Plant Circular RNA Database

Detail information of Os01g0512100_circ_g.7

			
						 General Information
					
						CircRNA Name
						Os01g0512100_circ_g.7
					
						ID in PlantcircBase
						osa_circ_001908
					
						Alias
						Os_ciR2140
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 18047494-18048149  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, find_circ
					
						Parent gene
						
							Os01g0512100						
					
						Parent gene annotation
						
							Similar to Chaperone protein dnaJ 15 (Protein ALTERED RESPONSE T
O GRAVITY) (AtARG1) (AtJ15) (AtDjB15). (Os01t0512100-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0512100_circ_g.1 Os01g0512100_circ_g.2 Os01g0512100_circ_g.3 Os01g0512100_circ_g.4 Os01g0512100_circ_g.5 Os01g0512100_circ_g.6 						
					
						Support reads
						6/3
					
						Tissues
						root/shoot, root, seed
					
						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
						Os01t0512100-01:4

General Information
CircRNA Name	Os01g0512100_circ_g.7
ID in PlantcircBase	osa_circ_001908
Alias	Os_ciR2140
Organism	Oryza sativa
Position	chr1: 18047494-18048149 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, find_circ
Parent gene	Os01g0512100
Parent gene annotation	Similar to Chaperone protein dnaJ 15 (Protein ALTERED RESPONSE T O GRAVITY) (AtARG1) (AtJ15) (AtDjB15). (Os01t0512100-01)
Parent gene strand	+
Alternative splicing	Os01g0512100_circ_g.1 Os01g0512100_circ_g.2 Os01g0512100_circ_g.3 Os01g0512100_circ_g.4 Os01g0512100_circ_g.5 Os01g0512100_circ_g.6
Support reads	6/3
Tissues	root/shoot, root, seed
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	Os01t0512100-01:4

			
						 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  
						
							TCTTTTCAATTTGGAGAGAGCTTTGATCGAGTTAAATGGTGTGCAGGCTTTAGCGCGGTTTCAA
GAAGTGACCAACAGATACACCCAAGAAAAAGAAGCGgaagatagtcagaagactggtaaggtga
catctgcaggcatgtatttcttgcattttcaagtgtatcgtatggattcaacagtgaatgcggt
atgtatgt

						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: 402
Transcript exons: 18047494-18047583,18047667-18047775,18047850-18047998,18
048096-18048149
GAAGATAGTCAGAAGACTGGTAAGGTGACATCTGCAGGCATGTATTTCTTGCATTTTCAAGTGT
ATCGTATGGATTCAACAGTGAATGCGTTGGCAATGGCCAAGGATCCTGAGGCTGCATTCTTTAA
AAGGTTGGAAGGTCTCCAGCCGTGCGAAGTGTCGGCTCTCAAATCTGGAACTCATATATTTGCT
GTATACGGTGATAATTTTTTCAAGCCAGCTAGCTATACAATTGAAGCAATGTGTGCAAAGAGTT
ACGAAGACACAACACAGAGGCTAAAGGAAATAGAGTCTAAAATTCTAGAGAAGAGAAATGATTT
GCGCCAATTTGAAACTGAGTACAGAAAAGCTTTAGCGCGGTTTCAAGAAGTGACCAACAGATAC
ACCCAAGAAAAAGAAGCG
						
						Genomic sequence
						
							GAAGATAGTCAGAAGACTGGTAAGGTGACATCTGCAGGCATGTATTTCTTGCATTTTCAAGTGT
ATCGTATGGATTCAACAGTGAATGCGGTATGTATGTTCTGCTATATAGCTTTAGTTTTTATGCT
CTTTGGGCCTGATGTGATGTGAGACTTTGCTGCTTCCTACTACAGTTGGCAATGGCCAAGGATC
CTGAGGCTGCATTCTTTAAAAGGTTGGAAGGTCTCCAGCCGTGCGAAGTGTCGGCTCTCAAATC
TGGAACTCATATATTTGCTGTATACGGTCTGCAAACTTACTTTATCTGTTTATATGAATGACAT
ACCTCCGTTCTGATCCATCCTAATTAATATGTTCAGGTGATAATTTTTTCAAGCCAGCTAGCTA
TACAATTGAAGCAATGTGTGCAAAGAGTTACGAAGACACAACACAGAGGCTAAAGGAAATAGAG
TCTAAAATTCTAGAGAAGAGAAATGATTTGCGCCAATTTGAAACTGAGTACAGAAAAGTCAGCC
ACTACATCTTTTTCTACATAACACATGAAATATGTATTTAGTTTTCTTTTCAATTTGGAGAGAG
CTTTGATCGAGTTAAATGGTGTGCAGGCTTTAGCGCGGTTTCAAGAAGTGACCAACAGATACAC
CCAAGAAAAAGAAGCG

