Plant Circular RNA Database

Detail information of Os03g0417900_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os03g0417900_circ_g.4
					
						ID in PlantcircBase
						osa_circ_020319
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 17378717-17381701  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os03g0417900						
					
						Parent gene annotation
						
							Similar to ARE1-like protein. (Os03t0417900-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0417900_circ_g.3 Os03g0417900_circ_g.5 Os03g0417900_circ_g.6 						
					
						Support reads
						1
					
						Tissues
						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
						Os03t0417900-01:5

General Information
CircRNA Name	Os03g0417900_circ_g.4
ID in PlantcircBase	osa_circ_020319
Alias	NA
Organism	Oryza sativa
Position	chr3: 17378717-17381701 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os03g0417900
Parent gene annotation	Similar to ARE1-like protein. (Os03t0417900-01)
Parent gene strand	-
Alternative splicing	Os03g0417900_circ_g.3 Os03g0417900_circ_g.5 Os03g0417900_circ_g.6
Support reads	1
Tissues	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	Os03t0417900-01:5

			
						 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  
						
							ATTTATTATAACATTCACCTTGTTCATGGTATCAATATAAGCTGCACGAACTTCCGCATATATC
TCCTTAGCATGTTCCTTAAGAAAAACTATCGTGTACctgatgctgatgaattattcggatcata
agcattatgccgattgcgtcataacagttcaggagcacagcattgaaatgttcatcaacaactt
ggataggt

									
								

					

