Plant Circular RNA Database

Detail information of Os01g0723400_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os01g0723400_circ_g.4
					
						ID in PlantcircBase
						osa_circ_003725
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 30167457-30167951  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0723400						
					
						Parent gene annotation
						
							NADP-malic enzyme, Splicing variant (Os01t0723400-01);Similar to
 Malic enzyme. (Os01t0723400-02);NADP-malic enzyme, Salt and osm
otic stress tolerance, Disease resistance (Os01t0723400-03);NADP
-malic enzyme, Splicing variant (Os01t0723400-04);NADP-malic enz
yme, Splicing variant (Os01t0723400-05)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0723400_circ_g.3 Os01g0723400_circ_g.5 Os01g0723400_circ_g.6 						
					
						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
						Os01t0723400-05:3
Os01t0723400-03:3
Os01t0723400-04:3
Os01t0723400-02:3
Os01t0723400-01:3

General Information
CircRNA Name	Os01g0723400_circ_g.4
ID in PlantcircBase	osa_circ_003725
Alias	NA
Organism	Oryza sativa
Position	chr1: 30167457-30167951 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0723400
Parent gene annotation	NADP-malic enzyme, Splicing variant (Os01t0723400-01);Similar to Malic enzyme. (Os01t0723400-02);NADP-malic enzyme, Salt and osm otic stress tolerance, Disease resistance (Os01t0723400-03);NADP -malic enzyme, Splicing variant (Os01t0723400-04);NADP-malic enz yme, Splicing variant (Os01t0723400-05)
Parent gene strand	+
Alternative splicing	Os01g0723400_circ_g.3 Os01g0723400_circ_g.5 Os01g0723400_circ_g.6
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	Os01t0723400-05:3 Os01t0723400-03:3 Os01t0723400-04:3 Os01t0723400-02:3 Os01t0723400-01:3

			
						 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  
						
							GATCCTTGAGGTGCTAAAAAACTGGCCAGAGAGGAGCATTCAGGTTATCGTTGTTACTGATGGT
GAGCGAATTTTGGGGCTTGGAGATCTTGGCTGCCAGgaaaggaaaatcatgcataacatccgac
aataccagctgcctctgcagaaatacatggctatgatggacctccaggtgactttccttattgt
tcatagta

						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: 333
Transcript exons: 30167457-30167531,30167620-30167771,30167846-30167951
GAAAGGAAAATCATGCATAACATCCGACAATACCAGCTGCCTCTGCAGAAATACATGGCTATGA
TGGACCTCCAGGAGGGGAATGAGAGGCTTTTCTACAAGCTCCTCATTGACAATGTTGAGGAGCT
ACTTCCTGTCGTTTACACTCCAACAGTTGGTGAGGCCTGCCAAAAGTATGGATCCATATTTAGC
CGTCCTCAGGGTCTTTATATCAGCTTGAAGGAGAAGGGAAAGATCCTTGAGGTGCTAAAAAACT
GGCCAGAGAGGAGCATTCAGGTTATCGTTGTTACTGATGGTGAGCGAATTTTGGGGCTTGGAGA
TCTTGGCTGCCAG
						
						Genomic sequence
						
							GAAAGGAAAATCATGCATAACATCCGACAATACCAGCTGCCTCTGCAGAAATACATGGCTATGA
TGGACCTCCAGGTGACTTTCCTTATTGTTCATAGTATAGCATTACAGCTCATTTGAGTTACGCA
GTTTGGTTACACTGTTCTTTCAATGCATATTGCAGGAGGGGAATGAGAGGCTTTTCTACAAGCT
CCTCATTGACAATGTTGAGGAGCTACTTCCTGTCGTTTACACTCCAACAGTTGGTGAGGCCTGC
CAAAAGTATGGATCCATATTTAGCCGTCCTCAGGGTCTTTATATCAGCTTGAAGGAGAAGTAAG
TTTCTCTACCTGGGTTGTTGTATTGTTTTGAGATTCCCGTGTTCATGTGCATCTGTAATTTTGC
TGCAGGGGAAAGATCCTTGAGGTGCTAAAAAACTGGCCAGAGAGGAGCATTCAGGTTATCGTTG
TTACTGATGGTGAGCGAATTTTGGGGCTTGGAGATCTTGGCTGCCAG

