Plant Circular RNA Database

Detail information of Os04g0433800_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0433800_circ_g.3
					
						ID in PlantcircBase
						osa_circ_023879
					
						Alias
						Os_ciR852
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 21552328-21553465  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os04g0433800						
					
						Parent gene annotation
						
							Similar to RECQ4A; ATP binding / ATP-dependent helicase/ helicas
e/ nucleic acid binding. (Os04t0433800-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0433800_circ_g.2 Os04g0433800_circ_g.4 Os04g0433800_circ_g.5 						
					
						Support reads
						32/5
					
						Tissues
						root/shoot, root
					
						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
						Os04t0433800-01:5

General Information
CircRNA Name	Os04g0433800_circ_g.3
ID in PlantcircBase	osa_circ_023879
Alias	Os_ciR852
Organism	Oryza sativa
Position	chr4: 21552328-21553465 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os04g0433800
Parent gene annotation	Similar to RECQ4A; ATP binding / ATP-dependent helicase/ helicas e/ nucleic acid binding. (Os04t0433800-01)
Parent gene strand	-
Alternative splicing	Os04g0433800_circ_g.2 Os04g0433800_circ_g.4 Os04g0433800_circ_g.5
Support reads	32/5
Tissues	root/shoot, root
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	Os04t0433800-01:5

			
						 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  
						
							AACAACCCTTTACCTGCAATAAATGCATGATCTGGTCTTGGATGAGCGATACGAGAGGAGAAAC
TACCAATGTAACGCCATTACAAATGAGTGCTGGAAGccttaatttagcagccactttctcacaa
tccatcctcgaaaggcaatatatgatgccgcattctttattatgatttgcatgtataaagttat
ggatatcc

									
								

					

						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: 132
Transcript exons: 21552328-21552372,21553379-21553465
CCTTAATTTAGCAGCCACTTTCTCACAATCCATCCTCGAAAGGCACTGCAATAAATGCATGATC
TGGTCTTGGATGAGCGATACGAGAGGAGAAACTACCAATGTAACGCCATTACAAATGAGTGCTG
GAAG
Transcript length: 624
Transcript exons: 21552328-21552463,21552540-21552691,21552765-21552885,21
553178-21553305,21553379-21553465
CCTTAATTTAGCAGCCACTTTCTCACAATCCATCCTCGAAAGGCAATATATGATGCCGCATTCT
TTATTATGATTTGCATGTATAAAGTTATGGATATCCTCGAGGCACTTCTTTGTCTTGGGCCATA
CAAAATACCTCAGATTTGGACGATTAAAACTTTGTCTGAAAATAATGCAGTTTGCAAGGCCTAG
AACTTGCACGACATCTTCCTTGACACTTGCAGTTGCTGTTGCAGTCAAGGCCAGGACTGGCGTC
TGCGGGAACTTCTGTTTTAAAATGCCTAGATGCTGGTAATCAGGTCGGAAATCATGACCCCACT
GGCTAACACAGTGGGCTTCATCAATGACAATTCTAGAGAGATGGCCTCGCGAATATAAATTTTC
CAATTGTCTCAACAGAGCATCACTCTTGGCTATCTTTTCAGGCGTAACATACAGTAACTTGTAC
GTGCATGTAGGAGACATTAATTCTCTTAATATCTCCTGCTGTTCTGACCACTCCATGCTGGCGC
TAAGGTAAGCTGCAGAAATATTTGCCTGCAATAAATGCATGATCTGGTCTTGGATGAGCGATAC
GAGAGGAGAAACTACCAATGTAACGCCATTACAAATGAGTGCTGGAAG
						
					

