Plant Circular RNA Database

Detail information of Os04g0195000_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os04g0195000_circ_g.4
					
						ID in PlantcircBase
						osa_circ_023070
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 6516546-6517028  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0195000						
					
						Parent gene annotation
						
							Similar to Vacuolar assembly protein VPS41 homolog. (Os04t019500
0-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						1
					
						Tissues
						shoot
					
						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
						Os04t0195000-01:2

General Information
CircRNA Name	Os04g0195000_circ_g.4
ID in PlantcircBase	osa_circ_023070
Alias	NA
Organism	Oryza sativa
Position	chr4: 6516546-6517028 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0195000
Parent gene annotation	Similar to Vacuolar assembly protein VPS41 homolog. (Os04t019500 0-01)
Parent gene strand	+
Alternative splicing	NA
Support reads	1
Tissues	shoot
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	Os04t0195000-01:2

			
						 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  
						
							TGCTAGTAAAAGTTGTGACAAAAGACATTTGTTGCATCTGTATTTACATGCTCTGTTTGAGACA
GACATGAATGCTGGAAAAGACTATCATGACATGCAGctcttgaagccagaagtattcgaattta
ttgagaagcacaacttgcatgatgccattcatgacaaggtatggttaaaattcccaaatgtagg
ataaaact

						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: 267
Transcript exons: 6516546-6516611,6516828-6517028
CTCTTGAAGCCAGAAGTATTCGAATTTATTGAGAAGCACAACTTGCATGATGCCATTCATGACA
AGGTTGTCAATCTTATGATATTGGATAGTAAAAGAACTGTAAACCTATTGATCCAGCATCGTGA
TACGATCCCCCCGAATGAAGTTGTAGGACAGTTGTTGCATGCTAGTAAAAGTTGTGACAAAAGA
CATTTGTTGCATCTGTATTTACATGCTCTGTTTGAGACAGACATGAATGCTGGAAAAGACTATC
ATGACATGCAG
						
						Genomic sequence
						
							CTCTTGAAGCCAGAAGTATTCGAATTTATTGAGAAGCACAACTTGCATGATGCCATTCATGACA
AGGTATGGTTAAAATTCCCAAATGTAGGATAAAACTGATCTCACTTGACTTTTTTTTTCAAGTT
TGCATTTGTGAATTGTCAAGTGTCATGGTAGCAATTGTCTAATAATGGTACTTACATATGGTTA
CAATGTAGTTGAACATGATAATATATTTTAGACAGAGACAGGCTTCAATAACCTCCATATATTC
ACTTATGGGCCTTGCGTATTTCGCAGGTTGTCAATCTTATGATATTGGATAGTAAAAGAACTGT
AAACCTATTGATCCAGCATCGTGATACGATCCCCCCGAATGAAGTTGTAGGACAGTTGTTGCAT
GCTAGTAAAAGTTGTGACAAAAGACATTTGTTGCATCTGTATTTACATGCTCTGTTTGAGACAG
ACATGAATGCTGGAAAAGACTATCATGACATGCAG

Sequences
Splice junction sequence	TGCTAGTAAAAGTTGTGACAAAAGACATTTGTTGCATCTGTATTTACATGCTCTGTTTGAGACA GACATGAATGCTGGAAAAGACTATCATGACATGCAGctcttgaagccagaagtattcgaattta ttgagaagcacaacttgcatgatgccattcatgacaaggtatggttaaaattcccaaatgtagg ataaaact
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: 267 Transcript exons: 6516546-6516611,6516828-6517028 CTCTTGAAGCCAGAAGTATTCGAATTTATTGAGAAGCACAACTTGCATGATGCCATTCATGACA AGGTTGTCAATCTTATGATATTGGATAGTAAAAGAACTGTAAACCTATTGATCCAGCATCGTGA TACGATCCCCCCGAATGAAGTTGTAGGACAGTTGTTGCATGCTAGTAAAAGTTGTGACAAAAGA CATTTGTTGCATCTGTATTTACATGCTCTGTTTGAGACAGACATGAATGCTGGAAAAGACTATC ATGACATGCAG
Genomic sequence	CTCTTGAAGCCAGAAGTATTCGAATTTATTGAGAAGCACAACTTGCATGATGCCATTCATGACA AGGTATGGTTAAAATTCCCAAATGTAGGATAAAACTGATCTCACTTGACTTTTTTTTTCAAGTT TGCATTTGTGAATTGTCAAGTGTCATGGTAGCAATTGTCTAATAATGGTACTTACATATGGTTA CAATGTAGTTGAACATGATAATATATTTTAGACAGAGACAGGCTTCAATAACCTCCATATATTC ACTTATGGGCCTTGCGTATTTCGCAGGTTGTCAATCTTATGATATTGGATAGTAAAAGAACTGT AAACCTATTGATCCAGCATCGTGATACGATCCCCCCGAATGAAGTTGTAGGACAGTTGTTGCAT GCTAGTAAAAGTTGTGACAAAAGACATTTGTTGCATCTGTATTTACATGCTCTGTTTGAGACAG ACATGAATGCTGGAAAAGACTATCATGACATGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.245327916

Conservation Information
Conserved circRNAs	NA
PMCS	0.245327916

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6516841-6517025(+)
6516607-6516974(-)
6516603-6517018(-)
						
						Potential amino acid sequence
						
							MILDSKRTVNLLIQHRDTIPPNEVVGQLLHASKSCDKRHLLHLYLHALFETDMNAGKDYHDMQL
LKPEVFEFIEKHNLHDAIHDKVVNLMILDSKRTVNLLIQHRDTIPPNEVVGQLLHASKSCDKRH
LLHLYLHALFETDMNAGKDYHDMQLLKPEVFEFIEKHNLHDAIHDKVVNLMILDSKRTVNLLIQ
HRDTIPPNEVVGQLLHASKSCDKRHLLHLYLHALFETDMNAGKDYHDMQLLKPEVFEFIEKHNL
HDAIHDKVVNLMILDSKRTVNLLIQHRDTIPPNEVVGQLLHASKSCDKRHLLHLYLHALFETDM
NAGKDYHDMQ(+)
MNGIMQVVLLNKFEYFWLQELHVMIVFSSIHVCLKQSM*(-)
MASCKLCFSINSNTSGFKSCMS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6516841-6517025(+) 6516607-6516974(-) 6516603-6517018(-)
Potential amino acid sequence	MILDSKRTVNLLIQHRDTIPPNEVVGQLLHASKSCDKRHLLHLYLHALFETDMNAGKDYHDMQL LKPEVFEFIEKHNLHDAIHDKVVNLMILDSKRTVNLLIQHRDTIPPNEVVGQLLHASKSCDKRH LLHLYLHALFETDMNAGKDYHDMQLLKPEVFEFIEKHNLHDAIHDKVVNLMILDSKRTVNLLIQ HRDTIPPNEVVGQLLHASKSCDKRHLLHLYLHALFETDMNAGKDYHDMQLLKPEVFEFIEKHNL HDAIHDKVVNLMILDSKRTVNLLIQHRDTIPPNEVVGQLLHASKSCDKRHLLHLYLHALFETDM NAGKDYHDMQ(+) MNGIMQVVLLNKFEYFWLQELHVMIVFSSIHVCLKQSM(-) MASCKLCFSINSNTSGFKSCMS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0195000_circ_g.4

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