Plant Circular RNA Database

Detail information of Os01g0749200_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os01g0749200_circ_g.1
					
						ID in PlantcircBase
						osa_circ_003880
					
						Alias
						Os_ciR6116
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 31367938-31368575  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os01g0749200						
					
						Parent gene annotation
						
							Chloroplast ribosome L13 protein, Chloroplast development under 
low temperature conditions (Os01t0749200-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0749200_circ_g.2 						
					
						Support reads
						2/1
					
						Tissues
						root/root
					
						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
						Os01t0749200-01:2

General Information
CircRNA Name	Os01g0749200_circ_g.1
ID in PlantcircBase	osa_circ_003880
Alias	Os_ciR6116
Organism	Oryza sativa
Position	chr1: 31367938-31368575 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os01g0749200
Parent gene annotation	Chloroplast ribosome L13 protein, Chloroplast development under low temperature conditions (Os01t0749200-01)
Parent gene strand	+
Alternative splicing	Os01g0749200_circ_g.2
Support reads	2/1
Tissues	root/root
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	Os01t0749200-01:2

			
						 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  
						
							GCCTGGTGGAATGAAAGAAGAAACTTTTGATCAGCTTCAGAAAAGGATTCCGGAGAGAATTATT
GAACATGCAGTGCGTGGCATGCTTCCTAAGGGCAGAgacatatggaacacaacatggtacccta
aggctgcagatcatgtaactactgagaagacatggtatgttgttgatgcaacagacaagattct
aggtaggc

						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: 357
Transcript exons: 31367938-31368123,31368405-31368575
GACATATGGAACACAACATGGTACCCTAAGGCTGCAGATCATGTAACTACTGAGAAGACATGGT
ATGTTGTTGATGCAACAGACAAGATTCTAGGTAGGCTTGCATCCACCATTGCAGTACACATCAG
AGGAAAGAATGAGGCCACATACACTCCAAGTGTGGACATGGGGGCTTTTGTTGTTGTGGTTAAT
GCAGAGAAGGTTGCTGTTTCTGGCAAAAAGCGGTCACAGAAGCTCTACAGGAGGCACTCTGGAC
GGCCTGGTGGAATGAAAGAAGAAACTTTTGATCAGCTTCAGAAAAGGATTCCGGAGAGAATTAT
TGAACATGCAGTGCGTGGCATGCTTCCTAAGGGCAGA
						
						Genomic sequence
						
							GACATATGGAACACAACATGGTACCCTAAGGCTGCAGATCATGTAACTACTGAGAAGACATGGT
ATGTTGTTGATGCAACAGACAAGATTCTAGGTAGGCTTGCATCCACCATTGCAGTACACATCAG
AGGAAAGAATGAGGCCACATACACTCCAAGTGTGGACATGGGGGCTTTTGTTGTTGTGGTATGT
ATGTTTCTTGAAATTAATTTATAAAGTTAAATAGTGCACACAATAAGATCCTCTGTAGTCCCAC
AAAAGGAAAAGAGGTTTAGCAGCACATACAAATAAGCACCAAAAGGTATCTGGAAGCTGAGGTC
CACCTGAAGGCATTTTGAAGCTGATTTCATGTATATATATTTATGTTACTGTGTGCTTTTAATA
CTAATGCATCTCTGAAGAGTAATTGCTACGCATATACTATTGTAAGTTCCTGAACTACCATGCT
GAACTCTATGTTCACATAGGTTAATGCAGAGAAGGTTGCTGTTTCTGGCAAAAAGCGGTCACAG
AAGCTCTACAGGAGGCACTCTGGACGGCCTGGTGGAATGAAAGAAGAAACTTTTGATCAGCTTC
AGAAAAGGATTCCGGAGAGAATTATTGAACATGCAGTGCGTGGCATGCTTCCTAAGGGCAGA