						Genomic sequence
						
							CCTTAATTTAGCAGCCACTTTCTCACAATCCATCCTCGAAAGGCAATATATGATGCCGCATTCT
TTATTATGATTTGCATGTATAAAGTTATGGATATCCTCGAGGCACTTCTTTGTCTTGGGCCATA
CAAAATACCTGCAAAAGTTGGGCTGAGATGGTCTGGTGCAATTGGAGTTGAATGTCAATGTCTT
CTGAATTCTGATAGACTTACCTCAGATTTGGACGATTAAAACTTTGTCTGAAAATAATGCAGTT
TGCAAGGCCTAGAACTTGCACGACATCTTCCTTGACACTTGCAGTTGCTGTTGCAGTCAAGGCC
AGGACTGGCGTCTGCGGGAACTTCTGTTTTAAAATGCCTAGATGCTGATGGATAAAGAACTGGA
TTAAAAGGTTGTCAATTATTTAACATGAAAATCTGCTTCCTGACAGAAAGTACCTGGTAATCAG
GTCGGAAATCATGACCCCACTGGCTAACACAGTGGGCTTCATCAATGACAATTCTAGAGAGATG
GCCTCGCGAATATAAATTTTCCAATTGTCTCAACAGAGCATCACTCCTGTACTCAGGAAATTAA
TGTGAGTTAGGCACATGAATTGGCAAAGCACACGTCACAAAAGAAAGGACTAATTGTGTGAGAA
GCTAATACAAGCTAAAGGTGTTGAATCTTCATAAAGAAAAACAAAGAAATGTAACCAATAGTCC
AATACTAGTGATCTGGAAATGCGAACTGCTGCATAGTGACAGCAGGTCATTATGAGCTTACTTA
TACTATATCAGAAAAGACTACCTTTCAAATAGTCAAGAAATCATATAACATGACTACGAATCAA
CAGCAGAATTCCACTTACTTGGCTATCTTTTCAGGCGTAACATACAGTAACTTGTACGTGCATG
TAGGAGACATTAATTCTCTTAATATCTCCTGCTGTTCTGACCACTCCATGCTGGCGCTAAGGTA
AGCTGCAGAAATATTTGCCTGTGATAAACAACACGTGAGCAATTAGAAAATCATCAAGAAATAA
GTAGAAGGAAACAAAACAACCCTTTACCTGCAATAAATGCATGATCTGGTCTTGGATGAGCGAT
ACGAGAGGAGAAACTACCAATGTAACGCCATTACAAATGAGTGCTGGAAG
						
					

			
		

