Plant Circular RNA Database

Detail information of BGIOSGA003599_circ_g.4

			
						 General Information
					
						CircRNA Name
						BGIOSGA003599_circ_g.4
					
						ID in PlantcircBase
						osi_circ_002090
					
						Alias
						1:19136470|19142410
					
						Organism
						
							Oryza sativa ssp. indica						
					
						Position
						
							chr1: 19136470-19142410  JBrowse»						
					
						Reference genome
						
							Oryza_indica.ASM465v1.42						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							BGIOSGA003599						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							BGIOSGA003599_circ_g.1 BGIOSGA003599_circ_g.2 BGIOSGA003599_circ_g.3 BGIOSGA003599_circ_g.5 BGIOSGA003599_circ_g.6 BGIOSGA003599_circ_g.7 BGIOSGA003599_circ_g.8 BGIOSGA003599_circ_g.9 						
					
						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
						BGIOSGA003599-TA:8

General Information
CircRNA Name	BGIOSGA003599_circ_g.4
ID in PlantcircBase	osi_circ_002090
Alias	1:19136470\|19142410
Organism	Oryza sativa ssp. indica
Position	chr1: 19136470-19142410 JBrowse»
Reference genome	Oryza_indica.ASM465v1.42
Type	e-circRNA
Identification method	find_circ
Parent gene	BGIOSGA003599
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	BGIOSGA003599_circ_g.1 BGIOSGA003599_circ_g.2 BGIOSGA003599_circ_g.3 BGIOSGA003599_circ_g.5 BGIOSGA003599_circ_g.6 BGIOSGA003599_circ_g.7 BGIOSGA003599_circ_g.8 BGIOSGA003599_circ_g.9
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	BGIOSGA003599-TA:8

			
						 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  
						
							GGAGATGAAGAAATATCAGAAGGACTTTTCGGGCTGGTGTGGTGAATGTAAACGTGAGAAGAAG
GAGAGGCAGATTCATGCTGTTAAAGCAACTAAGCTGgttcaaaggcacagagaatacagacaga
gaatactcaaccattataaggttagcgtttcagcatagctgacattattcgaattatctctaaa
tattttga

						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	GGAGATGAAGAAATATCAGAAGGACTTTTCGGGCTGGTGTGGTGAATGTAAACGTGAGAAGAAG GAGAGGCAGATTCATGCTGTTAAAGCAACTAAGCTGgttcaaaggcacagagaatacagacaga gaatactcaaccattataaggttagcgtttcagcatagctgacattattcgaattatctctaaa tattttga
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_001845* 						
					
						PMCS

Conservation Information
Conserved circRNAs	osa_circ_001845*
PMCS

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							19137552-19140017(-)
19137567-19142407(+)
19142389-19137644(+)
						
					

						Potential amino acid sequence
						
							MKWHPTLFTDLLSNQLCPFVPGTSCTLIMVEYSLSVFSVPLNQLSCFNSMNLPLLLLTFTFTTP
ARKVLLIFLHLPEHRASAPQKKIDSEPR*(-)
MRPSSFFLPTFLEAIRTNTEESFRSIMTEPVPGVYSFAMLQPNFCEMLLQEVENFEKWVHTMKF
KIMRPNTMNKYGAVLDDFGLEVMLNQFMEQFIAPMSTVLYPEVGGGTLDTHHAFVVEYGKDRDV
ELGFHVDDSEVTLNVCLGKQFSGGELYFRGIRCENHVNSETQHEEMFDYSHVPGRAVLHRGRHR
HGARPTSSGLRINLLLWCRSSVFREMKKYQKDFSGWCGECKREKKERQIHAVKATKLVQRHREY
RQRILNHYKSAAGSWYKRAQLVGQEVREECRVPLHKELYKMRPSSFFLPTFLEAIRTNTEESFR
SIMTEPVPGVYSFAMLQPNFCEMLLQEVENFEKWVHTMKFKIMRPNTMNKYGAVLDDFGLEVML
NQFMEQFIAPMSTVLYPEVGGGTLDTHHAFVVEYGKDRDVELGFHVDDSEVTLNVCLGKQFSGG
ELYFRGIRCENHVNSETQHEEMFDYSHVPGRAVLHRGRHRHGARPTSSGLRINLLLWCRSSVFR
EMKKYQKDFSGWCGECKREKKERQIHAVKATKLVQRHREYRQRILNHYKSAAGSWYKRAQLVGQ
EVREECRVPLHKELYKMRPSSFFLPTFLEAIRTNTEESFRSIMTEPVPGVYSFAMLQPNFCEML
LQEVENFEKWVHTMKFKIMRPNTMNKYGAVLDDFGLEVMLNQFMEQFIAPMSTVLYPEVGGGTL
DTHHAFVVEYGKDRDVELGFHVDDSEVTLNVCLGKQFSGGELYFRGIRCENHVNSETQHEEMFD
YSHVPGRAVLHRGRHRHGARPTSSGLRINLLLWCRSSVFREMKKYQKDFSGWCGECKREKKERQ
IHAVKATKLVQRHREYRQRILNHYKSAAGSWYKRAQLVGQEVREECRVPLHKELYKMRPSSFFL
PTFLEAIRTNTEESFRSIMTEPVPGVYSFAMLQPNFCEMLLQEVENFEKWVHTMKFKIMRPNTM
NKYGAVLDDFGLEVMLNQFMEQFIAPMSTVLYPEVGGGTLDTHHAFVVEYGKDRDVELGFHVDD
SEVTLNVCLGKQFSGGELYFRGIRCENHVNSETQHEEMFDYSHVPGRAVLHRGRHRHGARPTSS
GLRINLLLWCRSSVFREMKKYQKDFSGWCGECKREKKERQIHAVKATKL(+)
MLLKQLSWFKGTENTDREYSTIIRVQLVPGTKGHNWLDKRSVKSVGCHFIKSYTKCALHRSFYQ
HSLKLLGPIQKKALEAL*(+)
						
