Plant Circular RNA Database

Detail information of Os10g0573000_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os10g0573000_circ_g.3
					
						ID in PlantcircBase
						osa_circ_008123
					
						Alias
						Os10circ10502
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr10: 22751012-22752029  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl
					
						Parent gene
						
							Os10g0573000						
					
						Parent gene annotation
						
							Similar to Carbohydrate kinase-like protein. (Os10t0573000-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os10g0573000_circ_g.2 Os10g0573000_circ_g.4 						
					
						Support reads
						2/1
					
						Tissues
						leaf/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
						Os10t0573000-01:3

General Information
CircRNA Name	Os10g0573000_circ_g.3
ID in PlantcircBase	osa_circ_008123
Alias	Os10circ10502
Organism	Oryza sativa
Position	chr10: 22751012-22752029 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl
Parent gene	Os10g0573000
Parent gene annotation	Similar to Carbohydrate kinase-like protein. (Os10t0573000-01)
Parent gene strand	+
Alternative splicing	Os10g0573000_circ_g.2 Os10g0573000_circ_g.4
Support reads	2/1
Tissues	leaf/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	Os10t0573000-01:3

			
						 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  
						
							CCATCAAGCAAGCATGTGAAGATGCTCATAAGAATGGCTCACTTATTGCAGTTACAGCATCAGA
TGTGTCATGCATCAAGCGTTGCTACAATGATTTTTGgttgatttctcagggatggtggacgacg
agttccttcacagattgggcatacaaaagggtaccagaaaggttgtcaaccacgaggagagagg
gcgtgtct

									
								

					

						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: 593
Transcript exons: 22751012-22751277,22751390-22751507,22751821-22752029
GTTGATTTCTCAGGGATGGTGGACGACGAGTTCCTTCACAGATTGGGCATACAAAAGGGTACCA
GAAAGGTTGTCAACCACGAGGAGAGAGGGCGTGTCTTGCGCGCCATGGATGGTTGCAGCTACAA
GGCTGCCGCTGGAGGCTCACTGTCCAACTCGCTTGTCGCGCTATCAAGGCTTGGTAGTAGCCGC
TCCACTAACTACCCCGAGCTTAGAATCGCGATGGCTGGCAGTGTGGGCAGCGACCCACTTGGTA
GTTTTTACAGGGCAAAATTGCGCCGTGCTAATTTGCATTTCTTGTCTAAGCCGGTCAAAGATGG
GACTACTGGAACTGTGATTGTTCTAACAACTCCAGATGCACAACGAACTATGCTTGCATATCAG
GGAACATCGTCAACTTTGAGTTATGATTCAGATTTGGCCAGTCTAGTGTCCAAGTCAAATGTAG
TAATTGTGGAAGGCTACCTATTTGAGCTACCTCACACGATCGAAGCCATCAAGCAAGCATGTGA
AGATGCTCATAAGAATGGCTCACTTATTGCAGTTACAGCATCAGATGTGTCATGCATCAAGCGT
TGCTACAATGATTTTTG
						
					

						Genomic sequence
						
							GTTGATTTCTCAGGGATGGTGGACGACGAGTTCCTTCACAGATTGGGCATACAAAAGGGTACCA
GAAAGGTTGTCAACCACGAGGAGAGAGGGCGTGTCTTGCGCGCCATGGATGGTTGCAGCTACAA
GGCTGCCGCTGGAGGCTCACTGTCCAACTCGCTTGTCGCGCTATCAAGGCTTGGTAGTAGCCGC
TCCACTAACTACCCCGAGCTTAGAATCGCGATGGCTGGCAGTGTGGGCAGCGACCCACTTGGTA
GTTTTTACAGGTAGTTCACTAGTTTGACAACATATTTTTGCACGTACTGATGTCTTAATTGCTG
CACTAGAAGCTTCAGAGTGTTGGCTGACATCACACTGTTGGTTGAATTGTTCTATTAGGGCAAA
ATTGCGCCGTGCTAATTTGCATTTCTTGTCTAAGCCGGTCAAAGATGGGACTACTGGAACTGTG
ATTGTTCTAACAACTCCAGATGCACAACGAACTATGCTTGCATATCAGGTCAGTTGATATGTTT
GTACTTCAGGGTTGTTATTCCCCCTTCTAGGGACTTCTGTTGCAATATCAGACTAAATTTTAAT
TTTTGAAGATGAGTAGTTTAACCAGGTCTGCTTTTAGTATGAATGTATCAATGAGAACCACCAT
CAGATATCAACTTTACTTGACAGGTCTTATTACTTGTTAGCTGTACTTTTTGACTCATTGAACA
TTCACCGTGTATAATTTACTTACTGGACAACTATATAGAAGTGTTGCTGGCACTAATATAGGAG
TATGACCTTACTGTTCCCTTTTTGCGTGTGTGTATTTCCAGGGAACATCGTCAACTTTGAGTTA
TGATTCAGATTTGGCCAGTCTAGTGTCCAAGTCAAATGTAGTAATTGTGGAAGGCTACCTATTT
GAGCTACCTCACACGATCGAAGCCATCAAGCAAGCATGTGAAGATGCTCATAAGAATGGCTCAC
TTATTGCAGTTACAGCATCAGATGTGTCATGCATCAAGCGTTGCTACAATGATTTTTG
						
					

			
		

