Plant Circular RNA Database

Detail information of Os01g0680700_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os01g0680700_circ_g.4
					
						ID in PlantcircBase
						osa_circ_003243
					
						Alias
						Os01circ20310/Os_ciR1022
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 28018040-28018544  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, SMALT, Segemehl, circseq_cup, find_circ
					
						Parent gene
						
							Os01g0680700						
					
						Parent gene annotation
						
							Protein of unknown function DUF1639 family protein. (Os01t068070
0-01);Hypothetical conserved gene. (Os01t0680700-02);Hypothetica
l conserved gene. (Os01t0680700-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0680700_circ_g.5 						
					
						Support reads
						10/19/14/15
					
						Tissues
						leaf and panicle/root/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  
						
							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
						Os01t0680700-02:1
Os01t0680700-03:2
Os01t0680700-01:2

General Information
CircRNA Name	Os01g0680700_circ_g.4
ID in PlantcircBase	osa_circ_003243
Alias	Os01circ20310/Os_ciR1022
Organism	Oryza sativa
Position	chr1: 28018040-28018544 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, SMALT, Segemehl, circseq_cup, find_circ
Parent gene	Os01g0680700
Parent gene annotation	Protein of unknown function DUF1639 family protein. (Os01t068070 0-01);Hypothetical conserved gene. (Os01t0680700-02);Hypothetica l conserved gene. (Os01t0680700-03)
Parent gene strand	-
Alternative splicing	Os01g0680700_circ_g.5
Support reads	10/19/14/15
Tissues	leaf and panicle/root/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	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	Os01t0680700-02:1 Os01t0680700-03:2 Os01t0680700-01:2

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F: TGTGGCTTTCAGACTTGACG
 R: GTTCTTGGAATCCATGTGCAG
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	Yes 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	F: TGTGGCTTTCAGACTTGACG R: GTTCTTGGAATCCATGTGCAG 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  
						
							GTTCTTGGAATCCATGTGCAGCGCCGCGTCCAGGGCGGACTTGTGCGCCTTGTCCGGCGACCGC
TTGTACCCGCCGCCTGATCGCTCCTCCACGGCGGACcttcttcacacatttcttctctcgcacc
tcataccgtcctctcgtcaagtctgaaagccacatcccagggaatacatactgcacatcacatc
gggggcaa

									
								

					

						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: 151
Transcript exons: 28018040-28018094,28018449-28018544
CTTCTTCACACATTTCTTCTCTCGCACCTCATACCGTCCTCTCGTCAAGTCTGAATTGGAATCC
ATGTGCAGCGCCGCGTCCAGGGCGGACTTGTGCGCCTTGTCCGGCGACCGCTTGTACCCGCCGC
CTGATCGCTCCTCCACGGCGGAC
Transcript length: 217
Transcript exons: 28018040-28018095,28018384-28018544
CTTCTTCACACATTTCTTCTCTCGCACCTCATACCGTCCTCTCGTCAAGTCTGAAACGCCGGCG
CCGGCGCCGCCGTTTGCGGTCACCGACGAGTCGTGGTGGTGGTGATGGTGGTTGTTCTTGGAAT
CCATGTGCAGCGCCGCGTCCAGGGCGGACTTGTGCGCCTTGTCCGGCGACCGCTTGTACCCGCC
GCCTGATCGCTCCTCCACGGCGGAC
Transcript length: 222
Transcript exons: 28018040-28018108,28018375-28018482,28018500-28018544
CTTCTTCACACATTTCTTCTCTCGCACCTCATACCGTCCTCTCGTCAAGTCTGAAAGCCACATC
CCAGGCGATCTTCTCGCCGGCGCCGGCGCCGCCGTTTGCGGTCACCGACGAGTCGTGGTGGTGG
TGATGGTGGTTGTTCTTGGAATCCATGTGCAGCGCCGCGTCCAGGGCGGGGCGACCGCTTGTAC
CCGCCGCCTGATCGCTCCTCCACGGCGGAC
Transcript length: 223
Transcript exons: 28018040-28018077,28018360-28018544
CTTCTTCACACATTTCTTCTCTCGCACCTCATACCGTCCAAACCGCTCGGAGCCGATCTTCTCG
CCGGCGCCGGCGCCGCCGTTTGCGGTCACCGACGAGTCGTGGTGGTGGTGATGGTGGTTGTTCT
TGGAATCCATGTGCAGCGCCGCGTCCAGGGCGGACTTGTGCGCCTTGTCCGGCGACCGCTTGTA
CCCGCCGCCTGATCGCTCCTCCACGGCGGAC
Transcript length: 232
Transcript exons: 28018040-28018100,28018374-28018544
CTTCTTCACACATTTCTTCTCTCGCACCTCATACCGTCCTCTCGTCAAGTCTGAAAGCCACCCG
ATCTTCTCGCCGGCGCCGGCGCCGCCGTTTGCGGTCACCGACGAGTCGTGGTGGTGGTGATGGT
GGTTGTTCTTGGAATCCATGTGCAGCGCCGCGTCCAGGGCGGACTTGTGCGCCTTGTCCGGCGA
CCGCTTGTACCCGCCGCCTGATCGCTCCTCCACGGCGGAC
Transcript length: 388
Transcript exons: 28018040-28018117,28018235-28018544
CTTCTTCACACATTTCTTCTCTCGCACCTCATACCGTCCTCTCGTCAAGTCTGAAAGCCACATC
CCAGGGAATACATATTGGAGGGTCTTGTCCACGTTCTTGGCCCTCTTCTTGGGCCTCTGAGGCA
GCTTGGTGCCCTTCATGATCAAGAAGTCGTCCTCCTTCTCCTTGCGCGACAGCGAGATGTAGAT
CCGGGGCAGCTCAAACCGCTCGGAGCCGATCTTCTCGCCGGCGCCGGCGCCGCCGTTTGCGGTC
ACCGACGAGTCGTGGTGGTGGTGATGGTGGTTGTTCTTGGAATCCATGTGCAGCGCCGCGTCCA
GGGCGGACTTGTGCGCCTTGTCCGGCGACCGCTTGTACCCGCCGCCTGATCGCTCCTCCACGGC
GGAC
						
