Plant Circular RNA Database

Detail information of Os01g0957900_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0957900_circ_g.3
					
						ID in PlantcircBase
						osa_circ_005883
					
						Alias
						Os_ciR3274
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 42220623-42222520  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ
					
						Parent gene
						
							Os01g0957900						
					
						Parent gene annotation
						
							Armadillo-type fold domain containing protein. (Os01t0957900-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0957900_circ_g.2 Os01g0957900_circ_g.4 Os01g0957900_circ_g.5 Os01g0957900_circ_g.6 Os01g0957900_circ_g.7 Os01g0957900_circ_g.8 						
					
						Support reads
						3/3
					
						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
						Os01t0957900-01:4

General Information
CircRNA Name	Os01g0957900_circ_g.3
ID in PlantcircBase	osa_circ_005883
Alias	Os_ciR3274
Organism	Oryza sativa
Position	chr1: 42220623-42222520 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ
Parent gene	Os01g0957900
Parent gene annotation	Armadillo-type fold domain containing protein. (Os01t0957900-01)
Parent gene strand	+
Alternative splicing	Os01g0957900_circ_g.2 Os01g0957900_circ_g.4 Os01g0957900_circ_g.5 Os01g0957900_circ_g.6 Os01g0957900_circ_g.7 Os01g0957900_circ_g.8
Support reads	3/3
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	Os01t0957900-01:4

			
						 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  
						
							ATACTCAGTCAGAGCAAGAGAATATTGAATGCCAAACTAATGAGGTAGACAAGAAGGATGAAGA
GGGTACTGATGTAGATGAGGAGAAAAATAAAAAGAGgttgaagagtgcattggggcagctgtca
ttgctttggggccagataaaatcctttcactaattccaataggttttgatgaggaccggctaac
atgctcaa

									
								

					

						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: 821
Transcript exons: 42220623-42220833,42220907-42221088,42221215-42221454,42
222333-42222520
GTTGAAGAGTGCATTGGGGCAGCTGTCATTGCTTTGGGGCCAGATAAAATCCTTTCACTAATTC
CAATAGGTTTTGATGAGGACCGGCTAACATGCTCAAATACTTGGCTTCTGCCCATTTTAGATAA
GTATATCTATGGGGCCTCACCACAACAATTCCTAGAGCGCATTGTACCTCTAGCAGAATCTGTA
CAACAAGCTTCTAACATGGCCAAGTCAGCACGGAAATGTGAAGACTTGAAATCATGTTCCAATC
AGCTGTGGAATTTGCTTCCTGCCTTCTGCCGCTACCCAGTTGATATATGTCAGAATTTCGGTTC
TCTATCCAAGTTGCTACTAGAGATGTTGAAATGTGACAAGTATCTGTACAAATCCGCTGTTAAA
GCCCTGCAGCAACTTGTAGATGGAACTAGAAGATTAAGTAGCAGTGAGCAAAACAGAGAAATAT
ATGTGGAGCTTTCTACTTTGTTCTCCTCGAAAATTATTAACTTAAGCTGCCCAAGCTTTGAGAG
GTGCTCTAAAAAAGATGCTCGTAAGAACATGAAAGTTCTGGCATCACATTCTGTGTATCTTCTT
TCTACTGTCACAGATTATTTTCTAGATTCTTCACCAGAGAAGCGTTCTCATTTGAAGGATGCAT
TGAGATGTTTGGCTCAACTTTCTGGTAGCACGAACATTTGCAACCTTTTCCTTTCACTGGTTAA
AAGATTTGGTTTAGAAGATACTCAGTCAGAGCAAGAGAATATTGAATGCCAAACTAATGAGGTA
GACAAGAAGGATGAAGAGGGTACTGATGTAGATGAGGAGAAAAATAAAAAGAG
						
					