Sequences
Splice junction sequence	TCTTTTCAATTTGGAGAGAGCTTTGATCGAGTTAAATGGTGTGCAGGCTTTAGCGCGGTTTCAA GAAGTGACCAACAGATACACCCAAGAAAAAGAAGCGgaagatagtcagaagactggtaaggtga catctgcaggcatgtatttcttgcattttcaagtgtatcgtatggattcaacagtgaatgcggt atgtatgt
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: 402 Transcript exons: 18047494-18047583,18047667-18047775,18047850-18047998,18 048096-18048149 GAAGATAGTCAGAAGACTGGTAAGGTGACATCTGCAGGCATGTATTTCTTGCATTTTCAAGTGT ATCGTATGGATTCAACAGTGAATGCGTTGGCAATGGCCAAGGATCCTGAGGCTGCATTCTTTAA AAGGTTGGAAGGTCTCCAGCCGTGCGAAGTGTCGGCTCTCAAATCTGGAACTCATATATTTGCT GTATACGGTGATAATTTTTTCAAGCCAGCTAGCTATACAATTGAAGCAATGTGTGCAAAGAGTT ACGAAGACACAACACAGAGGCTAAAGGAAATAGAGTCTAAAATTCTAGAGAAGAGAAATGATTT GCGCCAATTTGAAACTGAGTACAGAAAAGCTTTAGCGCGGTTTCAAGAAGTGACCAACAGATAC ACCCAAGAAAAAGAAGCG
Genomic sequence	GAAGATAGTCAGAAGACTGGTAAGGTGACATCTGCAGGCATGTATTTCTTGCATTTTCAAGTGT ATCGTATGGATTCAACAGTGAATGCGGTATGTATGTTCTGCTATATAGCTTTAGTTTTTATGCT CTTTGGGCCTGATGTGATGTGAGACTTTGCTGCTTCCTACTACAGTTGGCAATGGCCAAGGATC CTGAGGCTGCATTCTTTAAAAGGTTGGAAGGTCTCCAGCCGTGCGAAGTGTCGGCTCTCAAATC TGGAACTCATATATTTGCTGTATACGGTCTGCAAACTTACTTTATCTGTTTATATGAATGACAT ACCTCCGTTCTGATCCATCCTAATTAATATGTTCAGGTGATAATTTTTTCAAGCCAGCTAGCTA TACAATTGAAGCAATGTGTGCAAAGAGTTACGAAGACACAACACAGAGGCTAAAGGAAATAGAG TCTAAAATTCTAGAGAAGAGAAATGATTTGCGCCAATTTGAAACTGAGTACAGAAAAGTCAGCC ACTACATCTTTTTCTACATAACACATGAAATATGTATTTAGTTTTCTTTTCAATTTGGAGAGAG CTTTGATCGAGTTAAATGGTGTGCAGGCTTTAGCGCGGTTTCAAGAAGTGACCAACAGATACAC CCAAGAAAAAGAAGCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_009632 						
					
						PMCS
						0.499071075

Conservation Information
Conserved circRNAs	osi_circ_009632
PMCS	0.499071075

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							18047534-18048146(+)
18047549-18048101(-)
18047699-18047945(-)
						
						Potential amino acid sequence
						
							MYFLHFQVYRMDSTVNALAMAKDPEAAFFKRLEGLQPCEVSALKSGTHIFAVYGDNFFKPASYT
IEAMCAKSYEDTTQRLKEIESKILEKRNDLRQFETEYRKALARFQEVTNRYTQEKEAEDSQKTG
KVTSAGMYFLHFQVYRMDSTVNALAMAKDPEAAFFKRLEGLQPCEVSALKSGTHIFAVYGDNFF
KPASYTIEAMCAKSYEDTTQRLKEIESKILEKRNDLRQFETEYRKALARFQEVTNRYTQEKEAE
DSQKTGKVTSAGMYFLHFQVYRMDSTVNALAMAKDPEAAFFKRLEGLQPCEVSALKSGTHIFAV
YGDNFFKPASYTIEAMCAKSYEDTTQRLKEIESKILEKRNDLRQFETEYRKALARFQEVTNRYT
QEKEAEDSQKTGKVTSAGMYFLHFQVYRMDSTVNALAMAKDPEAAFFKRLEGLQPCEVSALKSG
THIFAVYGDNFFKPASYTIEAMCAKSYEDTTQRLKEIESKILEKRNDLRQFETEYRKALARFQE
VTNRYTQEKEA(+)
MQEIHACRCHLTSLLTIFRFFFLGVSVGHFLKPR*(-)
MQPQDPWPLPTHSLLNPYDTLENARNTCLQMSPYQSSDYLPLLFLGCICWSLLETALKLFCTQF
QIGANHFSSLEF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	18047534-18048146(+) 18047549-18048101(-) 18047699-18047945(-)
Potential amino acid sequence	MYFLHFQVYRMDSTVNALAMAKDPEAAFFKRLEGLQPCEVSALKSGTHIFAVYGDNFFKPASYT IEAMCAKSYEDTTQRLKEIESKILEKRNDLRQFETEYRKALARFQEVTNRYTQEKEAEDSQKTG KVTSAGMYFLHFQVYRMDSTVNALAMAKDPEAAFFKRLEGLQPCEVSALKSGTHIFAVYGDNFF KPASYTIEAMCAKSYEDTTQRLKEIESKILEKRNDLRQFETEYRKALARFQEVTNRYTQEKEAE DSQKTGKVTSAGMYFLHFQVYRMDSTVNALAMAKDPEAAFFKRLEGLQPCEVSALKSGTHIFAV YGDNFFKPASYTIEAMCAKSYEDTTQRLKEIESKILEKRNDLRQFETEYRKALARFQEVTNRYT QEKEAEDSQKTGKVTSAGMYFLHFQVYRMDSTVNALAMAKDPEAAFFKRLEGLQPCEVSALKSG THIFAVYGDNFFKPASYTIEAMCAKSYEDTTQRLKEIESKILEKRNDLRQFETEYRKALARFQE VTNRYTQEKEA(+) MQEIHACRCHLTSLLTIFRFFFLGVSVGHFLKPR(-) MQPQDPWPLPTHSLLNPYDTLENARNTCLQMSPYQSSDYLPLLFLGCICWSLLETALKLFCTQF QIGANHFSSLEF(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os01g0512100_circ_g.7

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