					

						Genomic sequence
						
							CTTCTTCACACATTTCTTCTCTCGCACCTCATACCGTCCTCTCGTCAAGTCTGAAAGCCACATC
CCAGGGAATACATACTGCACATCACATCGGGGGCAACACGAGACACATGTTAGCTCTGTGATCA
GAACAGATGCAAGAATGGATCGGAGCAGATAAGATCAGGCCGGTTTGCGGAGCAAAGATTGGCA
TACTTGGAGGGTCTTGTCCACGTTCTTGGCCCTCTTCTTGGGCCTCTGAGGCAGCTTGGTGCCC
TTCATGATCAAGAAGTCGTCCTCCTTCTCCTTGCGCGACAGCGAGATGTAGATCCGGGGCAGCT
CAAACCGCTCGGAGCCGATCTTCTCGCCGGCGCCGGCGCCGCCGTTTGCGGTCACCGACGAGTC
GTGGTGGTGGTGATGGTGGTTGTTCTTGGAATCCATGTGCAGCGCCGCGTCCAGGGCGGACTTG
TGCGCCTTGTCCGGCGACCGCTTGTACCCGCCGCCTGATCGCTCCTCCACGGCGGAC
						
					

			
		

Sequences
Splice junction sequence	GTTCTTGGAATCCATGTGCAGCGCCGCGTCCAGGGCGGACTTGTGCGCCTTGTCCGGCGACCGC TTGTACCCGCCGCCTGATCGCTCCTCCACGGCGGACcttcttcacacatttcttctctcgcacc tcataccgtcctctcgtcaagtctgaaagccacatcccagggaatacatactgcacatcacatc gggggcaa
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: 151 Transcript exons: 28018040-28018094,28018449-28018544 CTTCTTCACACATTTCTTCTCTCGCACCTCATACCGTCCTCTCGTCAAGTCTGAATTGGAATCC ATGTGCAGCGCCGCGTCCAGGGCGGACTTGTGCGCCTTGTCCGGCGACCGCTTGTACCCGCCGC CTGATCGCTCCTCCACGGCGGAC Transcript length: 217 Transcript exons: 28018040-28018095,28018384-28018544 CTTCTTCACACATTTCTTCTCTCGCACCTCATACCGTCCTCTCGTCAAGTCTGAAACGCCGGCG CCGGCGCCGCCGTTTGCGGTCACCGACGAGTCGTGGTGGTGGTGATGGTGGTTGTTCTTGGAAT CCATGTGCAGCGCCGCGTCCAGGGCGGACTTGTGCGCCTTGTCCGGCGACCGCTTGTACCCGCC GCCTGATCGCTCCTCCACGGCGGAC Transcript length: 222 Transcript exons: 28018040-28018108,28018375-28018482,28018500-28018544 CTTCTTCACACATTTCTTCTCTCGCACCTCATACCGTCCTCTCGTCAAGTCTGAAAGCCACATC CCAGGCGATCTTCTCGCCGGCGCCGGCGCCGCCGTTTGCGGTCACCGACGAGTCGTGGTGGTGG TGATGGTGGTTGTTCTTGGAATCCATGTGCAGCGCCGCGTCCAGGGCGGGGCGACCGCTTGTAC CCGCCGCCTGATCGCTCCTCCACGGCGGAC Transcript length: 223 Transcript exons: 28018040-28018077,28018360-28018544 CTTCTTCACACATTTCTTCTCTCGCACCTCATACCGTCCAAACCGCTCGGAGCCGATCTTCTCG CCGGCGCCGGCGCCGCCGTTTGCGGTCACCGACGAGTCGTGGTGGTGGTGATGGTGGTTGTTCT TGGAATCCATGTGCAGCGCCGCGTCCAGGGCGGACTTGTGCGCCTTGTCCGGCGACCGCTTGTA CCCGCCGCCTGATCGCTCCTCCACGGCGGAC Transcript length: 232 Transcript exons: 28018040-28018100,28018374-28018544 CTTCTTCACACATTTCTTCTCTCGCACCTCATACCGTCCTCTCGTCAAGTCTGAAAGCCACCCG ATCTTCTCGCCGGCGCCGGCGCCGCCGTTTGCGGTCACCGACGAGTCGTGGTGGTGGTGATGGT GGTTGTTCTTGGAATCCATGTGCAGCGCCGCGTCCAGGGCGGACTTGTGCGCCTTGTCCGGCGA