Plant Circular RNA Database

Detail information of Os04g0349401_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0349401_circ_g.2
					
						ID in PlantcircBase
						osa_circ_023481
					
						Alias
						Os04circ03004/Os_ciR3901
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 16639509-16641971  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os04g0349401						
					
						Parent gene annotation
						
							Hypothetical conserved gene. (Os04t0349401-00)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0349401_circ_g.1 Os04g0349401_circ_g.3 Os04g0349401_circ_g.4 Os04g0349401_circ_g.5 						
					
						Support reads
						2/2
					
						Tissues
						leaf and panicle/root
					
						Exon boundary  
						
							No-No							"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
						Os04t0349401-00:4

General Information
CircRNA Name	Os04g0349401_circ_g.2
ID in PlantcircBase	osa_circ_023481
Alias	Os04circ03004/Os_ciR3901
Organism	Oryza sativa
Position	chr4: 16639509-16641971 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ui-circRNA
Identification method	SMALT, Segemehl, find_circ
Parent gene	Os04g0349401
Parent gene annotation	Hypothetical conserved gene. (Os04t0349401-00)
Parent gene strand	-
Alternative splicing	Os04g0349401_circ_g.1 Os04g0349401_circ_g.3 Os04g0349401_circ_g.4 Os04g0349401_circ_g.5
Support reads	2/2
Tissues	leaf and panicle/root
Exon boundary	No-No "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	Os04t0349401-00:4

			
						 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  
						
							CATATAGCTTATTACATCATGTCCATTGGACCATCAAATAATAGATTGTTAGATGTCGAATTTA
ATATGCAGCTTTTTCCGACAGTCTGCTGGACTGAAAaggtgaaggctataccaagatgcttgta
ttagtatactgcaagataatgtcaaatagcagtgtaaaaataagaacaaaacatcaaaaagaac
tcaaaatg

									
								

					

						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: 124
Transcript exons: ,16641849-16641971
CCAGATTCTTTCCCTCGAATTTCCATATAGCTTATTACATCATGTCCATTGGACCATCAAATAA
TAGATTGTTAGATGTCGAATTTAATATGCAGCTTTTTCCGACAGTCTGCTGGACTGAAA
						
					