						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
						
							CTGATGCTGATGAATTATTCGGATCATAAGCATTATGCCGATTGCGTCATAACAGTTCAGGAGC
ACAGCATTGAAATGTTCATCAACAACTTGGATAGGTCCTAAGGGAAAAGTAACAGACATCACTT
GTTTGATGTTTATGTTAAACATTTAAAACACATATTCATTGTCTATTTTCAGGTAGATGACAGT
GGTAATAGTATAAAATGGCTTGACTTGATATATTCAATTAATCAGTTTGGATTATCTATGACAT
GGAGCATTTATATGTCAGACATGATAAAATAAATGGATTATTTCCTAAAGTTAAATAAAATGAA
CAGATAGTATATTACTTTGGTTACTAGTGTAATGCAAAGCATATTCTCATTTTCTATCAACTCC
TGAAATCTCATCCTGCACATTTTCTAAATGACTGAGAAGAGTTATGCTCACTTGCTCAGCCAGA
AATGTTCATAACAAAGACTGGACTTTTAATTTTCAGCAAAATTTAAATCAGGGTAACCACAAAA
CATCTGAATTAAGATTGGCCTTGACAAACTAAATGTATGGTAGTTATTCAAGCCACTGTGGCAG
AACAATATTGATCAAAGTATGTCTCAATAGTATGACCAGCAAAAACAGGCATATAAATGTATGG
TAGTCTTTGCACGCATTGTGCTTCCTACGGGTAAAGGACGATGTAAAAGCGGTTTGGGGGAGTA
TCTACGCATCTTTGAACTTCAGGTTCTAAAATGCCAACTCCATCTGGGTTGATTCATAATTTTA
GGTGGATCAGATCCAAACAGGATGTAATAGCCACATGGACCACTATTTACAAATAATAACTGCC
TTGCGGTTTGAGCCATCATTTATGAGTGTCCCGTCACATCCCTTTAAATCTGATCCATCCAAAC
CTCATCAAATGGTAAATATGAATGTTCATTCACATGCTAGAACTGAGCGATGGATTTACACTAG
ATGCTTCTCCATTTAGATTACTACATCCACATAAGATAGACATTCAAAAATAGGACAAAACAAA
CCTGCAAATATGTCATTAAACAGTGATTCTTCACCAAAGAAATCATCAGAGAAAAGGTACCTGC
AGTTAGTGGATATCTATCAGGTTGCCACTCATTCAAAAGCCATTACGAATAAAAATACAAGGGA
AATCAGGCTTACTCTGAAGTAGCTGTATCAATCAAAAGTTTTTGCAAGCTTCTGAAAAGAACTT
CATATGGATATTTTTGAGACTTGGCTTCAGCTATGTGAGGTATCAAGGCAGGCTGATCAATTTC
CTGACATTCCAACAAAAGCCCACATGACAGACAGAAATGATGCTACTGTGCTGCTTCAACAATA
ATATGGTACTCAAAGTTCAAAATGGCAAGATCAAAATCTAAATAAAGTTAGGTGATGATTCTGT
CCAAAACTGCAACGAACATATATAGGCATGAAACAGTCAATAGCTTCTGTGAGAAGAATTCAAA
GCATGTTAAAATAATTCTTTTTGGTACAACAAGCAACAAGATTTTCTTGTCTGATCAACTATGG
CAAGAACATTGCATTCATAGAATTTGACTGGATCTATTACAGTAGAGAAATGTATCCACAAATT
TGATTATGGTGCTAACTGGATCCTCAATCCTTAAATTTGTGTTGGCATGTCATTTGTGTCCCTA
AACTTGGGGGTTGCATGGCACAATCATGTTACTGAACTTGTATAATCACCATAAATGGTGTGGG
CAAGTCCATATGTCTTGTTACAATGTTAGAGACAACTCAAAATGTGAACAAGACAGGACTAAGT
GTCTGGCAACTAGCCACATTTACTCTAGGATTATATTTATGGTCATGTGCCAATTATGCACTAT
AAGATGATTTACAATGATAGGTGTCTCGTGGCATGTTTGACCGCTAACTAAATAGCTTGTTATG
TTAGTCCATTAGTTCTTGTTGGAACCTTATAGCATCACATGACCCAGTTTAGCTCCCAGCCTCC
GTGTCATGCTTAACAAGTAGAATGCAGTTGAAGACAACCATAAGTATAGGATCGACTGATTACA
GCTAACAGTGAATTACTTGACAAACTACATTATCAAAAAAAAAAAAATCTAAATGTCAGTTGGA
GTGTCAGGAATAAAAATACCTTTAATATGTTTATCCTTTCACCCAAAGCAAAGACAGAAGAACG
GGTCTTCAGAGATTCTTTTCCCATGGAGAAAAGGAATCCTGTACTTCTAGTTTCAACTCCAAGT
AAGTCGGTAGAGGTTGCTATGTCCAGTTGTAGTTTCTCTAATGCTTGAATATACGCACGGAAAT
GTGCACTCAGCACCTGCAAATTGGTAATATGGTAAAAATGTCAAGAAAGCATTTGCTCCAAAAT
ATCTAAGAAGACACACAATGCAAGTGCTCTTGTTATTGTTATCGACTAGTACACTGCATTGCAC
AAGTCAAAAGTCATCGCACACAGACTAGTAGTGTTCCCTAACCTATGCAGAAAGTTTCAAAAGT
ATGTACATATGGAATTATTTTTTTATGAGTAAGGTTGATACCACAACAAGCACAGCAGTACATA
CAGAGAATTGCAAAAAGAACAGAATGAAGAAAAACGGACAGGGATGCAACTGTAACAATCCATC
GCCCAAAAGTCACCAATGACCAAACCCCACCTTGGGGAAGCAGCACAAGCGTGAAACAGCTAGC
TTGGGCCTTTGAACTCTTTGCCTAGGATTAACACATAGTTGCTAAATTTGGACCCTCAAGCATG
CCTGCTACTACTCTACACTTTGTACAGCAGTGCAGTAGTAAACCTTACCCTGGCAATGATTGGG
ACACAAAGCTGGACCAGGATCCAGGTCATACATTGATAATCTAATACCTATTCACACCATAGCT
ATGAGATTTATTATAACATTCACCTTGTTCATGGTATCAATATAAGCTGCACGAACTTCCGCAT
ATATCTCCTTAGCATGTTCCTTAAGAAAAACTATCGTGTAC
						
					

			
		