Sequences
Splice junction sequence	GCCTGGTGGAATGAAAGAAGAAACTTTTGATCAGCTTCAGAAAAGGATTCCGGAGAGAATTATT GAACATGCAGTGCGTGGCATGCTTCCTAAGGGCAGAgacatatggaacacaacatggtacccta aggctgcagatcatgtaactactgagaagacatggtatgttgttgatgcaacagacaagattct aggtaggc
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: 357 Transcript exons: 31367938-31368123,31368405-31368575 GACATATGGAACACAACATGGTACCCTAAGGCTGCAGATCATGTAACTACTGAGAAGACATGGT ATGTTGTTGATGCAACAGACAAGATTCTAGGTAGGCTTGCATCCACCATTGCAGTACACATCAG AGGAAAGAATGAGGCCACATACACTCCAAGTGTGGACATGGGGGCTTTTGTTGTTGTGGTTAAT GCAGAGAAGGTTGCTGTTTCTGGCAAAAAGCGGTCACAGAAGCTCTACAGGAGGCACTCTGGAC GGCCTGGTGGAATGAAAGAAGAAACTTTTGATCAGCTTCAGAAAAGGATTCCGGAGAGAATTAT TGAACATGCAGTGCGTGGCATGCTTCCTAAGGGCAGA
Genomic sequence	GACATATGGAACACAACATGGTACCCTAAGGCTGCAGATCATGTAACTACTGAGAAGACATGGT ATGTTGTTGATGCAACAGACAAGATTCTAGGTAGGCTTGCATCCACCATTGCAGTACACATCAG AGGAAAGAATGAGGCCACATACACTCCAAGTGTGGACATGGGGGCTTTTGTTGTTGTGGTATGT ATGTTTCTTGAAATTAATTTATAAAGTTAAATAGTGCACACAATAAGATCCTCTGTAGTCCCAC AAAAGGAAAAGAGGTTTAGCAGCACATACAAATAAGCACCAAAAGGTATCTGGAAGCTGAGGTC CACCTGAAGGCATTTTGAAGCTGATTTCATGTATATATATTTATGTTACTGTGTGCTTTTAATA CTAATGCATCTCTGAAGAGTAATTGCTACGCATATACTATTGTAAGTTCCTGAACTACCATGCT GAACTCTATGTTCACATAGGTTAATGCAGAGAAGGTTGCTGTTTCTGGCAAAAAGCGGTCACAG AAGCTCTACAGGAGGCACTCTGGACGGCCTGGTGGAATGAAAGAAGAAACTTTTGATCAGCTTC AGAAAAGGATTCCGGAGAGAATTATTGAACATGCAGTGCGTGGCATGCTTCCTAAGGGCAGA

			
						 Conservation Information
					
						Conserved circRNAs
						
							zma_circ_001498 						
					
						PMCS
						0.598565788

Conservation Information
Conserved circRNAs	zma_circ_001498
PMCS	0.598565788

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							31368104-31368572(+)
31368545-31367980(+)
31367981-31368446(-)
31367944-31368514(-)
						
						Potential amino acid sequence
						
							MGAFVVVVNAEKVAVSGKKRSQKLYRRHSGRPGGMKEETFDQLQKRIPERIIEHAVRGMLPKGR
DIWNTTWYPKAADHVTTEKTWYVVDATDKILGRLASTIAVHIRGKNEATYTPSVDMGAFVVVVN
AEKVAVSGKKRSQKLYRRHSGRPGGMKEETFDQLQKRIPERIIEHAVRGMLPKGRDIWNTTWYP
KAADHVTTEKTWYVVDATDKILGRLASTIAVHIRGKNEATYTPSVDMGAFVVVVNAEKVAVSGK
KRSQKLYRRHSGRPGGMKEETFDQLQKRIPERIIEHAVRGMLPKGRDIWNTTWYPKAADHVTTE
KTWYVVDATDKILGRLASTIAVHIRGKNEATYTPSVDMGAFVVVVNAEKVAVSGKKRSQKLYRR
HSGRPGGMKEETFDQLQKRIPERIIEHAVRGMLPKGR(+)
MQCVACFLRAETYGTQHGTLRLQIM*(+)
MICSLRVPCCVPYVSALRKHATHCMFNNSLRNPFLKLIKSFFFHSTRPSRVPPVELL*(-)
MSLPLGSMPRTACSIILSGILF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	31368104-31368572(+) 31368545-31367980(+) 31367981-31368446(-) 31367944-31368514(-)
Potential amino acid sequence	MGAFVVVVNAEKVAVSGKKRSQKLYRRHSGRPGGMKEETFDQLQKRIPERIIEHAVRGMLPKGR DIWNTTWYPKAADHVTTEKTWYVVDATDKILGRLASTIAVHIRGKNEATYTPSVDMGAFVVVVN AEKVAVSGKKRSQKLYRRHSGRPGGMKEETFDQLQKRIPERIIEHAVRGMLPKGRDIWNTTWYP KAADHVTTEKTWYVVDATDKILGRLASTIAVHIRGKNEATYTPSVDMGAFVVVVNAEKVAVSGK KRSQKLYRRHSGRPGGMKEETFDQLQKRIPERIIEHAVRGMLPKGRDIWNTTWYPKAADHVTTE KTWYVVDATDKILGRLASTIAVHIRGKNEATYTPSVDMGAFVVVVNAEKVAVSGKKRSQKLYRR HSGRPGGMKEETFDQLQKRIPERIIEHAVRGMLPKGR(+) MQCVACFLRAETYGTQHGTLRLQIM(+) MICSLRVPCCVPYVSALRKHATHCMFNNSLRNPFLKLIKSFFFHSTRPSRVPPVELL(-) MSLPLGSMPRTACSIILSGILF*(-)
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 Os01g0749200_circ_g.1

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