Plant Circular RNA Database

Detail information of Os06g0178900_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os06g0178900_circ_g.3
					
						ID in PlantcircBase
						osa_circ_029898
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr6: 3922004-3922988  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os06g0178900						
					
						Parent gene annotation
						
							Vacuolar H+-pyrophosphatase (EC 3.6.1.1) (Ovp2). (Os06t0178900-0
1)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						1
					
						Tissues
						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
						Os06t0178950-00:3
Os06t0178900-01:3
Os06t0178950-00:3

General Information
CircRNA Name	Os06g0178900_circ_g.3
ID in PlantcircBase	osa_circ_029898
Alias	NA
Organism	Oryza sativa
Position	chr6: 3922004-3922988 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os06g0178900
Parent gene annotation	Vacuolar H+-pyrophosphatase (EC 3.6.1.1) (Ovp2). (Os06t0178900-0 1)
Parent gene strand	+
Alternative splicing	NA
Support reads	1
Tissues	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	Os06t0178950-00:3 Os06t0178900-01:3 Os06t0178950-00:3

			
						 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  
						
							TGCTGGTGGTATTGCCGAGATGGCTGGTATGAGCCACAGAATCCGTGAGAGAACTGATGCCCTT
GATGCTGCTGGCAACACAACTGCTGCTATTGGGAAGgtgattgctgacaatgtcggtgacaatg
ttggtgatattgctggaatgggatcagatctctttgggtcatacgccgaatcatcctgtgctgc
tcttgttg

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							GTGATTGCTGACAATGTCGGTGACAATGTTGGTGATATTGCTGGAATGGGATCAGATCTCTTTG
GGTCATACGCCGAATCATCCTGTGCTGCTCTTGTTGTTGCATCTATCTCATCTTTTGGAATCAA
CCATGATTTCACTGGGATGTGCTACCCACTGCTTGTCAGCTCTGTTGGCATCATTGTTTGTTTG
ATCACCACACTCTTTGCAACTGATTTCTTTGAGATCAAGGCAGTGAAAGAAATTGAACCTGCTC
TGAAGAAGCAGCTCATCATCTCCACTGCTTTGATGACTGTTGGTATTGCAATAATCAGCTGGTT
GGCCCTTCCAGCAAAGTTCACCATCTTCAATTTTGGTGCTCAGAAGGAAGTTACCAACTGGTAA
ACTACTTGTCTAACTTTCTTTGTTTGTGAAATGTTGTCTAGTTTTGTTATTTGTTTGTGAAATG
TATTCTTTCTGATTAATTTGCTGTGGTTTCACAGGGGCTTGTTCTTCTGCGTTGCAATTGGTCT
GTGGGCTGGTCTGATCATTGGTTTTGTGACAGAGTACTACACTAGCAATGCATACAGGTAAGAA
ACCTATTAGTTTCCAATTATGATGTCTTTCACCATTGTTACATTACATGTTTTAATCCCTACTG
CTTCTTTTTGGCAGCCCTGTGCAAGATGTTGCAGATTCCTGCAGAACTGGTGCTGCCACTAATG
TCATATTTGGTCTTGCTCTGGGATACAAATCAGTTATCATCCCAATTTTTGCTATTGCTGTCAG
CATATATGTTAGTTTCTCTATTGCTGCAATGTACGGCATAGCCGTTGCCGCTCTTGGCATGCTA
AGCACCATTGCAACAGGCCTTGCCATTGATGCTTATGGTCCTATCAGTGACAATGCTGGTGGTA
TTGCCGAGATGGCTGGTATGAGCCACAGAATCCGTGAGAGAACTGATGCCCTTGATGCTGCTGG
CAACACAACTGCTGCTATTGGGAAG