Sequences
Splice junction sequence	AACAACCCTTTACCTGCAATAAATGCATGATCTGGTCTTGGATGAGCGATACGAGAGGAGAAAC TACCAATGTAACGCCATTACAAATGAGTGCTGGAAGccttaatttagcagccactttctcacaa tccatcctcgaaaggcaatatatgatgccgcattctttattatgatttgcatgtataaagttat ggatatcc
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: 132 Transcript exons: 21552328-21552372,21553379-21553465 CCTTAATTTAGCAGCCACTTTCTCACAATCCATCCTCGAAAGGCACTGCAATAAATGCATGATC TGGTCTTGGATGAGCGATACGAGAGGAGAAACTACCAATGTAACGCCATTACAAATGAGTGCTG GAAG Transcript length: 624 Transcript exons: 21552328-21552463,21552540-21552691,21552765-21552885,21 553178-21553305,21553379-21553465 CCTTAATTTAGCAGCCACTTTCTCACAATCCATCCTCGAAAGGCAATATATGATGCCGCATTCT TTATTATGATTTGCATGTATAAAGTTATGGATATCCTCGAGGCACTTCTTTGTCTTGGGCCATA CAAAATACCTCAGATTTGGACGATTAAAACTTTGTCTGAAAATAATGCAGTTTGCAAGGCCTAG AACTTGCACGACATCTTCCTTGACACTTGCAGTTGCTGTTGCAGTCAAGGCCAGGACTGGCGTC TGCGGGAACTTCTGTTTTAAAATGCCTAGATGCTGGTAATCAGGTCGGAAATCATGACCCCACT GGCTAACACAGTGGGCTTCATCAATGACAATTCTAGAGAGATGGCCTCGCGAATATAAATTTTC CAATTGTCTCAACAGAGCATCACTCTTGGCTATCTTTTCAGGCGTAACATACAGTAACTTGTAC GTGCATGTAGGAGACATTAATTCTCTTAATATCTCCTGCTGTTCTGACCACTCCATGCTGGCGC TAAGGTAAGCTGCAGAAATATTTGCCTGCAATAAATGCATGATCTGGTCTTGGATGAGCGATAC GAGAGGAGAAACTACCAATGTAACGCCATTACAAATGAGTGCTGGAAG
Genomic sequence	CCTTAATTTAGCAGCCACTTTCTCACAATCCATCCTCGAAAGGCAATATATGATGCCGCATTCT TTATTATGATTTGCATGTATAAAGTTATGGATATCCTCGAGGCACTTCTTTGTCTTGGGCCATA CAAAATACCTGCAAAAGTTGGGCTGAGATGGTCTGGTGCAATTGGAGTTGAATGTCAATGTCTT CTGAATTCTGATAGACTTACCTCAGATTTGGACGATTAAAACTTTGTCTGAAAATAATGCAGTT TGCAAGGCCTAGAACTTGCACGACATCTTCCTTGACACTTGCAGTTGCTGTTGCAGTCAAGGCC AGGACTGGCGTCTGCGGGAACTTCTGTTTTAAAATGCCTAGATGCTGATGGATAAAGAACTGGA TTAAAAGGTTGTCAATTATTTAACATGAAAATCTGCTTCCTGACAGAAAGTACCTGGTAATCAG GTCGGAAATCATGACCCCACTGGCTAACACAGTGGGCTTCATCAATGACAATTCTAGAGAGATG GCCTCGCGAATATAAATTTTCCAATTGTCTCAACAGAGCATCACTCCTGTACTCAGGAAATTAA TGTGAGTTAGGCACATGAATTGGCAAAGCACACGTCACAAAAGAAAGGACTAATTGTGTGAGAA GCTAATACAAGCTAAAGGTGTTGAATCTTCATAAAGAAAAACAAAGAAATGTAACCAATAGTCC AATACTAGTGATCTGGAAATGCGAACTGCTGCATAGTGACAGCAGGTCATTATGAGCTTACTTA TACTATATCAGAAAAGACTACCTTTCAAATAGTCAAGAAATCATATAACATGACTACGAATCAA CAGCAGAATTCCACTTACTTGGCTATCTTTTCAGGCGTAACATACAGTAACTTGTACGTGCATG TAGGAGACATTAATTCTCTTAATATCTCCTGCTGTTCTGACCACTCCATGCTGGCGCTAAGGTA AGCTGCAGAAATATTTGCCTGTGATAAACAACACGTGAGCAATTAGAAAATCATCAAGAAATAA GTAGAAGGAAACAAAACAACCCTTTACCTGCAATAAATGCATGATCTGGTCTTGGATGAGCGAT ACGAGAGGAGAAACTACCAATGTAACGCCATTACAAATGAGTGCTGGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005468* osi_circ_014378 						
					
						PMCS
						0.40586827

Conservation Information
Conserved circRNAs	osi_circ_005468* osi_circ_014378
PMCS	0.40586827

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21553389-21552330(+)
21553393-21552397(+)
21553395-21552330(-)
						
