Plant Circular RNA Database

Detail information of Os03g0704200_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os03g0704200_circ_g.2
					
						ID in PlantcircBase
						osa_circ_021158
					
						Alias
						Os03circ23598/Os_ciR1592
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 28309559-28311071  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os03g0704200						
					
						Parent gene annotation
						
							Zinc finger, MYND-type domain containing protein. (Os03t0704200-
01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0704200_circ_g.1 Os03g0704200_circ_g.3 						
					
						Support reads
						4/9/3
					
						Tissues
						panicle/root/shoot, root, seed
					
						Exon boundary  
						
							Yes-No							"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
						Os03t0704200-01:6

General Information
CircRNA Name	Os03g0704200_circ_g.2
ID in PlantcircBase	osa_circ_021158
Alias	Os03circ23598/Os_ciR1592
Organism	Oryza sativa
Position	chr3: 28309559-28311071 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, SMALT, Segemehl, find_circ
Parent gene	Os03g0704200
Parent gene annotation	Zinc finger, MYND-type domain containing protein. (Os03t0704200- 01)
Parent gene strand	-
Alternative splicing	Os03g0704200_circ_g.1 Os03g0704200_circ_g.3
Support reads	4/9/3
Tissues	panicle/root/shoot, root, seed
Exon boundary	Yes-No "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	Os03t0704200-01:6

			
						 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  
						
							ATTTCCTTAAGATCAAGCTCGAATGAAGGAAGAATCAGTTGGACAAGATTGGCCATCTGAGCAT
ATAAAACCAGTTGATTTTTATCAACCTCGGAGATGTttccagatgaaactaaggaagagacttt
gtcagataatagtagtacatcgctagccatcttttgtaactcttccccatctctagaagtgcta
catttctg

									
								

					

						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: 157
Transcript exons: 28309559-28309632,28310989-28311071
TTCCAGATGAAACTAAGGAAGAGACTTTGTCAGATAATAGTAGTACATCGCTAGCCATCTTTTG
TAACTCTTCCCTCGAATGAAGGAAGAATCAGTTGGACAAGATTGGCCATCTGAGCATATAAAAC
CAGTTGATTTTTATCAACCTCGGAGATGT
Transcript length: 159
Transcript exons: 28309559-28309632,28310987-28311071
TTCCAGATGAAACTAAGGAAGAGACTTTGTCAGATAATAGTAGTACATCGCTAGCCATCTTTTG
TAACTCTTCCAGCTCGAATGAAGGAAGAATCAGTTGGACAAGATTGGCCATCTGAGCATATAAA
ACCAGTTGATTTTTATCAACCTCGGAGATGT
						
					

						Genomic sequence
						
							TTCCAGATGAAACTAAGGAAGAGACTTTGTCAGATAATAGTAGTACATCGCTAGCCATCTTTTG
TAACTCTTCCCCATCTCTAGAAGTGCTACATTTCTGGCATGTATAACCTTTGTTTCCTACAGAT
GTTAAATCCAGATAAAAATGTAAGATCAATGATAACTGAAACAGTATTAAAGCTGCAGCTGACA
TTATGTTTGAATAATCCAATCTATTACATCTCTTCAGTTAGTATTTTTCCTTCGTGATGTTAAC
CAACCTGCATTAGGCAGAAGAAATCCATCACACTTTTGGTCATTGCATCTGTATCCCTCAAGGA
GCGCATCTTCCTCAGAATCCTGTAAGGTTGGGGAAAAAATTATAGCTAGAGAACACTTCATTAT
CAAGAATGTGTCAGCTTCCCATAGGACATCCAAGAATAGTAAGCAATGAAATCAAAAACCTTAA
CACAACGGGGACATGTGCAAGTGAAGTAGTAGTGCTTGAGATCGTCCTGTCTCTTCATAGTGGT
TGCCGCAGTTTCAATGTAACTTATTGATACCTAACCAAAGATGCGTAACTGACATTGCCCAGAG
AAGAAACCCCAAGAAACATGGATTGCAAGCAGAGGAATATATGATAATAAGGAAAAAAACAAAA
GTATATTCATTACCTCCTCATTTTTACTTATAGGTTGCAATGCACGAACATATGCTGTCCGACC
TTCAAATATCAAAACTGCATTTGGTACACAACTAAGTATACCAGGAAAGGGTAGATGCAATAAT
AATTATTTATTAAATGATAAAATCGGAGGAAGATGCTAAACGATGAATAAAGGAATAGTATATC
ACCTGTGGTTAATAATAGATAAAACAGGGTATAGTCCAGTCCCAAGGGGCCTCAGTTCAGGATC
ACATATGGTATGAGCGTTGCAGGCAAACTGCACATATGAGGCAGAGGATATATTATTCATGCTT
ACTTCTAAAGGTCTAGCCAGATAATCACCAAAATAGTCCTAGCCACTGCTTAAGGGTGAGACTG
GAAGACAACAAATATGAAAAACGGAAGAATAAACATGGACAGAACAATTATTCTTTTTTTTTCC
AAAGCTTCTTGGCTTATTCTGGTTTATTTTTCAAAAGGCAGATTCAAGACACGATTCTACTATA
CTCAAATAAGAGTATAAGACCACAGGGAGGTGTCCTAGATAACTTGGATCCTCATGGTTTTGGA
ACAAAATTAATCACATCCAACTAGGTCCCAATAGGTTTTAGATGGAAGGTACAAGCAAAATCTC
AAAAATAACACCAGGAAACAACTGTATTTTTTAAGCTCAATTATTCATTGGATACATTGTCTTC
TATAGTAGTTAAAACATTTTTTATAACCTTATGACTTTGAGTAGCATTACCTTGGAAAAGGTAT
GTGTAATTTCCTTAAGATCAAGCTCGAATGAAGGAAGAATCAGTTGGACAAGATTGGCCATCTG
AGCATATAAAACCAGTTGATTTTTATCAACCTCGGAGATGT
						
