Plant Circular RNA Database

Detail information of BGIOSGA006535_circ_g.3

			
						 General Information
					
						CircRNA Name
						BGIOSGA006535_circ_g.3
					
						ID in PlantcircBase
						osi_circ_003889
					
						Alias
						2:15998211|16008607
					
						Organism
						
							Oryza sativa ssp. indica						
					
						Position
						
							chr2: 15998211-16008607  JBrowse»						
					
						Reference genome
						
							Oryza_indica.ASM465v1.42						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							BGIOSGA006535						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							BGIOSGA006535_circ_g.1 BGIOSGA006535_circ_g.2 BGIOSGA006535_circ_g.4 BGIOSGA006535_circ_g.5 BGIOSGA006535_circ_g.6 BGIOSGA006535_circ_g.7 BGIOSGA006535_circ_g.8 BGIOSGA006535_circ_g.9 BGIOSGA006535_circ_g.10 BGIOSGA006535_circ_g.11 BGIOSGA006535_circ_g.12 BGIOSGA006535_circ_g.13 BGIOSGA006535_circ_g.14 BGIOSGA006535_circ_g.15 BGIOSGA006535_circ_g.16 BGIOSGA006535_circ_g.17 BGIOSGA006535_circ_g.18 BGIOSGA006535_circ_g.19 BGIOSGA006535_circ_g.20 BGIOSGA006535_circ_g.21 BGIOSGA006535_circ_g.22 BGIOSGA006535_circ_g.23 						
					
						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  
						
							CT-AC							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
						BGIOSGA006535-TA:11

General Information
CircRNA Name	BGIOSGA006535_circ_g.3
ID in PlantcircBase	osi_circ_003889
Alias	2:15998211\|16008607
Organism	Oryza sativa ssp. indica
Position	chr2: 15998211-16008607 JBrowse»
Reference genome	Oryza_indica.ASM465v1.42
Type	e-circRNA
Identification method	find_circ
Parent gene	BGIOSGA006535
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	BGIOSGA006535_circ_g.1 BGIOSGA006535_circ_g.2 BGIOSGA006535_circ_g.4 BGIOSGA006535_circ_g.5 BGIOSGA006535_circ_g.6 BGIOSGA006535_circ_g.7 BGIOSGA006535_circ_g.8 BGIOSGA006535_circ_g.9 BGIOSGA006535_circ_g.10 BGIOSGA006535_circ_g.11 BGIOSGA006535_circ_g.12 BGIOSGA006535_circ_g.13 BGIOSGA006535_circ_g.14 BGIOSGA006535_circ_g.15 BGIOSGA006535_circ_g.16 BGIOSGA006535_circ_g.17 BGIOSGA006535_circ_g.18 BGIOSGA006535_circ_g.19 BGIOSGA006535_circ_g.20 BGIOSGA006535_circ_g.21 BGIOSGA006535_circ_g.22 BGIOSGA006535_circ_g.23
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	CT-AC 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	BGIOSGA006535-TA:11

			
						 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  
						
							GAGTAGCCATTGTGTTCAAACAAGCATTGTACTTGTGTGAATCCAAAGCATTTTCACTAAAAAG
CTCCTCCAATGCTCTTTCATGGTCAGTGGTGAAACCcttgaatacccatcatcagagccacgtg
gccgagcccatgtaccacctgtccgtctggatctcatagaatgagctggttggtgagctgggct
agttctga

						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
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	GAGTAGCCATTGTGTTCAAACAAGCATTGTACTTGTGTGAATCCAAAGCATTTTCACTAAAAAG CTCCTCCAATGCTCTTTCATGGTCAGTGGTGAAACCcttgaatacccatcatcagagccacgtg gccgagcccatgtaccacctgtccgtctggatctcatagaatgagctggttggtgagctgggct agttctga
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	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_014574* 						
					
						PMCS

Conservation Information
Conserved circRNAs	osa_circ_014574*
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							16008519-16008525(-)
16008505-15998274(+)
16008591-15998279(+)
						
						Potential amino acid sequence
						
							MATRISTVFASMREFPRVHYRVAKTIDASVTTTLRDLVPTKLAAAVWNCLSKLKTSIPDYPQTE
TCELLIVDRSVDQIAPIIHEWTYDAMCHDLLCMDGNKYVHEVPSKNGSSTEKKDVLLEDHDPIW
VELRHAHIADASERLHDKMSNFVSKNKAAQLQQARTGGEISNRDLQKMVQALPQYSDQIEKLSL
HVEIAGKLNSIIREQGLRDVGQLEQDLVFGDAGTKELINFLRTQLGVSRENKLRLLMIYAAINP
EKFESDKGEKLMQLAGLSTDDMIAVSNMRCLCGPDTKKSSGGGFTLKFDVHKKKHGLRKERTGE
ESTWALSRFYPVLEDLIEKLSKGELPKDEYYCMNDPSPSFHGLPMSSSVRTSPAHQPAHSMRSR
RTGGTWARPRGSDDGYSRVSPLTMKEHWRSFLVKMLWIHTSTMLV*(-)
MRVAIVFKQALYLCESKAFSLKSSSNALSWSVVKPLNTHHQSHVAEPMYHLSVWIS*(+)
MVSGETLEYPSSEPRGRAHVPPVRLDLIE*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	16008519-16008525(-) 16008505-15998274(+) 16008591-15998279(+)
Potential amino acid sequence	MATRISTVFASMREFPRVHYRVAKTIDASVTTTLRDLVPTKLAAAVWNCLSKLKTSIPDYPQTE TCELLIVDRSVDQIAPIIHEWTYDAMCHDLLCMDGNKYVHEVPSKNGSSTEKKDVLLEDHDPIW VELRHAHIADASERLHDKMSNFVSKNKAAQLQQARTGGEISNRDLQKMVQALPQYSDQIEKLSL HVEIAGKLNSIIREQGLRDVGQLEQDLVFGDAGTKELINFLRTQLGVSRENKLRLLMIYAAINP EKFESDKGEKLMQLAGLSTDDMIAVSNMRCLCGPDTKKSSGGGFTLKFDVHKKKHGLRKERTGE ESTWALSRFYPVLEDLIEKLSKGELPKDEYYCMNDPSPSFHGLPMSSSVRTSPAHQPAHSMRSR RTGGTWARPRGSDDGYSRVSPLTMKEHWRSFLVKMLWIHTSTMLV(-) MRVAIVFKQALYLCESKAFSLKSSSNALSWSVVKPLNTHHQSHVAEPMYHLSVWIS(+) MVSGETLEYPSSEPRGRAHVPPVRLDLIE*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Huang et al., 2021

circRNA

Detail information of BGIOSGA006535_circ_g.3

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