					

						Sponge-miRNAs
						
							osa-miR5083 						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	19137552-19140017(-) 19137567-19142407(+) 19142389-19137644(+)
Potential amino acid sequence	MKWHPTLFTDLLSNQLCPFVPGTSCTLIMVEYSLSVFSVPLNQLSCFNSMNLPLLLLTFTFTTP ARKVLLIFLHLPEHRASAPQKKIDSEPR(-) MRPSSFFLPTFLEAIRTNTEESFRSIMTEPVPGVYSFAMLQPNFCEMLLQEVENFEKWVHTMKF KIMRPNTMNKYGAVLDDFGLEVMLNQFMEQFIAPMSTVLYPEVGGGTLDTHHAFVVEYGKDRDV ELGFHVDDSEVTLNVCLGKQFSGGELYFRGIRCENHVNSETQHEEMFDYSHVPGRAVLHRGRHR HGARPTSSGLRINLLLWCRSSVFREMKKYQKDFSGWCGECKREKKERQIHAVKATKLVQRHREY RQRILNHYKSAAGSWYKRAQLVGQEVREECRVPLHKELYKMRPSSFFLPTFLEAIRTNTEESFR SIMTEPVPGVYSFAMLQPNFCEMLLQEVENFEKWVHTMKFKIMRPNTMNKYGAVLDDFGLEVML NQFMEQFIAPMSTVLYPEVGGGTLDTHHAFVVEYGKDRDVELGFHVDDSEVTLNVCLGKQFSGG ELYFRGIRCENHVNSETQHEEMFDYSHVPGRAVLHRGRHRHGARPTSSGLRINLLLWCRSSVFR EMKKYQKDFSGWCGECKREKKERQIHAVKATKLVQRHREYRQRILNHYKSAAGSWYKRAQLVGQ EVREECRVPLHKELYKMRPSSFFLPTFLEAIRTNTEESFRSIMTEPVPGVYSFAMLQPNFCEML LQEVENFEKWVHTMKFKIMRPNTMNKYGAVLDDFGLEVMLNQFMEQFIAPMSTVLYPEVGGGTL DTHHAFVVEYGKDRDVELGFHVDDSEVTLNVCLGKQFSGGELYFRGIRCENHVNSETQHEEMFD YSHVPGRAVLHRGRHRHGARPTSSGLRINLLLWCRSSVFREMKKYQKDFSGWCGECKREKKERQ IHAVKATKLVQRHREYRQRILNHYKSAAGSWYKRAQLVGQEVREECRVPLHKELYKMRPSSFFL PTFLEAIRTNTEESFRSIMTEPVPGVYSFAMLQPNFCEMLLQEVENFEKWVHTMKFKIMRPNTM NKYGAVLDDFGLEVMLNQFMEQFIAPMSTVLYPEVGGGTLDTHHAFVVEYGKDRDVELGFHVDD SEVTLNVCLGKQFSGGELYFRGIRCENHVNSETQHEEMFDYSHVPGRAVLHRGRHRHGARPTSS GLRINLLLWCRSSVFREMKKYQKDFSGWCGECKREKKERQIHAVKATKL(+) MLLKQLSWFKGTENTDREYSTIIRVQLVPGTKGHNWLDKRSVKSVGCHFIKSYTKCALHRSFYQ HSLKLLGPIQKKALEAL(+)
Sponge-miRNAs	osa-miR5083
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Huang et al., 2021

circRNA

Detail information of BGIOSGA003599_circ_g.4

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