Plant Circular RNA Database

Detail information of Os06g0167500_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os06g0167500_circ_g.4
					
						ID in PlantcircBase
						osa_circ_029815
					
						Alias
						Os_ciR1161
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr6: 3415001-3416249  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ
					
						Parent gene
						
							Os06g0167500						
					
						Parent gene annotation
						
							Leucine-rich repeat, plant specific containing protein. (Os06t01
67500-01);Hypothetical conserved gene. (Os06t0167500-02);Hypothe
tical conserved gene. (Os06t0167500-03)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os06g0167500_circ_g.1 Os06g0167500_circ_g.2 Os06g0167500_circ_g.3 Os06g0167500_circ_g.5 						
					
						Support reads
						16/5
					
						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
						Os06t0167500-02:3
Os06t0167500-03:3
Os06t0167500-01:3

General Information
CircRNA Name	Os06g0167500_circ_g.4
ID in PlantcircBase	osa_circ_029815
Alias	Os_ciR1161
Organism	Oryza sativa
Position	chr6: 3415001-3416249 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ
Parent gene	Os06g0167500
Parent gene annotation	Leucine-rich repeat, plant specific containing protein. (Os06t01 67500-01);Hypothetical conserved gene. (Os06t0167500-02);Hypothe tical conserved gene. (Os06t0167500-03)
Parent gene strand	+
Alternative splicing	Os06g0167500_circ_g.1 Os06g0167500_circ_g.2 Os06g0167500_circ_g.3 Os06g0167500_circ_g.5
Support reads	16/5
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	Os06t0167500-02:3 Os06t0167500-03:3 Os06t0167500-01:3

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F: ATAGTTGCCCAGGTGGAAAAA
 R: CCTAGCAGTTCTGCTGATAGAA
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	Yes 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	F: ATAGTTGCCCAGGTGGAAAAA R: CCTAGCAGTTCTGCTGATAGAA 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  
						
							CTGATTGTTACAGTGGCCTTACTCATTATTTTGTGAACATGTCTTTTATGCATAGAAATTATAT
TGGAACTTCGATTGGTGCAGGAAGCTCAGTTGGCAGttatgtaggtgaaaacaatttcaatgga
tctctgcctgatcaaatgcctcaatcactagttgctctgtaagtctgctgtttgcatttgctga
ttgaagtg

						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: 180
Transcript exons: 3415001-3415066,3416046-3416114,3416205-3416249
TTATGTAGGTGAAAACAATTTCAATGGATCTCTGCCTGATCAAATGCCTCAATCACTAGTTGCT
CTGGATGTCACATATAATCCTTTGCTTAGGGGAAGGCTTCCTAGCAGTTCTGCTGATAGAAAGA
TGCGGATAAATTATATTGGAACTTCGATTGGTGCAGGAAGCTCAGTTGGCAG
						
						Genomic sequence
						
							TTATGTAGGTGAAAACAATTTCAATGGATCTCTGCCTGATCAAATGCCTCAATCACTAGTTGCT
CTGTAAGTCTGCTGTTTGCATTTGCTGATTGAAGTGTAGGAAAAAGCATTTTATAATGTGAACT
TCATGGATGGAAAACAAATGGCACGATTTTTCCACCTGGGCAACTATTATATGTTATATTTTCA
TCAGCTACTGTTGCAAGCAATCCCTACTACTTAAAATATTTCGTACTCTGTCAAGGTGCATACT
GTTACACAACCGTCTTCAAATACTAAATGAGAAAGAACGGCAATATAGCACAAATCCTTTCCTT
GTCAGCTAATCCTTCTTCTCCCAAGCTGATAAGAGGATAAGAGAAATCCTTTCCTTGTCAGCTA
ATCCTCCTTCACCCAAGCTAATAAGAGGAAAAGAGAAGGCAGAATTAGATGCAACTCTATTTGC
CATTTTACATTTCATGCAATGTGGTCAAGTTCAGCATGCTCATAGTGCCTAATTTGATGGTGGA
GCATGTGGGGGACACGGTACCCGGGTGCCCTAGAGGAGGCCTTTGGGTTGTACTGCATAGGGTG
GGTCGAGTGCCTTAGGCCCATGCAACATTTTTGTATAGAAAGGGATAAGAGATAAGAAAGTCTA
TCCAATCCCATGTAAATAGATGGTAGATACCCGGATTATTATGGATATCGCGCCATACATGCCG
CCGGATGCCCTAGCACTATATAAAAGGCATCGGTAGGAACCCTAGAGAGGTTAGACACCATTAT
ACCCACCATCAGCCACTCCATTGTTGATTTGCACACACCTCGTAGATCCAATCTACGCTAACTG
GACTAGGGTATTACCTCATTCGAGGGCCTGAACTAGTATAAATTTGTGTCACCATCTCTCCTTG
TTCTCGTGCACCCTATAAATTATATTACCGATCATAAAAATCGACAGAGCATATGTTGAAGTAG
GATAGATTTTCTTCCCTAGTACAAAGTACAATCTGATATTAAACCTGTCTAACAATTCTCCTTT
CCTTTTTATTGAAAACTACAGGGATGTCACATATAATCCTTTGCTTAGGGGAAGGCTTCCTAGC
AGTTCTGCTGATAGAAAGATGCGGATGTATGCCATTTACTTGTATTAAGCACTAGACTCAACTG
ATTGTTACAGTGGCCTTACTCATTATTTTGTGAACATGTCTTTTATGCATAGAAATTATATTGG
AACTTCGATTGGTGCAGGAAGCTCAGTTGGCAG

