Plant Circular RNA Database

Detail information of BGIOSGA004145_circ_g.3

			
						 General Information
					
						CircRNA Name
						BGIOSGA004145_circ_g.3
					
						ID in PlantcircBase
						osi_circ_002270
					
						Alias
						1:30026325|30027031
					
						Organism
						
							Oryza sativa ssp. indica						
					
						Position
						
							chr1: 30026325-30027031  JBrowse»						
					
						Reference genome
						
							Oryza_indica.ASM465v1.42						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							BGIOSGA004145						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							BGIOSGA004145_circ_g.1 BGIOSGA004145_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						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
						BGIOSGA004145-TA:2

General Information
CircRNA Name	BGIOSGA004145_circ_g.3
ID in PlantcircBase	osi_circ_002270
Alias	1:30026325\|30027031
Organism	Oryza sativa ssp. indica
Position	chr1: 30026325-30027031 JBrowse»
Reference genome	Oryza_indica.ASM465v1.42
Type	e-circRNA
Identification method	find_circ
Parent gene	BGIOSGA004145
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	BGIOSGA004145_circ_g.1 BGIOSGA004145_circ_g.2
Support reads	NA
Tissues	leaf
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	BGIOSGA004145-TA: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  
						
							ATGCGTCAAAAGCAGAAGTTCATCACCCAGAGATACTTGTTGACCATGATGTGTACCTACCGCC
TTCTCCAAGCTCTCATGATTCCCATGAGAGGTTTTGtgagtactctatgcaactgaatgcttct
cgcatcaaagtgcttcaagctcaggatgatttggttaattccatgaaagaggatgctacaaagc
aactcctg

						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
						
							TGAGTACTCTATGCAACTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCAGGATGATTTGGTT
AATTCCATGAAAGAGGATGCTACAAAGCAACTCCTGCGTGTCAGCCACAACCACCATGAATACA
AGAACCTTTTGAAAGAACTCGTCGTTCAGGTTTGTATGAAATGTTGAATACATCATCTGCTAGA
TTCTTATCCATTAAGCCTTTTTGAGCGATCCTTCTGATAATTGTGGACCCCAAGAGGGTTTCAC
CTATATAGTTAAGTTCGATACGCAGAACTGAATTATTGGATATTGAAGTGTTAAATCACATTGT
AGTTTTGCAACTCTAACTGCATGCACAAAAGAGCTAGTGCTAAAAGAACATCTGTTTATGATTC
ACCTTTAAACTTCTCTTATGGACGTGCCAATTTAATTGATGGAATTAAGTTTGAAATGCCATCT
CCTTGTTTGTTCACTACTGTTATTAACAAAATAATCATTCATCATATTGACTGGAAATACAGGG
TTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAAGACCATCATCATGTG
GAATCTGTACTGCATTCAGCAAAGAATGAATATGCGTCAAAAGCAGAAGTTCATCACCCAGAGA
TACTTGTTGACCATGATGTGTACCTACCGCCTTCTCCAAGCTCTCATGATTCCCATGAGAGGTT
TTG

Sequences
Splice junction sequence	ATGCGTCAAAAGCAGAAGTTCATCACCCAGAGATACTTGTTGACCATGATGTGTACCTACCGCC TTCTCCAAGCTCTCATGATTCCCATGAGAGGTTTTGtgagtactctatgcaactgaatgcttct cgcatcaaagtgcttcaagctcaggatgatttggttaattccatgaaagaggatgctacaaagc aactcctg
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	TGAGTACTCTATGCAACTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCAGGATGATTTGGTT AATTCCATGAAAGAGGATGCTACAAAGCAACTCCTGCGTGTCAGCCACAACCACCATGAATACA AGAACCTTTTGAAAGAACTCGTCGTTCAGGTTTGTATGAAATGTTGAATACATCATCTGCTAGA TTCTTATCCATTAAGCCTTTTTGAGCGATCCTTCTGATAATTGTGGACCCCAAGAGGGTTTCAC CTATATAGTTAAGTTCGATACGCAGAACTGAATTATTGGATATTGAAGTGTTAAATCACATTGT AGTTTTGCAACTCTAACTGCATGCACAAAAGAGCTAGTGCTAAAAGAACATCTGTTTATGATTC ACCTTTAAACTTCTCTTATGGACGTGCCAATTTAATTGATGGAATTAAGTTTGAAATGCCATCT CCTTGTTTGTTCACTACTGTTATTAACAAAATAATCATTCATCATATTGACTGGAAATACAGGG TTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAAGACCATCATCATGTG GAATCTGTACTGCATTCAGCAAAGAATGAATATGCGTCAAAAGCAGAAGTTCATCACCCAGAGA TACTTGTTGACCATGATGTGTACCTACCGCCTTCTCCAAGCTCTCATGATTCCCATGAGAGGTT TTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_003086* 						
					