Sequences
Splice junction sequence	CCATCAAGCAAGCATGTGAAGATGCTCATAAGAATGGCTCACTTATTGCAGTTACAGCATCAGA TGTGTCATGCATCAAGCGTTGCTACAATGATTTTTGgttgatttctcagggatggtggacgacg agttccttcacagattgggcatacaaaagggtaccagaaaggttgtcaaccacgaggagagagg gcgtgtct
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: 593 Transcript exons: 22751012-22751277,22751390-22751507,22751821-22752029 GTTGATTTCTCAGGGATGGTGGACGACGAGTTCCTTCACAGATTGGGCATACAAAAGGGTACCA GAAAGGTTGTCAACCACGAGGAGAGAGGGCGTGTCTTGCGCGCCATGGATGGTTGCAGCTACAA GGCTGCCGCTGGAGGCTCACTGTCCAACTCGCTTGTCGCGCTATCAAGGCTTGGTAGTAGCCGC TCCACTAACTACCCCGAGCTTAGAATCGCGATGGCTGGCAGTGTGGGCAGCGACCCACTTGGTA GTTTTTACAGGGCAAAATTGCGCCGTGCTAATTTGCATTTCTTGTCTAAGCCGGTCAAAGATGG GACTACTGGAACTGTGATTGTTCTAACAACTCCAGATGCACAACGAACTATGCTTGCATATCAG GGAACATCGTCAACTTTGAGTTATGATTCAGATTTGGCCAGTCTAGTGTCCAAGTCAAATGTAG TAATTGTGGAAGGCTACCTATTTGAGCTACCTCACACGATCGAAGCCATCAAGCAAGCATGTGA AGATGCTCATAAGAATGGCTCACTTATTGCAGTTACAGCATCAGATGTGTCATGCATCAAGCGT TGCTACAATGATTTTTG
Genomic sequence	GTTGATTTCTCAGGGATGGTGGACGACGAGTTCCTTCACAGATTGGGCATACAAAAGGGTACCA GAAAGGTTGTCAACCACGAGGAGAGAGGGCGTGTCTTGCGCGCCATGGATGGTTGCAGCTACAA GGCTGCCGCTGGAGGCTCACTGTCCAACTCGCTTGTCGCGCTATCAAGGCTTGGTAGTAGCCGC TCCACTAACTACCCCGAGCTTAGAATCGCGATGGCTGGCAGTGTGGGCAGCGACCCACTTGGTA GTTTTTACAGGTAGTTCACTAGTTTGACAACATATTTTTGCACGTACTGATGTCTTAATTGCTG CACTAGAAGCTTCAGAGTGTTGGCTGACATCACACTGTTGGTTGAATTGTTCTATTAGGGCAAA ATTGCGCCGTGCTAATTTGCATTTCTTGTCTAAGCCGGTCAAAGATGGGACTACTGGAACTGTG ATTGTTCTAACAACTCCAGATGCACAACGAACTATGCTTGCATATCAGGTCAGTTGATATGTTT GTACTTCAGGGTTGTTATTCCCCCTTCTAGGGACTTCTGTTGCAATATCAGACTAAATTTTAAT TTTTGAAGATGAGTAGTTTAACCAGGTCTGCTTTTAGTATGAATGTATCAATGAGAACCACCAT CAGATATCAACTTTACTTGACAGGTCTTATTACTTGTTAGCTGTACTTTTTGACTCATTGAACA TTCACCGTGTATAATTTACTTACTGGACAACTATATAGAAGTGTTGCTGGCACTAATATAGGAG TATGACCTTACTGTTCCCTTTTTGCGTGTGTGTATTTCCAGGGAACATCGTCAACTTTGAGTTA TGATTCAGATTTGGCCAGTCTAGTGTCCAAGTCAAATGTAGTAATTGTGGAAGGCTACCTATTT GAGCTACCTCACACGATCGAAGCCATCAAGCAAGCATGTGAAGATGCTCATAAGAATGGCTCAC TTATTGCAGTTACAGCATCAGATGTGTCATGCATCAAGCGTTGCTACAATGATTTTTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_008739 						
					
						PMCS
						0.399971094

Conservation Information
Conserved circRNAs	osi_circ_008739
PMCS	0.399971094

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							22751028-22751457(+)
22751952-22751013(+)
						
						Potential amino acid sequence
						
							MVDDEFLHRLGIQKGTRKVVNHEERGRVLRAMDGCSYKAAAGGSLSNSLVALSRLGSSRSTNYP
ELRIAMAGSVGSDPLGSFYRAKLRRANLHFLSKPVKDGTTGTVIVLTTPDAQRTMLAYQGTSST
LSYDSDLASLVSKSNVVIVEGYLFELPHTIEAIKQACEDAHKNGSLIAVTASDVSCIKRCYNDF
WLISQGWWTTSSFTDWAYKRVPERLSTTRREGVSCAPWMVAATRLPLEAHCPTRLSRYQGLVVA
APLTTPSLESRWLAVWAATHLVVFTGQNCAVLICISCLSRSKMGLLEL*(+)
MLIRMAHLLQLQHQMCHASSVATMIFG*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	22751028-22751457(+) 22751952-22751013(+)
Potential amino acid sequence	MVDDEFLHRLGIQKGTRKVVNHEERGRVLRAMDGCSYKAAAGGSLSNSLVALSRLGSSRSTNYP ELRIAMAGSVGSDPLGSFYRAKLRRANLHFLSKPVKDGTTGTVIVLTTPDAQRTMLAYQGTSST LSYDSDLASLVSKSNVVIVEGYLFELPHTIEAIKQACEDAHKNGSLIAVTASDVSCIKRCYNDF WLISQGWWTTSSFTDWAYKRVPERLSTTRREGVSCAPWMVAATRLPLEAHCPTRLSRYQGLVVA APLTTPSLESRWLAVWAATHLVVFTGQNCAVLICISCLSRSKMGLLEL(+) MLIRMAHLLQLQHQMCHASSVATMIFG(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os10g0573000_circ_g.3

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