						Genomic sequence
						
							GTTGAAGAGTGCATTGGGGCAGCTGTCATTGCTTTGGGGCCAGATAAAATCCTTTCACTAATTC
CAATAGGTTTTGATGAGGACCGGCTAACATGCTCAAATACTTGGCTTCTGCCCATTTTAGATAA
GTATATCTATGGGGCCTCACCACAACAATTCCTAGAGCGCATTGTACCTCTAGCAGAATCTGTA
CAACAAGCTTCTAACATGGGTAGGTAAAGCCAATTCATTAGGTCTTAAATACATACGCAACATG
ATTTCCTAACCTTCTGCTTTAACTTCAGCCAAGTCAGCACGGAAATGTGAAGACTTGAAATCAT
GTTCCAATCAGCTGTGGAATTTGCTTCCTGCCTTCTGCCGCTACCCAGTTGATATATGTCAGAA
TTTCGGTTCTCTATCCAAGTTGCTACTAGAGATGTTGAAATGTGACAAGTATCTGTACAAATCC
GCTGTTAAAGCCCTGCAGGTGCAGTTTTCATTTACAGATATACTGCATTTTTCTTATCTTATCT
ATACTCATTTTCTTTCTGGAATTTCGAACTACAAGGCTGCTCCATGTCTTCTCTCAGACAACAT
GTTTTATTTTTCTCAGCAACTTGTAGATGGAACTAGAAGATTAAGTAGCAGTGAGCAAAACAGA
GAAATATATGTGGAGCTTTCTACTTTGTTCTCCTCGAAAATTATTAACTTAAGCTGCCCAAGCT
TTGAGAGGTGCTCTAAAAAAGATGCTCGTAAGAACATGAAAGTTCTGGCATCACATTCTGTGTA
TCTTCTTTCTACTGTCACAGATTATTTTCTAGATTCTTCACCAGAGAAGCGTTCTCATTTGAAG
GTGTGTCACTTAATATTTCTAATTATTATCAGTTGATGAGCATGTTAGATGTCTTCAAACCAAT
TAAGTCTAAAAAACCCCTACTTAAATCAGTCACGGACGGACTCACATATTGAAACATTACTGTA
TTTTCTATTATTTGGCATTTGAAGTTTGATTGATCTATGCACATTAGAGTACCACTGATTTAAA
TGAGGTTTTGTGTCACAAACTTGAGAAAGGCTTAACGCCGCTTGATGCAGCCCAATATTGACTG
CTGCAGGCTGTGCCCTACACAATTAAAGAGAGATTATATTAGTAGAACATGGTTATTTTGTTGT
GTTTGTACTTTTTTACTATCATTTAACCATGTTTGGTTGATATAGATAAAACCAATAAAGGTGT
ATCAGGGATGAGTTATATAAGTAAATTTTATAAATGCACTTTTGCATATTATTATCAATACATA
AGAAAAGGAACCACAACCTTATTTCTTCTCAGCAAGGCGCACTCAAATGACTAAATAGCAAATA
CCAAGTGAAAAATGTCTGAGAGATTAATATCCTGGTCCAGTTGGTTATTCCATATCCATGTGCA
CGGTGTGCCCATGAATGGCTCAGTCCAATGGCACTGAATACTTGTTACAGTTGGTTTGATACTT
TGATGCACTGTATTCTTGTAGTGTATATTAACAAAATACAGTTTTACCTTGAATACATGATTTC
TCCAACTTCCTTAGCTGTTTGTACCTGGGAGAGGTTGAGCTGTACTAGTTGTGTCAGTAAATTA
GGTTATGTACCCTTTGCTCTAGCACACCTTCTATTTATCCCTGAAAACAACATTAGTTTTTAGA
CTACATATTGCACAATATTTATCATATCATCTTTGTCTTCTTGCAGGATGCATTGAGATGTTTG
GCTCAACTTTCTGGTAGCACGAACATTTGCAACCTTTTCCTTTCACTGGTTAAAAGATTTGGTT
TAGAAGATACTCAGTCAGAGCAAGAGAATATTGAATGCCAAACTAATGAGGTAGACAAGAAGGA
TGAAGAGGGTACTGATGTAGATGAGGAGAAAAATAAAAAGAG
						
					

			
		

