVGVGLHQ ERRPVELHRRVVLLM(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Ye et al., 2016;Chu et al., 2017; this study

circRNA

Detail information of Os01g0830700_circ_g.3

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