Sequences
Splice junction sequence	TGCTGGTGGTATTGCCGAGATGGCTGGTATGAGCCACAGAATCCGTGAGAGAACTGATGCCCTT GATGCTGCTGGCAACACAACTGCTGCTATTGGGAAGgtgattgctgacaatgtcggtgacaatg ttggtgatattgctggaatgggatcagatctctttgggtcatacgccgaatcatcctgtgctgc tcttgttg
Assembled circRNA sequence	NA 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	NA
Genomic sequence	GTGATTGCTGACAATGTCGGTGACAATGTTGGTGATATTGCTGGAATGGGATCAGATCTCTTTG GGTCATACGCCGAATCATCCTGTGCTGCTCTTGTTGTTGCATCTATCTCATCTTTTGGAATCAA CCATGATTTCACTGGGATGTGCTACCCACTGCTTGTCAGCTCTGTTGGCATCATTGTTTGTTTG ATCACCACACTCTTTGCAACTGATTTCTTTGAGATCAAGGCAGTGAAAGAAATTGAACCTGCTC TGAAGAAGCAGCTCATCATCTCCACTGCTTTGATGACTGTTGGTATTGCAATAATCAGCTGGTT GGCCCTTCCAGCAAAGTTCACCATCTTCAATTTTGGTGCTCAGAAGGAAGTTACCAACTGGTAA ACTACTTGTCTAACTTTCTTTGTTTGTGAAATGTTGTCTAGTTTTGTTATTTGTTTGTGAAATG TATTCTTTCTGATTAATTTGCTGTGGTTTCACAGGGGCTTGTTCTTCTGCGTTGCAATTGGTCT GTGGGCTGGTCTGATCATTGGTTTTGTGACAGAGTACTACACTAGCAATGCATACAGGTAAGAA ACCTATTAGTTTCCAATTATGATGTCTTTCACCATTGTTACATTACATGTTTTAATCCCTACTG CTTCTTTTTGGCAGCCCTGTGCAAGATGTTGCAGATTCCTGCAGAACTGGTGCTGCCACTAATG TCATATTTGGTCTTGCTCTGGGATACAAATCAGTTATCATCCCAATTTTTGCTATTGCTGTCAG CATATATGTTAGTTTCTCTATTGCTGCAATGTACGGCATAGCCGTTGCCGCTCTTGGCATGCTA AGCACCATTGCAACAGGCCTTGCCATTGATGCTTATGGTCCTATCAGTGACAATGCTGGTGGTA TTGCCGAGATGGCTGGTATGAGCCACAGAATCCGTGAGAGAACTGATGCCCTTGATGCTGCTGG CAACACAACTGCTGCTATTGGGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.52374055

Conservation Information
Conserved circRNAs	NA
PMCS	0.52374055

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3922050-3922985(+)
3922111-3922980(-)
						
