Plant Circular RNA Database

Detail information of Os03g0143800_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os03g0143800_circ_g.1
					
						ID in PlantcircBase
						osa_circ_017886
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 2439558-2439770  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os03g0143800						
					
						Parent gene annotation
						
							PIROGI/Specifically Rac1-associated protein 1 (PIR/SRA1)-like pr
otein, Homolog of SCAR/WAVE complex components, Control of epide
rmal cell morphogenesis (Os03t0143800-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0143800_circ_g.2 Os03g0143800_circ_g.3 Os03g0143800_circ_g.4 Os03g0143800_circ_g.5 Os03g0143800_circ_g.6 Os03g0143800_circ_g.7 Os03g0143800_circ_g.8 Os03g0143800_circ_g.9 Os03g0143800_circ_g.10 Os03g0143800_circ_g.11 Os03g0143800_circ_g.12 Os03g0143800_circ_g.13 						
					
						Support reads
						1
					
						Tissues
						shoot
					
						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
						Os03t0143800-01:1

General Information
CircRNA Name	Os03g0143800_circ_g.1
ID in PlantcircBase	osa_circ_017886
Alias	NA
Organism	Oryza sativa
Position	chr3: 2439558-2439770 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os03g0143800
Parent gene annotation	PIROGI/Specifically Rac1-associated protein 1 (PIR/SRA1)-like pr otein, Homolog of SCAR/WAVE complex components, Control of epide rmal cell morphogenesis (Os03t0143800-01)
Parent gene strand	+
Alternative splicing	Os03g0143800_circ_g.2 Os03g0143800_circ_g.3 Os03g0143800_circ_g.4 Os03g0143800_circ_g.5 Os03g0143800_circ_g.6 Os03g0143800_circ_g.7 Os03g0143800_circ_g.8 Os03g0143800_circ_g.9 Os03g0143800_circ_g.10 Os03g0143800_circ_g.11 Os03g0143800_circ_g.12 Os03g0143800_circ_g.13
Support reads	1
Tissues	shoot
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	Os03t0143800-01:1

			
						 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  
						
							CAGGATATGGGAGCAGTGTGCCTGGAAATTTTCGCGCCCTTGTAAAGAACCACCTTCAGATTCT
CAACATGGATCGACAACATTTTTTGACTATGAAAAGatgataatattgaagtcatcagatggtg
cggataatgactggtcaagagatattaaggggaacatgtatgatattgttgttgaaggctttca
gcttctta

						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: 213
Transcript exons: 2439558-2439770
ATGATAATATTGAAGTCATCAGATGGTGCGGATAATGACTGGTCAAGAGATATTAAGGGGAACA
TGTATGATATTGTTGTTGAAGGCTTTCAGCTTCTTAGCCGATGGACTGGCAGGATATGGGAGCA
GTGTGCCTGGAAATTTTCGCGCCCTTGTAAAGAACCACCTTCAGATTCTCAACATGGATCGACA
ACATTTTTTGACTATGAAAAG
						
						Genomic sequence
						
							ATGATAATATTGAAGTCATCAGATGGTGCGGATAATGACTGGTCAAGAGATATTAAGGGGAACA
TGTATGATATTGTTGTTGAAGGCTTTCAGCTTCTTAGCCGATGGACTGGCAGGATATGGGAGCA
GTGTGCCTGGAAATTTTCGCGCCCTTGTAAAGAACCACCTTCAGATTCTCAACATGGATCGACA
ACATTTTTTGACTATGAAAAG

Sequences
Splice junction sequence	CAGGATATGGGAGCAGTGTGCCTGGAAATTTTCGCGCCCTTGTAAAGAACCACCTTCAGATTCT CAACATGGATCGACAACATTTTTTGACTATGAAAAGatgataatattgaagtcatcagatggtg cggataatgactggtcaagagatattaaggggaacatgtatgatattgttgttgaaggctttca gcttctta
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: 213 Transcript exons: 2439558-2439770 ATGATAATATTGAAGTCATCAGATGGTGCGGATAATGACTGGTCAAGAGATATTAAGGGGAACA TGTATGATATTGTTGTTGAAGGCTTTCAGCTTCTTAGCCGATGGACTGGCAGGATATGGGAGCA GTGTGCCTGGAAATTTTCGCGCCCTTGTAAAGAACCACCTTCAGATTCTCAACATGGATCGACA ACATTTTTTGACTATGAAAAG
Genomic sequence	ATGATAATATTGAAGTCATCAGATGGTGCGGATAATGACTGGTCAAGAGATATTAAGGGGAACA TGTATGATATTGTTGTTGAAGGCTTTCAGCTTCTTAGCCGATGGACTGGCAGGATATGGGAGCA GTGTGCCTGGAAATTTTCGCGCCCTTGTAAAGAACCACCTTCAGATTCTCAACATGGATCGACA ACATTTTTTGACTATGAAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.565172229

Conservation Information
Conserved circRNAs	NA
PMCS	0.565172229

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2439559-2439767(+)
2439581-2439558(+)
2439624-2439763(-)
2439578-2439657(-)
						
						Potential amino acid sequence
						
							MIILKSSDGADNDWSRDIKGNMYDIVVEGFQLLSRWTGRIWEQCAWKFSRPCKEPPSDSQHGST
TFFDYEKMIILKSSDGADNDWSRDIKGNMYDIVVEGFQLLSRWTGRIWEQCAWKFSRPCKEPPS
DSQHGSTTFFDYEKMIILKSSDGADNDWSRDIKGNMYDIVVEGFQLLSRWTGRIWEQCAWKFSR
PCKEPPSDSQHGSTTFFDYEKMIILKSSDGADNDWSRDIKGNMYDIVVEGFQLLSRWTGRIWEQ
CAWKFSRPCKEPPSDSQHGSTTFFDYEK(+)
MVRIMTGQEILRGTCMILLLKAFSFLADGLAGYGSSVPGNFRALVKNHLQILNMDRQHFLTMKR
*(+)
MFPLISLDQSLSAPSDDFNIIIFS*(-)
MTSILSSFHSQKMLSIHVENLKVVLYKGAKISRHTAPISCQSIG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2439559-2439767(+) 2439581-2439558(+) 2439624-2439763(-) 2439578-2439657(-)
Potential amino acid sequence	MIILKSSDGADNDWSRDIKGNMYDIVVEGFQLLSRWTGRIWEQCAWKFSRPCKEPPSDSQHGST TFFDYEKMIILKSSDGADNDWSRDIKGNMYDIVVEGFQLLSRWTGRIWEQCAWKFSRPCKEPPS DSQHGSTTFFDYEKMIILKSSDGADNDWSRDIKGNMYDIVVEGFQLLSRWTGRIWEQCAWKFSR PCKEPPSDSQHGSTTFFDYEKMIILKSSDGADNDWSRDIKGNMYDIVVEGFQLLSRWTGRIWEQ CAWKFSRPCKEPPSDSQHGSTTFFDYEK(+) MVRIMTGQEILRGTCMILLLKAFSFLADGLAGYGSSVPGNFRALVKNHLQILNMDRQHFLTMKR (+) MFPLISLDQSLSAPSDDFNIIIFS(-) MTSILSSFHSQKMLSIHVENLKVVLYKGAKISRHTAPISCQSIG*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os03g0143800_circ_g.1

Address

Any questions?

Supported by