Sequences
Splice junction sequence	ATACTCAGTCAGAGCAAGAGAATATTGAATGCCAAACTAATGAGGTAGACAAGAAGGATGAAGA GGGTACTGATGTAGATGAGGAGAAAAATAAAAAGAGgttgaagagtgcattggggcagctgtca ttgctttggggccagataaaatcctttcactaattccaataggttttgatgaggaccggctaac atgctcaa
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: 821 Transcript exons: 42220623-42220833,42220907-42221088,42221215-42221454,42 222333-42222520 GTTGAAGAGTGCATTGGGGCAGCTGTCATTGCTTTGGGGCCAGATAAAATCCTTTCACTAATTC CAATAGGTTTTGATGAGGACCGGCTAACATGCTCAAATACTTGGCTTCTGCCCATTTTAGATAA GTATATCTATGGGGCCTCACCACAACAATTCCTAGAGCGCATTGTACCTCTAGCAGAATCTGTA CAACAAGCTTCTAACATGGCCAAGTCAGCACGGAAATGTGAAGACTTGAAATCATGTTCCAATC AGCTGTGGAATTTGCTTCCTGCCTTCTGCCGCTACCCAGTTGATATATGTCAGAATTTCGGTTC TCTATCCAAGTTGCTACTAGAGATGTTGAAATGTGACAAGTATCTGTACAAATCCGCTGTTAAA GCCCTGCAGCAACTTGTAGATGGAACTAGAAGATTAAGTAGCAGTGAGCAAAACAGAGAAATAT ATGTGGAGCTTTCTACTTTGTTCTCCTCGAAAATTATTAACTTAAGCTGCCCAAGCTTTGAGAG GTGCTCTAAAAAAGATGCTCGTAAGAACATGAAAGTTCTGGCATCACATTCTGTGTATCTTCTT TCTACTGTCACAGATTATTTTCTAGATTCTTCACCAGAGAAGCGTTCTCATTTGAAGGATGCAT TGAGATGTTTGGCTCAACTTTCTGGTAGCACGAACATTTGCAACCTTTTCCTTTCACTGGTTAA AAGATTTGGTTTAGAAGATACTCAGTCAGAGCAAGAGAATATTGAATGCCAAACTAATGAGGTA GACAAGAAGGATGAAGAGGGTACTGATGTAGATGAGGAGAAAAATAAAAAGAG
Genomic sequence	GTTGAAGAGTGCATTGGGGCAGCTGTCATTGCTTTGGGGCCAGATAAAATCCTTTCACTAATTC CAATAGGTTTTGATGAGGACCGGCTAACATGCTCAAATACTTGGCTTCTGCCCATTTTAGATAA GTATATCTATGGGGCCTCACCACAACAATTCCTAGAGCGCATTGTACCTCTAGCAGAATCTGTA CAACAAGCTTCTAACATGGGTAGGTAAAGCCAATTCATTAGGTCTTAAATACATACGCAACATG ATTTCCTAACCTTCTGCTTTAACTTCAGCCAAGTCAGCACGGAAATGTGAAGACTTGAAATCAT GTTCCAATCAGCTGTGGAATTTGCTTCCTGCCTTCTGCCGCTACCCAGTTGATATATGTCAGAA TTTCGGTTCTCTATCCAAGTTGCTACTAGAGATGTTGAAATGTGACAAGTATCTGTACAAATCC GCTGTTAAAGCCCTGCAGGTGCAGTTTTCATTTACAGATATACTGCATTTTTCTTATCTTATCT ATACTCATTTTCTTTCTGGAATTTCGAACTACAAGGCTGCTCCATGTCTTCTCTCAGACAACAT GTTTTATTTTTCTCAGCAACTTGTAGATGGAACTAGAAGATTAAGTAGCAGTGAGCAAAACAGA GAAATATATGTGGAGCTTTCTACTTTGTTCTCCTCGAAAATTATTAACTTAAGCTGCCCAAGCT TTGAGAGGTGCTCTAAAAAAGATGCTCGTAAGAACATGAAAGTTCTGGCATCACATTCTGTGTA TCTTCTTTCTACTGTCACAGATTATTTTCTAGATTCTTCACCAGAGAAGCGTTCTCATTTGAAG GTGTGTCACTTAATATTTCTAATTATTATCAGTTGATGAGCATGTTAGATGTCTTCAAACCAAT TAAGTCTAAAAAACCCCTACTTAAATCAGTCACGGACGGACTCACATATTGAAACATTACTGTA TTTTCTATTATTTGGCATTTGAAGTTTGATTGATCTATGCACATTAGAGTACCACTGATTTAAA TGAGGTTTTGTGTCACAAACTTGAGAAAGGCTTAACGCCGCTTGATGCAGCCCAATATTGACTG CTGCAGGCTGTGCCCTACACAATTAAAGAGAGATTATATTAGTAGAACATGGTTATTTTGTTGT GTTTGTACTTTTTTACTATCATTTAACCATGTTTGGTTGATATAGATAAAACCAATAAAGGTGT ATCAGGGATGAGTTATATAAGTAAATTTTATAAATGCACTTTTGCATATTATTATCAATACATA AGAAAAGGAACCACAACCTTATTTCTTCTCAGCAAGGCGCACTCAAATGACTAAATAGCAAATA CCAAGTGAAAAATGTCTGAGAGATTAATATCCTGGTCCAGTTGGTTATTCCATATCCATGTGCA CGGTGTGCCCATGAATGGCTCAGTCCAATGGCACTGAATACTTGTTACAGTTGGTTTGATACTT TGATGCACTGTATTCTTGTAGTGTATATTAACAAAATACAGTTTTACCTTGAATACATGATTTC TCCAACTTCCTTAGCTGTTTGTACCTGGGAGAGGTTGAGCTGTACTAGTTGTGTCAGTAAATTA GGTTATGTACCCTTTGCTCTAGCACACCTTCTATTTATCCCTGAAAACAACATTAGTTTTTAGA CTACATATTGCACAATATTTATCATATCATCTTTGTCTTCTTGCAGGATGCATTGAGATGTTTG GCTCAACTTTCTGGTAGCACGAACATTTGCAACCTTTTCCTTTCACTGGTTAAAAGATTTGGTT TAGAAGATACTCAGTCAGAGCAAGAGAATATTGAATGCCAAACTAATGAGGTAGACAAGAAGGA TGAAGAGGGTACTGATGTAGATGAGGAGAAAAATAAAAAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002693* osi_circ_011220 						
					