Sequences
Splice junction sequence	GATCCTTGAGGTGCTAAAAAACTGGCCAGAGAGGAGCATTCAGGTTATCGTTGTTACTGATGGT GAGCGAATTTTGGGGCTTGGAGATCTTGGCTGCCAGgaaaggaaaatcatgcataacatccgac aataccagctgcctctgcagaaatacatggctatgatggacctccaggtgactttccttattgt tcatagta
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: 333 Transcript exons: 30167457-30167531,30167620-30167771,30167846-30167951 GAAAGGAAAATCATGCATAACATCCGACAATACCAGCTGCCTCTGCAGAAATACATGGCTATGA TGGACCTCCAGGAGGGGAATGAGAGGCTTTTCTACAAGCTCCTCATTGACAATGTTGAGGAGCT ACTTCCTGTCGTTTACACTCCAACAGTTGGTGAGGCCTGCCAAAAGTATGGATCCATATTTAGC CGTCCTCAGGGTCTTTATATCAGCTTGAAGGAGAAGGGAAAGATCCTTGAGGTGCTAAAAAACT GGCCAGAGAGGAGCATTCAGGTTATCGTTGTTACTGATGGTGAGCGAATTTTGGGGCTTGGAGA TCTTGGCTGCCAG
Genomic sequence	GAAAGGAAAATCATGCATAACATCCGACAATACCAGCTGCCTCTGCAGAAATACATGGCTATGA TGGACCTCCAGGTGACTTTCCTTATTGTTCATAGTATAGCATTACAGCTCATTTGAGTTACGCA GTTTGGTTACACTGTTCTTTCAATGCATATTGCAGGAGGGGAATGAGAGGCTTTTCTACAAGCT CCTCATTGACAATGTTGAGGAGCTACTTCCTGTCGTTTACACTCCAACAGTTGGTGAGGCCTGC CAAAAGTATGGATCCATATTTAGCCGTCCTCAGGGTCTTTATATCAGCTTGAAGGAGAAGTAAG TTTCTCTACCTGGGTTGTTGTATTGTTTTGAGATTCCCGTGTTCATGTGCATCTGTAATTTTGC TGCAGGGGAAAGATCCTTGAGGTGCTAAAAAACTGGCCAGAGAGGAGCATTCAGGTTATCGTTG TTACTGATGGTGAGCGAATTTTGGGGCTTGGAGATCTTGGCTGCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.514052222

Conservation Information
Conserved circRNAs	NA
PMCS	0.514052222

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30167470-30167948(+)
30167912-30167517(+)
30167476-30167867(-)
30167514-30167893(-)
						
						Potential amino acid sequence
						
							MHNIRQYQLPLQKYMAMMDLQEGNERLFYKLLIDNVEELLPVVYTPTVGEACQKYGSIFSRPQG
LYISLKEKGKILEVLKNWPERSIQVIVVTDGERILGLGDLGCQERKIMHNIRQYQLPLQKYMAM
MDLQEGNERLFYKLLIDNVEELLPVVYTPTVGEACQKYGSIFSRPQGLYISLKEKGKILEVLKN
WPERSIQVIVVTDGERILGLGDLGCQERKIMHNIRQYQLPLQKYMAMMDLQEGNERLFYKLLID
NVEELLPVVYTPTVGEACQKYGSIFSRPQGLYISLKEKGKILEVLKNWPERSIQVIVVTDGERI
LGLGDLGCQERKIMHNIRQYQLPLQKYMAMMDLQEGNERLFYKLLIDNVEELLPVVYTPTVGEA
CQKYGSIFSRPQGLYISLKEKGKILEVLKNWPERSIQVIVVTDGERILGLGDLGCQ(+)
MVSEFWGLEILAARKGKSCITSDNTSCLCRNTWL*(+)
MHDFPFLAAKISKPQNSLTISNNDNLNAPLWPVF*(-)
MYFCRGSWYCRMLCMIFLSWQPRSPSPKIRSPSVTTIT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	30167470-30167948(+) 30167912-30167517(+) 30167476-30167867(-) 30167514-30167893(-)
Potential amino acid sequence	MHNIRQYQLPLQKYMAMMDLQEGNERLFYKLLIDNVEELLPVVYTPTVGEACQKYGSIFSRPQG LYISLKEKGKILEVLKNWPERSIQVIVVTDGERILGLGDLGCQERKIMHNIRQYQLPLQKYMAM MDLQEGNERLFYKLLIDNVEELLPVVYTPTVGEACQKYGSIFSRPQGLYISLKEKGKILEVLKN WPERSIQVIVVTDGERILGLGDLGCQERKIMHNIRQYQLPLQKYMAMMDLQEGNERLFYKLLID NVEELLPVVYTPTVGEACQKYGSIFSRPQGLYISLKEKGKILEVLKNWPERSIQVIVVTDGERI LGLGDLGCQERKIMHNIRQYQLPLQKYMAMMDLQEGNERLFYKLLIDNVEELLPVVYTPTVGEA CQKYGSIFSRPQGLYISLKEKGKILEVLKNWPERSIQVIVVTDGERILGLGDLGCQ(+) MVSEFWGLEILAARKGKSCITSDNTSCLCRNTWL(+) MHDFPFLAAKISKPQNSLTISNNDNLNAPLWPVF(-) MYFCRGSWYCRMLCMIFLSWQPRSPSPKIRSPSVTTIT*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0723400_circ_g.4

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