						Potential amino acid sequence
						
							MHDLVLDERYERRNYQCNAITNECWKP*(+)
MIWSWMSDTRGETTNVTPLQMSAGSLNLAATFSQSILERQYMMPHSLL*(+)
MHLLQANISAAYLSASMEWSEQQEILRELMSPTCTYKLLYVTPEKIAKSDALLRQLENLYSRGH
LSRIVIDEAHCVSQWGHDFRPDYQHLGILKQKFPQTPVLALTATATASVKEDVVQVLGLANCII
FRQSFNRPNLRYFVWPKTKKCLEDIHNFIHANHNKECGIIYCLSRMDCEKVAAKLRLPALICNG
VTLVVSPLVSLIQDQIMHLLQANISAAYLSASMEWSEQQEILRELMSPTCTYKLLYVTPEKIAK
SDALLRQLENLYSRGHLSRIVIDEAHCVSQWGHDFRPDYQHLGILKQKFPQTPVLALTATATAS
VKEDVVQVLGLANCIIFRQSFNRPNLRYFVWPKTKKCLEDIHNFIHANHNKECGIIYCLSRMDC
EKVAAKLRLPALICNGVTLVVSPLVSLIQDQIMHLLQANISAAYLSASMEWSEQQEILRELMSP
TCTYKLLYVTPEKIAKSDALLRQLENLYSRGHLSRIVIDEAHCVSQWGHDFRPDYQHLGILKQK
FPQTPVLALTATATASVKEDVVQVLGLANCIIFRQSFNRPNLRYFVWPKTKKCLEDIHNFIHAN
HNKECGIIYCLSRMDCEKVAAKLRLPALICNGVTLVVSPLVSLIQDQIMHLLQANISAAYLSAS
MEWSEQQEILRELMSPTCTYKLLYVTPEKIAKSDALLRQLENLYSRGHLSRIVIDEAHCVSQWG
HDFRPDYQHLGILKQKFPQTPVLALTATATASVKEDVVQVLGLANCIIFRQSFNRPNLRYFVWP
KTKKCLEDIHNFIHANHNKECGIIYCLSRMDCEKVAAKLR(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21553389-21552330(+) 21553393-21552397(+) 21553395-21552330(-)
Potential amino acid sequence	MHDLVLDERYERRNYQCNAITNECWKP(+) MIWSWMSDTRGETTNVTPLQMSAGSLNLAATFSQSILERQYMMPHSLL(+) MHLLQANISAAYLSASMEWSEQQEILRELMSPTCTYKLLYVTPEKIAKSDALLRQLENLYSRGH LSRIVIDEAHCVSQWGHDFRPDYQHLGILKQKFPQTPVLALTATATASVKEDVVQVLGLANCII FRQSFNRPNLRYFVWPKTKKCLEDIHNFIHANHNKECGIIYCLSRMDCEKVAAKLRLPALICNG VTLVVSPLVSLIQDQIMHLLQANISAAYLSASMEWSEQQEILRELMSPTCTYKLLYVTPEKIAK SDALLRQLENLYSRGHLSRIVIDEAHCVSQWGHDFRPDYQHLGILKQKFPQTPVLALTATATAS VKEDVVQVLGLANCIIFRQSFNRPNLRYFVWPKTKKCLEDIHNFIHANHNKECGIIYCLSRMDC EKVAAKLRLPALICNGVTLVVSPLVSLIQDQIMHLLQANISAAYLSASMEWSEQQEILRELMSP TCTYKLLYVTPEKIAKSDALLRQLENLYSRGHLSRIVIDEAHCVSQWGHDFRPDYQHLGILKQK FPQTPVLALTATATASVKEDVVQVLGLANCIIFRQSFNRPNLRYFVWPKTKKCLEDIHNFIHAN HNKECGIIYCLSRMDCEKVAAKLRLPALICNGVTLVVSPLVSLIQDQIMHLLQANISAAYLSAS MEWSEQQEILRELMSPTCTYKLLYVTPEKIAKSDALLRQLENLYSRGHLSRIVIDEAHCVSQWG HDFRPDYQHLGILKQKFPQTPVLALTATATASVKEDVVQVLGLANCIIFRQSFNRPNLRYFVWP KTKKCLEDIHNFIHANHNKECGIIYCLSRMDCEKVAAKLR(-)
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 Os04g0433800_circ_g.3

Address

Any questions?

Supported by