					

			
		

Sequences
Splice junction sequence	ATTTCCTTAAGATCAAGCTCGAATGAAGGAAGAATCAGTTGGACAAGATTGGCCATCTGAGCAT ATAAAACCAGTTGATTTTTATCAACCTCGGAGATGTttccagatgaaactaaggaagagacttt gtcagataatagtagtacatcgctagccatcttttgtaactcttccccatctctagaagtgcta catttctg
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: 157 Transcript exons: 28309559-28309632,28310989-28311071 TTCCAGATGAAACTAAGGAAGAGACTTTGTCAGATAATAGTAGTACATCGCTAGCCATCTTTTG TAACTCTTCCCTCGAATGAAGGAAGAATCAGTTGGACAAGATTGGCCATCTGAGCATATAAAAC CAGTTGATTTTTATCAACCTCGGAGATGT Transcript length: 159 Transcript exons: 28309559-28309632,28310987-28311071 TTCCAGATGAAACTAAGGAAGAGACTTTGTCAGATAATAGTAGTACATCGCTAGCCATCTTTTG TAACTCTTCCAGCTCGAATGAAGGAAGAATCAGTTGGACAAGATTGGCCATCTGAGCATATAAA ACCAGTTGATTTTTATCAACCTCGGAGATGT
Genomic sequence	TTCCAGATGAAACTAAGGAAGAGACTTTGTCAGATAATAGTAGTACATCGCTAGCCATCTTTTG TAACTCTTCCCCATCTCTAGAAGTGCTACATTTCTGGCATGTATAACCTTTGTTTCCTACAGAT GTTAAATCCAGATAAAAATGTAAGATCAATGATAACTGAAACAGTATTAAAGCTGCAGCTGACA TTATGTTTGAATAATCCAATCTATTACATCTCTTCAGTTAGTATTTTTCCTTCGTGATGTTAAC CAACCTGCATTAGGCAGAAGAAATCCATCACACTTTTGGTCATTGCATCTGTATCCCTCAAGGA GCGCATCTTCCTCAGAATCCTGTAAGGTTGGGGAAAAAATTATAGCTAGAGAACACTTCATTAT CAAGAATGTGTCAGCTTCCCATAGGACATCCAAGAATAGTAAGCAATGAAATCAAAAACCTTAA CACAACGGGGACATGTGCAAGTGAAGTAGTAGTGCTTGAGATCGTCCTGTCTCTTCATAGTGGT TGCCGCAGTTTCAATGTAACTTATTGATACCTAACCAAAGATGCGTAACTGACATTGCCCAGAG AAGAAACCCCAAGAAACATGGATTGCAAGCAGAGGAATATATGATAATAAGGAAAAAAACAAAA GTATATTCATTACCTCCTCATTTTTACTTATAGGTTGCAATGCACGAACATATGCTGTCCGACC TTCAAATATCAAAACTGCATTTGGTACACAACTAAGTATACCAGGAAAGGGTAGATGCAATAAT AATTATTTATTAAATGATAAAATCGGAGGAAGATGCTAAACGATGAATAAAGGAATAGTATATC ACCTGTGGTTAATAATAGATAAAACAGGGTATAGTCCAGTCCCAAGGGGCCTCAGTTCAGGATC ACATATGGTATGAGCGTTGCAGGCAAACTGCACATATGAGGCAGAGGATATATTATTCATGCTT ACTTCTAAAGGTCTAGCCAGATAATCACCAAAATAGTCCTAGCCACTGCTTAAGGGTGAGACTG GAAGACAACAAATATGAAAAACGGAAGAATAAACATGGACAGAACAATTATTCTTTTTTTTTCC AAAGCTTCTTGGCTTATTCTGGTTTATTTTTCAAAAGGCAGATTCAAGACACGATTCTACTATA CTCAAATAAGAGTATAAGACCACAGGGAGGTGTCCTAGATAACTTGGATCCTCATGGTTTTGGA ACAAAATTAATCACATCCAACTAGGTCCCAATAGGTTTTAGATGGAAGGTACAAGCAAAATCTC AAAAATAACACCAGGAAACAACTGTATTTTTTAAGCTCAATTATTCATTGGATACATTGTCTTC TATAGTAGTTAAAACATTTTTTATAACCTTATGACTTTGAGTAGCATTACCTTGGAAAAGGTAT GTGTAATTTCCTTAAGATCAAGCTCGAATGAAGGAAGAATCAGTTGGACAAGATTGGCCATCTG AGCATATAAAACCAGTTGATTTTTATCAACCTCGGAGATGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005048* osi_circ_013479 						
					
						PMCS
						0.362515874

Conservation Information
Conserved circRNAs	osi_circ_005048* osi_circ_013479
PMCS	0.362515874

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os03g0704200_circ_g.2

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