						Genomic sequence
						
							AGGTGAAGGCTATACCAAGATGCTTGTATTAGTATACTGCAAGATAATGTCAAATAGCAGTGTA
AAAATAAGAACAAAACATCAAAAAGAACTCAAAATGTAAGATAGCAAGTATACCTGACCAAAAA
AAGGGCAATTGTTTTCTTCAGTAATGGCGATCATGTTTTCTTCTATGATGTGCCCCATCATGGT
ATATCTCACGCTGCCCCGTAGACGCCTCATCAATCATGCTTGTTGCAGGATCAACATCAGAATA
TGCGCTTTGGGGATCAGATCTATCACTGAACTTATCTTGAGTCACAGACACTGATCTATGCCGG
GTATGACTAGTTGTACTTACATCATTGCTTCTGACTCTTGACATGCGGTCATATTCTCTCTGAG
GACCATCTTGTACAACTGCTTGATTCAGAATAATAGTCTGACCCATTTTTGTTGTACTTATAAC
CATATTTCCTATGATCATCAGAATTTCTTTGGTGTCCGCTGTTCTCATGATGGTGAGAATACCT
TTGATCTACTGTGCTTTCTGAATCTTTAATACTTCTATTCTCATGATCAGATACTTTCTGGTAC
TGGCGTTGATGACTTCCATTTCTTAAGTCCTTATATGAATCCCTCGTGCCATGGTTCCTTGATG
AAACTATTCCAAAAGAATTAGCACATGGTAATTTTTCACAACTGACTGATGGAATACCAAAACT
GTCCTTACCATAAGAACTGCTTGTAGGATTAAAACTTCCTTGGTATGTGCCATCATGAGGACTA
TTCTTAAGCACACTCTGTGCAATATCACCAGGCACATCCAAATGGCAACCAATCCCTCCTGCCT
GTTTGATCTCTTCCATATGCTCATCAATTATGTCTCTTAAAATCTTCAACAGAGAAGGAAAAAA
AATTAAATCCATATATCGATCACATATTGCAGAATCAACTGAGTATAAGTAACATAACATGCAC
TGAAGGGTCATCTGAGTATATGACACATTGAACAATCTAGATGGTATAAGAATAATTAAATATG
AAATCTAAGCGTAACTAACTTGAGATTGAAAATGAATAAATAAATCAATTGAGATGATGTTCCC
TGACTTCGAACCCTAATAGAAAGTGAGCTGTCATCAACAAAAGAGAGTGTTGAGTAATGTTCCA
CCTGAAAAGTTACATAGACCCTCCATGTAAATCTGAATTATCATGGTCACAACACAACATTTGG
ACTGGCTTTTTGATAGTAACACACAGATAAAAATAATAATATGCTAGGAAATATTTTCAAAGAC
ATCTGATGGATTTGTTTTTCTTGTGATCAGTCACACAATCTTTTACTTATAATAATACCCAAGA
TTTCAAACGTTTGCAAGCAGGATCCCATAGAGAACTATATTTAGGGGCCATTGGACATACATAA
ATGATTCATATATCAGAAAACTTGAGGATGATAAAGACAAATGATATTTTTGAGAAACAAATCC
AAACGAACCTCTTTTGGATTTCTCTTCGCTTTCTTGCCACGGTACGACGTTCTTCTTCGCTTGT
AATCTCGCTCTTCAGCTAAAAGCTCCTCTCTAGTCTTGACTCTACCAAATTCCTTTTCAAGATG
GCAATAAAGAGAGCTAAGATACACTAAAATGATATTATGAGCACCATCTTGTACAGAAAACAAA
GTCAAGAGGATCAACACTATGTTCTTAATTTTTTTTTTAAGAAAATGTGCATTTAGATAGTAAA
TAACAAAGCAAAGAGATCAGAGCATGTTAGTCAAATGTTCAAATATAAAGTATCTACAGATCAT
TAAGGATCATAAAAACTATAAATGCAACTGTTTCATGAGTCAATATTTTTTTCTTAAGAGCTGT
TCAATAATAGGTACATACAACTCCTGGAACAACTAGAAAATATAAAAACATTGAGCATGAGCAT
GGTATCTACTATCTAGATATTAAAACCTACTACTGACAGAGTGGTTGCATGCCTTTACCTGGCT
ATCTACTCGGCGTGATATAATACCATCATACTCCAGAACAGCTCTGTAGTTTGGTCGTTTTGAT
CGCTCCTCGCGGCCTCGTTCCAGTGCTTTTGAATATTCCAGTAAACTACCAACAAATGAATATA
TGGGGTCATGGAAGGAAAAGCTTTGTGAAACCAAGCAGAAGTGCAAAACTAATCATATGCTGGG
AATGCAAATTACTGTGAGGGATCAGGCTGTTAAATATTATTAATAACTATTTTAATTATGTGCA
TTCATGACAGGCAGCCTACATGTAGCATAAAACCAATGTACTTGAATTCATATATATCAGAGCA
ACATATTTGAAACACAGATAACTTGTGATTACTAACCCAGATTCTTTCCCTCGAATTTCCATAT
AGCTTATTACATCATGTCCATTGGACCATCAAATAATAGATTGTTAGATGTCGAATTTAATATG
CAGCTTTTTCCGACAGTCTGCTGGACTGAAA
						
					

			
		