Sequences
Splice junction sequence	ATTTATTATAACATTCACCTTGTTCATGGTATCAATATAAGCTGCACGAACTTCCGCATATATC TCCTTAGCATGTTCCTTAAGAAAAACTATCGTGTACctgatgctgatgaattattcggatcata agcattatgccgattgcgtcataacagttcaggagcacagcattgaaatgttcatcaacaactt ggataggt
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	CTGATGCTGATGAATTATTCGGATCATAAGCATTATGCCGATTGCGTCATAACAGTTCAGGAGC ACAGCATTGAAATGTTCATCAACAACTTGGATAGGTCCTAAGGGAAAAGTAACAGACATCACTT GTTTGATGTTTATGTTAAACATTTAAAACACATATTCATTGTCTATTTTCAGGTAGATGACAGT GGTAATAGTATAAAATGGCTTGACTTGATATATTCAATTAATCAGTTTGGATTATCTATGACAT GGAGCATTTATATGTCAGACATGATAAAATAAATGGATTATTTCCTAAAGTTAAATAAAATGAA CAGATAGTATATTACTTTGGTTACTAGTGTAATGCAAAGCATATTCTCATTTTCTATCAACTCC TGAAATCTCATCCTGCACATTTTCTAAATGACTGAGAAGAGTTATGCTCACTTGCTCAGCCAGA AATGTTCATAACAAAGACTGGACTTTTAATTTTCAGCAAAATTTAAATCAGGGTAACCACAAAA CATCTGAATTAAGATTGGCCTTGACAAACTAAATGTATGGTAGTTATTCAAGCCACTGTGGCAG AACAATATTGATCAAAGTATGTCTCAATAGTATGACCAGCAAAAACAGGCATATAAATGTATGG TAGTCTTTGCACGCATTGTGCTTCCTACGGGTAAAGGACGATGTAAAAGCGGTTTGGGGGAGTA TCTACGCATCTTTGAACTTCAGGTTCTAAAATGCCAACTCCATCTGGGTTGATTCATAATTTTA GGTGGATCAGATCCAAACAGGATGTAATAGCCACATGGACCACTATTTACAAATAATAACTGCC TTGCGGTTTGAGCCATCATTTATGAGTGTCCCGTCACATCCCTTTAAATCTGATCCATCCAAAC CTCATCAAATGGTAAATATGAATGTTCATTCACATGCTAGAACTGAGCGATGGATTTACACTAG ATGCTTCTCCATTTAGATTACTACATCCACATAAGATAGACATTCAAAAATAGGACAAAACAAA CCTGCAAATATGTCATTAAACAGTGATTCTTCACCAAAGAAATCATCAGAGAAAAGGTACCTGC AGTTAGTGGATATCTATCAGGTTGCCACTCATTCAAAAGCCATTACGAATAAAAATACAAGGGA AATCAGGCTTACTCTGAAGTAGCTGTATCAATCAAAAGTTTTTGCAAGCTTCTGAAAAGAACTT CATATGGATATTTTTGAGACTTGGCTTCAGCTATGTGAGGTATCAAGGCAGGCTGATCAATTTC CTGACATTCCAACAAAAGCCCACATGACAGACAGAAATGATGCTACTGTGCTGCTTCAACAATA ATATGGTACTCAAAGTTCAAAATGGCAAGATCAAAATCTAAATAAAGTTAGGTGATGATTCTGT CCAAAACTGCAACGAACATATATAGGCATGAAACAGTCAATAGCTTCTGTGAGAAGAATTCAAA GCATGTTAAAATAATTCTTTTTGGTACAACAAGCAACAAGATTTTCTTGTCTGATCAACTATGG CAAGAACATTGCATTCATAGAATTTGACTGGATCTATTACAGTAGAGAAATGTATCCACAAATT TGATTATGGTGCTAACTGGATCCTCAATCCTTAAATTTGTGTTGGCATGTCATTTGTGTCCCTA AACTTGGGGGTTGCATGGCACAATCATGTTACTGAACTTGTATAATCACCATAAATGGTGTGGG CAAGTCCATATGTCTTGTTACAATGTTAGAGACAACTCAAAATGTGAACAAGACAGGACTAAGT GTCTGGCAACTAGCCACATTTACTCTAGGATTATATTTATGGTCATGTGCCAATTATGCACTAT AAGATGATTTACAATGATAGGTGTCTCGTGGCATGTTTGACCGCTAACTAAATAGCTTGTTATG TTAGTCCATTAGTTCTTGTTGGAACCTTATAGCATCACATGACCCAGTTTAGCTCCCAGCCTCC GTGTCATGCTTAACAAGTAGAATGCAGTTGAAGACAACCATAAGTATAGGATCGACTGATTACA GCTAACAGTGAATTACTTGACAAACTACATTATCAAAAAAAAAAAAATCTAAATGTCAGTTGGA GTGTCAGGAATAAAAATACCTTTAATATGTTTATCCTTTCACCCAAAGCAAAGACAGAAGAACG GGTCTTCAGAGATTCTTTTCCCATGGAGAAAAGGAATCCTGTACTTCTAGTTTCAACTCCAAGT AAGTCGGTAGAGGTTGCTATGTCCAGTTGTAGTTTCTCTAATGCTTGAATATACGCACGGAAAT GTGCACTCAGCACCTGCAAATTGGTAATATGGTAAAAATGTCAAGAAAGCATTTGCTCCAAAAT ATCTAAGAAGACACACAATGCAAGTGCTCTTGTTATTGTTATCGACTAGTACACTGCATTGCAC AAGTCAAAAGTCATCGCACACAGACTAGTAGTGTTCCCTAACCTATGCAGAAAGTTTCAAAAGT ATGTACATATGGAATTATTTTTTTATGAGTAAGGTTGATACCACAACAAGCACAGCAGTACATA CAGAGAATTGCAAAAAGAACAGAATGAAGAAAAACGGACAGGGATGCAACTGTAACAATCCATC GCCCAAAAGTCACCAATGACCAAACCCCACCTTGGGGAAGCAGCACAAGCGTGAAACAGCTAGC TTGGGCCTTTGAACTCTTTGCCTAGGATTAACACATAGTTGCTAAATTTGGACCCTCAAGCATG CCTGCTACTACTCTACACTTTGTACAGCAGTGCAGTAGTAAACCTTACCCTGGCAATGATTGGG ACACAAAGCTGGACCAGGATCCAGGTCATACATTGATAATCTAATACCTATTCACACCATAGCT ATGAGATTTATTATAACATTCACCTTGTTCATGGTATCAATATAAGCTGCACGAACTTCCGCAT ATATCTCCTTAGCATGTTCCTTAAGAAAAACTATCGTGTAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_013148 						
					
