Plant Circular RNA Database

Detail information of Os03g0644000_circ_g.6

			
						 General Information
					
						CircRNA Name
						Os03g0644000_circ_g.6
					
						ID in PlantcircBase
						osa_circ_020770
					
						Alias
						Os_ciR2405
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 24837596-24838063  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							i-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os03g0644000						
					
						Parent gene annotation
						
							ATG6/Beclin-1 protein, Abiotic stresses (heat,cold and drought) 
and hormone (abscisic acid) response (Os03t0644000-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0644000_circ_g.1 Os03g0644000_circ_g.2 Os03g0644000_circ_g.3 Os03g0644000_circ_g.4 Os03g0644000_circ_g.5 Os03g0644000_circ_g.7 Os03g0644000_circ_g.8 Os03g0644000_circ_g.9 						
					
						Support reads
						4/1
					
						Tissues
						root/root
					
						Exon boundary  
						
							No-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  
						
							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
						0

General Information
CircRNA Name	Os03g0644000_circ_g.6
ID in PlantcircBase	osa_circ_020770
Alias	Os_ciR2405
Organism	Oryza sativa
Position	chr3: 24837596-24838063 JBrowse»
Reference genome	IRGSP-1.0.38
Type	i-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os03g0644000
Parent gene annotation	ATG6/Beclin-1 protein, Abiotic stresses (heat,cold and drought) and hormone (abscisic acid) response (Os03t0644000-01)
Parent gene strand	+
Alternative splicing	Os03g0644000_circ_g.1 Os03g0644000_circ_g.2 Os03g0644000_circ_g.3 Os03g0644000_circ_g.4 Os03g0644000_circ_g.5 Os03g0644000_circ_g.7 Os03g0644000_circ_g.8 Os03g0644000_circ_g.9
Support reads	4/1
Tissues	root/root
Exon boundary	No-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	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	0

			
						 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  
						
							CACACATGTTTTGTTATATCGCTACAACAATTGCTAGTGGTTTTGTGCAATCTGAAATATTTGG
TTGGCTCATGTTATTTGTGAAGTTCTACAGTTACTTgttaaaattttaattaaccttttcattt
tgtcctttcttgaatgttcttattattaactctgaagtttctctacaagaatcagtgatataga
gtcttcag

						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: 468
Transcript exons: 24837596-24838063
GTTAAAATTTTAATTAACCTTTTCATTTTGTCCTTTCTTGAATGTTCTTATTATTAACTCTGAA
GTTTCTCTACAAGAATCAGTGATATAGAGTCTTCAGTGATTTATAATTTGCTTTTGGGTGTGCA
TGTGCATACTTGCAGGAGGCTCTCGACTCTTCTCTGTCTCTCTTTTTTTTCTGATGAGTCGTAA
CATTGTTATAGGCTATGAATACAACTGTTATATTGAAAACATTAATGTGTACCTATATTTGTCA
CCTGAAACTAGACATTATTCAACAGAGTGTCAGTGTGCTATTCAATATAATTGGCAATTCGACA
TCAGAAAATAGGAGTATCATTATTTGGGAATAATAACATAATACATCCCACACATGTTTTGTTA
TATCGCTACAACAATTGCTAGTGGTTTTGTGCAATCTGAAATATTTGGTTGGCTCATGTTATTT
GTGAAGTTCTACAGTTACTT
						
						Genomic sequence
						
							GTTAAAATTTTAATTAACCTTTTCATTTTGTCCTTTCTTGAATGTTCTTATTATTAACTCTGAA
GTTTCTCTACAAGAATCAGTGATATAGAGTCTTCAGTGATTTATAATTTGCTTTTGGGTGTGCA
TGTGCATACTTGCAGGAGGCTCTCGACTCTTCTCTGTCTCTCTTTTTTTTCTGATGAGTCGTAA
CATTGTTATAGGCTATGAATACAACTGTTATATTGAAAACATTAATGTGTACCTATATTTGTCA
CCTGAAACTAGACATTATTCAACAGAGTGTCAGTGTGCTATTCAATATAATTGGCAATTCGACA
TCAGAAAATAGGAGTATCATTATTTGGGAATAATAACATAATACATCCCACACATGTTTTGTTA
TATCGCTACAACAATTGCTAGTGGTTTTGTGCAATCTGAAATATTTGGTTGGCTCATGTTATTT
GTGAAGTTCTACAGTTACTT

Sequences
Splice junction sequence	CACACATGTTTTGTTATATCGCTACAACAATTGCTAGTGGTTTTGTGCAATCTGAAATATTTGG TTGGCTCATGTTATTTGTGAAGTTCTACAGTTACTTgttaaaattttaattaaccttttcattt tgtcctttcttgaatgttcttattattaactctgaagtttctctacaagaatcagtgatataga gtcttcag
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: 468 Transcript exons: 24837596-24838063 GTTAAAATTTTAATTAACCTTTTCATTTTGTCCTTTCTTGAATGTTCTTATTATTAACTCTGAA GTTTCTCTACAAGAATCAGTGATATAGAGTCTTCAGTGATTTATAATTTGCTTTTGGGTGTGCA TGTGCATACTTGCAGGAGGCTCTCGACTCTTCTCTGTCTCTCTTTTTTTTCTGATGAGTCGTAA CATTGTTATAGGCTATGAATACAACTGTTATATTGAAAACATTAATGTGTACCTATATTTGTCA CCTGAAACTAGACATTATTCAACAGAGTGTCAGTGTGCTATTCAATATAATTGGCAATTCGACA TCAGAAAATAGGAGTATCATTATTTGGGAATAATAACATAATACATCCCACACATGTTTTGTTA TATCGCTACAACAATTGCTAGTGGTTTTGTGCAATCTGAAATATTTGGTTGGCTCATGTTATTT GTGAAGTTCTACAGTTACTT
Genomic sequence	GTTAAAATTTTAATTAACCTTTTCATTTTGTCCTTTCTTGAATGTTCTTATTATTAACTCTGAA GTTTCTCTACAAGAATCAGTGATATAGAGTCTTCAGTGATTTATAATTTGCTTTTGGGTGTGCA TGTGCATACTTGCAGGAGGCTCTCGACTCTTCTCTGTCTCTCTTTTTTTTCTGATGAGTCGTAA CATTGTTATAGGCTATGAATACAACTGTTATATTGAAAACATTAATGTGTACCTATATTTGTCA CCTGAAACTAGACATTATTCAACAGAGTGTCAGTGTGCTATTCAATATAATTGGCAATTCGACA TCAGAAAATAGGAGTATCATTATTTGGGAATAATAACATAATACATCCCACACATGTTTTGTTA TATCGCTACAACAATTGCTAGTGGTTTTGTGCAATCTGAAATATTTGGTTGGCTCATGTTATTT GTGAAGTTCTACAGTTACTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.23393807

Conservation Information
Conserved circRNAs	NA
PMCS	0.23393807

			
						 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
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os03g0644000_circ_g.6

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