Sequences
Splice junction sequence	CATATAGCTTATTACATCATGTCCATTGGACCATCAAATAATAGATTGTTAGATGTCGAATTTA ATATGCAGCTTTTTCCGACAGTCTGCTGGACTGAAAaggtgaaggctataccaagatgcttgta ttagtatactgcaagataatgtcaaatagcagtgtaaaaataagaacaaaacatcaaaaagaac tcaaaatg
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: 124 Transcript exons: ,16641849-16641971 CCAGATTCTTTCCCTCGAATTTCCATATAGCTTATTACATCATGTCCATTGGACCATCAAATAA TAGATTGTTAGATGTCGAATTTAATATGCAGCTTTTTCCGACAGTCTGCTGGACTGAAA
Genomic sequence	AGGTGAAGGCTATACCAAGATGCTTGTATTAGTATACTGCAAGATAATGTCAAATAGCAGTGTA AAAATAAGAACAAAACATCAAAAAGAACTCAAAATGTAAGATAGCAAGTATACCTGACCAAAAA AAGGGCAATTGTTTTCTTCAGTAATGGCGATCATGTTTTCTTCTATGATGTGCCCCATCATGGT ATATCTCACGCTGCCCCGTAGACGCCTCATCAATCATGCTTGTTGCAGGATCAACATCAGAATA TGCGCTTTGGGGATCAGATCTATCACTGAACTTATCTTGAGTCACAGACACTGATCTATGCCGG GTATGACTAGTTGTACTTACATCATTGCTTCTGACTCTTGACATGCGGTCATATTCTCTCTGAG GACCATCTTGTACAACTGCTTGATTCAGAATAATAGTCTGACCCATTTTTGTTGTACTTATAAC CATATTTCCTATGATCATCAGAATTTCTTTGGTGTCCGCTGTTCTCATGATGGTGAGAATACCT TTGATCTACTGTGCTTTCTGAATCTTTAATACTTCTATTCTCATGATCAGATACTTTCTGGTAC TGGCGTTGATGACTTCCATTTCTTAAGTCCTTATATGAATCCCTCGTGCCATGGTTCCTTGATG AAACTATTCCAAAAGAATTAGCACATGGTAATTTTTCACAACTGACTGATGGAATACCAAAACT GTCCTTACCATAAGAACTGCTTGTAGGATTAAAACTTCCTTGGTATGTGCCATCATGAGGACTA TTCTTAAGCACACTCTGTGCAATATCACCAGGCACATCCAAATGGCAACCAATCCCTCCTGCCT GTTTGATCTCTTCCATATGCTCATCAATTATGTCTCTTAAAATCTTCAACAGAGAAGGAAAAAA AATTAAATCCATATATCGATCACATATTGCAGAATCAACTGAGTATAAGTAACATAACATGCAC TGAAGGGTCATCTGAGTATATGACACATTGAACAATCTAGATGGTATAAGAATAATTAAATATG AAATCTAAGCGTAACTAACTTGAGATTGAAAATGAATAAATAAATCAATTGAGATGATGTTCCC TGACTTCGAACCCTAATAGAAAGTGAGCTGTCATCAACAAAAGAGAGTGTTGAGTAATGTTCCA CCTGAAAAGTTACATAGACCCTCCATGTAAATCTGAATTATCATGGTCACAACACAACATTTGG ACTGGCTTTTTGATAGTAACACACAGATAAAAATAATAATATGCTAGGAAATATTTTCAAAGAC ATCTGATGGATTTGTTTTTCTTGTGATCAGTCACACAATCTTTTACTTATAATAATACCCAAGA TTTCAAACGTTTGCAAGCAGGATCCCATAGAGAACTATATTTAGGGGCCATTGGACATACATAA ATGATTCATATATCAGAAAACTTGAGGATGATAAAGACAAATGATATTTTTGAGAAACAAATCC AAACGAACCTCTTTTGGATTTCTCTTCGCTTTCTTGCCACGGTACGACGTTCTTCTTCGCTTGT AATCTCGCTCTTCAGCTAAAAGCTCCTCTCTAGTCTTGACTCTACCAAATTCCTTTTCAAGATG GCAATAAAGAGAGCTAAGATACACTAAAATGATATTATGAGCACCATCTTGTACAGAAAACAAA GTCAAGAGGATCAACACTATGTTCTTAATTTTTTTTTTAAGAAAATGTGCATTTAGATAGTAAA TAACAAAGCAAAGAGATCAGAGCATGTTAGTCAAATGTTCAAATATAAAGTATCTACAGATCAT TAAGGATCATAAAAACTATAAATGCAACTGTTTCATGAGTCAATATTTTTTTCTTAAGAGCTGT TCAATAATAGGTACATACAACTCCTGGAACAACTAGAAAATATAAAAACATTGAGCATGAGCAT GGTATCTACTATCTAGATATTAAAACCTACTACTGACAGAGTGGTTGCATGCCTTTACCTGGCT ATCTACTCGGCGTGATATAATACCATCATACTCCAGAACAGCTCTGTAGTTTGGTCGTTTTGAT CGCTCCTCGCGGCCTCGTTCCAGTGCTTTTGAATATTCCAGTAAACTACCAACAAATGAATATA TGGGGTCATGGAAGGAAAAGCTTTGTGAAACCAAGCAGAAGTGCAAAACTAATCATATGCTGGG AATGCAAATTACTGTGAGGGATCAGGCTGTTAAATATTATTAATAACTATTTTAATTATGTGCA TTCATGACAGGCAGCCTACATGTAGCATAAAACCAATGTACTTGAATTCATATATATCAGAGCA ACATATTTGAAACACAGATAACTTGTGATTACTAACCCAGATTCTTTCCCTCGAATTTCCATAT AGCTTATTACATCATGTCCATTGGACCATCAAATAATAGATTGTTAGATGTCGAATTTAATATG CAGCTTTTTCCGACAGTCTGCTGGACTGAAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_014257 						
					
						PMCS
						0.20536372

Conservation Information
Conserved circRNAs	osi_circ_014257
PMCS	0.20536372

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015

circRNA

Detail information of Os04g0349401_circ_g.2

Address

Any questions?

Supported by