						PMCS

Conservation Information
Conserved circRNAs	osa_circ_003086*
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30026917-30026990(-)
30026336-30027028(+)
30026897-30026341(+)
						
						Potential amino acid sequence
						
							MQYRFHMMMVFFAATEKYRWLFQPKQTLNDEFFQKVLVFMVVVADTQELLCSILFHGINQIILS
LKHFDARSIQLHRVLTKPLMGIMRAWRRR*(-)
MQLNASRIKVLQAQDDLVNSMKEDATKQLLRVSHNHHEYKNLLKELVVQGLLRLKEPAVLLRCR
KEDHHHVESVLHSAKNEYASKAEVHHPEILVDHDVYLPPSPSSHDSHERFCEYSMQLNASRIKV
LQAQDDLVNSMKEDATKQLLRVSHNHHEYKNLLKELVVQGLLRLKEPAVLLRCRKEDHHHVESV
LHSAKNEYASKAEVHHPEILVDHDVYLPPSPSSHDSHERFCEYSMQLNASRIKVLQAQDDLVNS
MKEDATKQLLRVSHNHHEYKNLLKELVVQGLLRLKEPAVLLRCRKEDHHHVESVLHSAKNEYAS
KAEVHHPEILVDHDVYLPPSPSSHDSHERFCEYSMQLNASRIKVLQAQDDLVNSMKEDATKQLL
RVSHNHHEYKNLLKELVVQGLLRLKEPAVLLRCRKEDHHHVESVLHSAKNEYASKAEVHHPEIL
VDHDVYLPPSPSSHDSHERF(+)
MWNLYCIQQRMNMRQKQKFITQRYLLTMMCTYRLLQALMIPMRGFVSTLCN*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	30026917-30026990(-) 30026336-30027028(+) 30026897-30026341(+)
Potential amino acid sequence	MQYRFHMMMVFFAATEKYRWLFQPKQTLNDEFFQKVLVFMVVVADTQELLCSILFHGINQIILS LKHFDARSIQLHRVLTKPLMGIMRAWRRR(-) MQLNASRIKVLQAQDDLVNSMKEDATKQLLRVSHNHHEYKNLLKELVVQGLLRLKEPAVLLRCR KEDHHHVESVLHSAKNEYASKAEVHHPEILVDHDVYLPPSPSSHDSHERFCEYSMQLNASRIKV LQAQDDLVNSMKEDATKQLLRVSHNHHEYKNLLKELVVQGLLRLKEPAVLLRCRKEDHHHVESV LHSAKNEYASKAEVHHPEILVDHDVYLPPSPSSHDSHERFCEYSMQLNASRIKVLQAQDDLVNS MKEDATKQLLRVSHNHHEYKNLLKELVVQGLLRLKEPAVLLRCRKEDHHHVESVLHSAKNEYAS KAEVHHPEILVDHDVYLPPSPSSHDSHERFCEYSMQLNASRIKVLQAQDDLVNSMKEDATKQLL RVSHNHHEYKNLLKELVVQGLLRLKEPAVLLRCRKEDHHHVESVLHSAKNEYASKAEVHHPEIL VDHDVYLPPSPSSHDSHERF(+) MWNLYCIQQRMNMRQKQKFITQRYLLTMMCTYRLLQALMIPMRGFVSTLCN(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Huang et al., 2021

circRNA

Detail information of BGIOSGA004145_circ_g.3

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