Sequences
Splice junction sequence	CTGATTGTTACAGTGGCCTTACTCATTATTTTGTGAACATGTCTTTTATGCATAGAAATTATAT TGGAACTTCGATTGGTGCAGGAAGCTCAGTTGGCAGttatgtaggtgaaaacaatttcaatgga tctctgcctgatcaaatgcctcaatcactagttgctctgtaagtctgctgtttgcatttgctga ttgaagtg
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: 180 Transcript exons: 3415001-3415066,3416046-3416114,3416205-3416249 TTATGTAGGTGAAAACAATTTCAATGGATCTCTGCCTGATCAAATGCCTCAATCACTAGTTGCT CTGGATGTCACATATAATCCTTTGCTTAGGGGAAGGCTTCCTAGCAGTTCTGCTGATAGAAAGA TGCGGATAAATTATATTGGAACTTCGATTGGTGCAGGAAGCTCAGTTGGCAG
Genomic sequence	TTATGTAGGTGAAAACAATTTCAATGGATCTCTGCCTGATCAAATGCCTCAATCACTAGTTGCT CTGTAAGTCTGCTGTTTGCATTTGCTGATTGAAGTGTAGGAAAAAGCATTTTATAATGTGAACT TCATGGATGGAAAACAAATGGCACGATTTTTCCACCTGGGCAACTATTATATGTTATATTTTCA TCAGCTACTGTTGCAAGCAATCCCTACTACTTAAAATATTTCGTACTCTGTCAAGGTGCATACT GTTACACAACCGTCTTCAAATACTAAATGAGAAAGAACGGCAATATAGCACAAATCCTTTCCTT GTCAGCTAATCCTTCTTCTCCCAAGCTGATAAGAGGATAAGAGAAATCCTTTCCTTGTCAGCTA ATCCTCCTTCACCCAAGCTAATAAGAGGAAAAGAGAAGGCAGAATTAGATGCAACTCTATTTGC CATTTTACATTTCATGCAATGTGGTCAAGTTCAGCATGCTCATAGTGCCTAATTTGATGGTGGA GCATGTGGGGGACACGGTACCCGGGTGCCCTAGAGGAGGCCTTTGGGTTGTACTGCATAGGGTG GGTCGAGTGCCTTAGGCCCATGCAACATTTTTGTATAGAAAGGGATAAGAGATAAGAAAGTCTA TCCAATCCCATGTAAATAGATGGTAGATACCCGGATTATTATGGATATCGCGCCATACATGCCG CCGGATGCCCTAGCACTATATAAAAGGCATCGGTAGGAACCCTAGAGAGGTTAGACACCATTAT ACCCACCATCAGCCACTCCATTGTTGATTTGCACACACCTCGTAGATCCAATCTACGCTAACTG GACTAGGGTATTACCTCATTCGAGGGCCTGAACTAGTATAAATTTGTGTCACCATCTCTCCTTG TTCTCGTGCACCCTATAAATTATATTACCGATCATAAAAATCGACAGAGCATATGTTGAAGTAG GATAGATTTTCTTCCCTAGTACAAAGTACAATCTGATATTAAACCTGTCTAACAATTCTCCTTT CCTTTTTATTGAAAACTACAGGGATGTCACATATAATCCTTTGCTTAGGGGAAGGCTTCCTAGC AGTTCTGCTGATAGAAAGATGCGGATGTATGCCATTTACTTGTATTAAGCACTAGACTCAACTG ATTGTTACAGTGGCCTTACTCATTATTTTGTGAACATGTCTTTTATGCATAGAAATTATATTGG AACTTCGATTGGTGCAGGAAGCTCAGTTGGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_016706 						
					
						PMCS
						0.313556952

Conservation Information
Conserved circRNAs	osi_circ_016706
PMCS	0.313556952

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3415045-3416246(+)
						
						Potential amino acid sequence
						
							MPQSLVALDVTYNPLLRGRLPSSSADRKMRINYIGTSIGAGSSVGSYVGENNFNGSLPDQMPQS
LVALDVTYNPLLRGRLPSSSADRKMRINYIGTSIGAGSSVGSYVGENNFNGSLPDQMPQSLVAL
DVTYNPLLRGRLPSSSADRKMRINYIGTSIGAGSSVGSYVGENNFNGSLPDQMPQSLVALDVTY
NPLLRGRLPSSSADRKMRINYIGTSIGAGSSVG(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3415045-3416246(+)
Potential amino acid sequence	MPQSLVALDVTYNPLLRGRLPSSSADRKMRINYIGTSIGAGSSVGSYVGENNFNGSLPDQMPQS LVALDVTYNPLLRGRLPSSSADRKMRINYIGTSIGAGSSVGSYVGENNFNGSLPDQMPQSLVAL DVTYNPLLRGRLPSSSADRKMRINYIGTSIGAGSSVGSYVGENNFNGSLPDQMPQSLVALDVTY NPLLRGRLPSSSADRKMRINYIGTSIGAGSSVG(+)
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 Os06g0167500_circ_g.4

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