						PMCS
						0.34793506

Conservation Information
Conserved circRNAs	osi_circ_002693* osi_circ_011220
PMCS	0.34793506

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							42220831-42220680(+)
42220743-42222459(-)
						
						Potential amino acid sequence
						
							MAKSARKCEDLKSCSNQLWNLLPAFCRYPVDICQNFGSLSKLLLEMLKCDKYLYKSAVKALQQL
VDGTRRLSSSEQNREIYVELSTLFSSKIINLSCPSFERCSKKDARKNMKVLASHSVYLLSTVTD
YFLDSSPEKRSHLKDALRCLAQLSGSTNICNLFLSLVKRFGLEDTQSEQENIECQTNEVDKKDE
EGTDVDEEKNKKRLKSALGQLSLLWGQIKSFH*(+)
MGRSQVFEHVSRSSSKPIGISERILSGPKAMTAAPMHSSTSFYFSPHLHQYPLHPSCLPH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	42220831-42220680(+) 42220743-42222459(-)
Potential amino acid sequence	MAKSARKCEDLKSCSNQLWNLLPAFCRYPVDICQNFGSLSKLLLEMLKCDKYLYKSAVKALQQL VDGTRRLSSSEQNREIYVELSTLFSSKIINLSCPSFERCSKKDARKNMKVLASHSVYLLSTVTD YFLDSSPEKRSHLKDALRCLAQLSGSTNICNLFLSLVKRFGLEDTQSEQENIECQTNEVDKKDE EGTDVDEEKNKKRLKSALGQLSLLWGQIKSFH(+) MGRSQVFEHVSRSSSKPIGISERILSGPKAMTAAPMHSSTSFYFSPHLHQYPLHPSCLPH(-)
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 Os01g0957900_circ_g.3

Address

Any questions?

Supported by