						Potential amino acid sequence
						
							MGSDLFGSYAESSCAALVVASISSFGINHDFTGMCYPLLVSSVGIIVCLITTLFATDFFEIKAV
KEIEPALKKQLIISTALMTVGIAIISWLALPAKFTIFNFGAQKEVTNWGLFFCVAIGLWAGLII
GFVTEYYTSNAYSPVQDVADSCRTGAATNVIFGLALGYKSVIIPIFAIAVSIYVSFSIAAMYGI
AVAALGMLSTIATGLAIDAYGPISDNAGGIAEMAGMSHRIRERTDALDAAGNTTAAIGKVIADN
VGDNVGDIAGMGSDLFGSYAESSCAALVVASISSFGINHDFTGMCYPLLVSSVGIIVCLITTLF
ATDFFEIKAVKEIEPALKKQLIISTALMTVGIAIISWLALPAKFTIFNFGAQKEVTNWGLFFCV
AIGLWAGLIIGFVTEYYTSNAYSPVQDVADSCRTGAATNVIFGLALGYKSVIIPIFAIAVSIYV
SFSIAAMYGIAVAALGMLSTIATGLAIDAYGPISDNAGGIAEMAGMSHRIRERTDALDAAGNTT
AAIGKVIADNVGDNVGDIAGMGSDLFGSYAESSCAALVVASISSFGINHDFTGMCYPLLVSSVG
IIVCLITTLFATDFFEIKAVKEIEPALKKQLIISTALMTVGIAIISWLALPAKFTIFNFGAQKE
VTNWGLFFCVAIGLWAGLIIGFVTEYYTSNAYSPVQDVADSCRTGAATNVIFGLALGYKSVIIP
IFAIAVSIYVSFSIAAMYGIAVAALGMLSTIATGLAIDAYGPISDNAGGIAEMAGMSHRIRERT
DALDAAGNTTAAIGKVIADNVGDNVGDIAGMGSDLFGSYAESSCAALVVASISSFGINHDFTGM
CYPLLVSSVGIIVCLITTLFATDFFEIKAVKEIEPALKKQLIISTALMTVGIAIISWLALPAKF
TIFNFGAQKEVTNWGLFFCVAIGLWAGLIIGFVTEYYTSNAYSPVQDVADSCRTGAATNVIFGL
ALGYKSVIIPIFAIAVSIYVSFSIAAMYGIAVAALGMLSTIATGLAIDAYGPISDNAGGIAEMA
GMSHRIRERTDALDAAGNTTAAIGK(+)
MQQQEQHRMIRRMTQRDLIPFQQYHQHCHRHCQQSPSQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3922050-3922985(+) 3922111-3922980(-)
Potential amino acid sequence	MGSDLFGSYAESSCAALVVASISSFGINHDFTGMCYPLLVSSVGIIVCLITTLFATDFFEIKAV KEIEPALKKQLIISTALMTVGIAIISWLALPAKFTIFNFGAQKEVTNWGLFFCVAIGLWAGLII GFVTEYYTSNAYSPVQDVADSCRTGAATNVIFGLALGYKSVIIPIFAIAVSIYVSFSIAAMYGI AVAALGMLSTIATGLAIDAYGPISDNAGGIAEMAGMSHRIRERTDALDAAGNTTAAIGKVIADN VGDNVGDIAGMGSDLFGSYAESSCAALVVASISSFGINHDFTGMCYPLLVSSVGIIVCLITTLF ATDFFEIKAVKEIEPALKKQLIISTALMTVGIAIISWLALPAKFTIFNFGAQKEVTNWGLFFCV AIGLWAGLIIGFVTEYYTSNAYSPVQDVADSCRTGAATNVIFGLALGYKSVIIPIFAIAVSIYV SFSIAAMYGIAVAALGMLSTIATGLAIDAYGPISDNAGGIAEMAGMSHRIRERTDALDAAGNTT AAIGKVIADNVGDNVGDIAGMGSDLFGSYAESSCAALVVASISSFGINHDFTGMCYPLLVSSVG IIVCLITTLFATDFFEIKAVKEIEPALKKQLIISTALMTVGIAIISWLALPAKFTIFNFGAQKE VTNWGLFFCVAIGLWAGLIIGFVTEYYTSNAYSPVQDVADSCRTGAATNVIFGLALGYKSVIIP IFAIAVSIYVSFSIAAMYGIAVAALGMLSTIATGLAIDAYGPISDNAGGIAEMAGMSHRIRERT DALDAAGNTTAAIGKVIADNVGDNVGDIAGMGSDLFGSYAESSCAALVVASISSFGINHDFTGM CYPLLVSSVGIIVCLITTLFATDFFEIKAVKEIEPALKKQLIISTALMTVGIAIISWLALPAKF TIFNFGAQKEVTNWGLFFCVAIGLWAGLIIGFVTEYYTSNAYSPVQDVADSCRTGAATNVIFGL ALGYKSVIIPIFAIAVSIYVSFSIAAMYGIAVAALGMLSTIATGLAIDAYGPISDNAGGIAEMA GMSHRIRERTDALDAAGNTTAAIGK(+) MQQQEQHRMIRRMTQRDLIPFQQYHQHCHRHCQQSPSQ*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os06g0178900_circ_g.3

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