CCGCTTGTACCCGCCGCCTGATCGCTCCTCCACGGCGGAC Transcript length: 388 Transcript exons: 28018040-28018117,28018235-28018544 CTTCTTCACACATTTCTTCTCTCGCACCTCATACCGTCCTCTCGTCAAGTCTGAAAGCCACATC CCAGGGAATACATATTGGAGGGTCTTGTCCACGTTCTTGGCCCTCTTCTTGGGCCTCTGAGGCA GCTTGGTGCCCTTCATGATCAAGAAGTCGTCCTCCTTCTCCTTGCGCGACAGCGAGATGTAGAT CCGGGGCAGCTCAAACCGCTCGGAGCCGATCTTCTCGCCGGCGCCGGCGCCGCCGTTTGCGGTC ACCGACGAGTCGTGGTGGTGGTGATGGTGGTTGTTCTTGGAATCCATGTGCAGCGCCGCGTCCA GGGCGGACTTGTGCGCCTTGTCCGGCGACCGCTTGTACCCGCCGCCTGATCGCTCCTCCACGGC GGAC
Genomic sequence	CTTCTTCACACATTTCTTCTCTCGCACCTCATACCGTCCTCTCGTCAAGTCTGAAAGCCACATC CCAGGGAATACATACTGCACATCACATCGGGGGCAACACGAGACACATGTTAGCTCTGTGATCA GAACAGATGCAAGAATGGATCGGAGCAGATAAGATCAGGCCGGTTTGCGGAGCAAAGATTGGCA TACTTGGAGGGTCTTGTCCACGTTCTTGGCCCTCTTCTTGGGCCTCTGAGGCAGCTTGGTGCCC TTCATGATCAAGAAGTCGTCCTCCTTCTCCTTGCGCGACAGCGAGATGTAGATCCGGGGCAGCT CAAACCGCTCGGAGCCGATCTTCTCGCCGGCGCCGGCGCCGCCGTTTGCGGTCACCGACGAGTC GTGGTGGTGGTGATGGTGGTTGTTCTTGGAATCCATGTGCAGCGCCGCGTCCAGGGCGGACTTG TGCGCCTTGTCCGGCGACCGCTTGTACCCGCCGCCTGATCGCTCCTCCACGGCGGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002301* osi_circ_010565 						
					
						PMCS
						0.590794215

Conservation Information
Conserved circRNAs	osi_circ_002301* osi_circ_010565
PMCS	0.590794215

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							28018459-28018090(+)
28018054-28018413(-)
28018461-28018361(-)
						
						Potential amino acid sequence
						
							MCSAASRADLCALSGDRLYPPPDRSSTADLLHTFLLSHLIPSSRQV*(+)
MCEEGPPWRSDQAAGTSGRRTRRTSPPWTRRCTWIPRTTTITTTTTRR*(-)
MDSKNNHHHHHHDSSVTANGGAGAGEKIGSERFELPRIYISLSRKEKEDDFLIMKGTKLPQRPK
KRAKNVDKTLQYVFPGMWLSDLTRGRYEVREKKCVKKVRRGGAIRRRVQAVAGQGAQVRPGRGA
AHGFQEQPPSPPPRLVGDRKRRRRRRREDRLRAV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	28018459-28018090(+) 28018054-28018413(-) 28018461-28018361(-)
Potential amino acid sequence	MCSAASRADLCALSGDRLYPPPDRSSTADLLHTFLLSHLIPSSRQV(+) MCEEGPPWRSDQAAGTSGRRTRRTSPPWTRRCTWIPRTTTITTTTTRR(-) MDSKNNHHHHHHDSSVTANGGAGAGEKIGSERFELPRIYISLSRKEKEDDFLIMKGTKLPQRPK KRAKNVDKTLQYVFPGMWLSDLTRGRYEVREKKCVKKVRRGGAIRRRVQAVAGQGAQVRPGRGA AHGFQEQPPSPPPRLVGDRKRRRRRRREDRLRAV*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os01g0680700_circ_g.4

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