						PMCS
						0.105443021

Conservation Information
Conserved circRNAs	osi_circ_013148
PMCS	0.105443021

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							17381020-17378742(+)
17381630-17381683(-)
						
						Potential amino acid sequence
						
							MCTQHLVHGINISCTNFRIYLLSMFLKKNYRVPDADELFGS*(+)
MNKVLSAHFRAYIQALEKLQLDIATSTDLLGVETRSTGFLFSMGKESLKTRSSVFALGERINIL
KEIDQPALIPHIAEAKSQKYPYEVLFRSLQKLLIDTATSEYLFSDDFFGEESLFNDIFAGPIQV
VDEHFNAVLLNCYDAIGIMLMIRIIHQHQVHDSFS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	17381020-17378742(+) 17381630-17381683(-)
Potential amino acid sequence	MCTQHLVHGINISCTNFRIYLLSMFLKKNYRVPDADELFGS(+) MNKVLSAHFRAYIQALEKLQLDIATSTDLLGVETRSTGFLFSMGKESLKTRSSVFALGERINIL KEIDQPALIPHIAEAKSQKYPYEVLFRSLQKLLIDTATSEYLFSDDFFGEESLFNDIFAGPIQV VDEHFNAVLLNCYDAIGIMLMIRIIHQHQVHDSFS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os03g0417900_circ_g.4

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