Plant Circular RNA Database

Detail information of Os06g0335500_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os06g0335500_circ_g.4
					
						ID in PlantcircBase
						osa_circ_030741
					
						Alias
						Os_ciR1776
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr6: 13346607-13348348  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os06g0335500						
					
						Parent gene annotation
						
							AUX/IAA protein family protein. (Os06t0335500-01);Similar to Aux
in-responsive protein IAA21. (Os06t0335500-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os06g0335500_circ_g.1 Os06g0335500_circ_g.2 Os06g0335500_circ_g.3 Os06g0335500_circ_g.5 Os06g0335500_circ_g.6 Os06g0335500_circ_g.7 Os06g0335500_circ_g.8 						
					
						Support reads
						8/3
					
						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  
						
							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
						Os06t0335500-01:3
Os06t0335500-02:2

General Information
CircRNA Name	Os06g0335500_circ_g.4
ID in PlantcircBase	osa_circ_030741
Alias	Os_ciR1776
Organism	Oryza sativa
Position	chr6: 13346607-13348348 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os06g0335500
Parent gene annotation	AUX/IAA protein family protein. (Os06t0335500-01);Similar to Aux in-responsive protein IAA21. (Os06t0335500-02)
Parent gene strand	+
Alternative splicing	Os06g0335500_circ_g.1 Os06g0335500_circ_g.2 Os06g0335500_circ_g.3 Os06g0335500_circ_g.5 Os06g0335500_circ_g.6 Os06g0335500_circ_g.7 Os06g0335500_circ_g.8
Support reads	8/3
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	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	Os06t0335500-01:3 Os06t0335500-02:2

			
						 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  
						
							CACTTGACGTCTATTTTTTTTTATTTGTTGTATTGCAGAATGTTCACAGACAGCTGTAGGAGGC
TGAGGATTATGAAGGGGTCAGATGCAGTGGGCCTTGggcacaggtggtaggatggccaccaatc
cgcagctacaggaagaacaccatggcgatgagccagcctgctctgaaaggcaaagacgacggcg
aggcgaag

									
								

					

						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: 446
Transcript exons: 13346607-13346848,13347537-13347678,13348287-13348348
GGCACAGGTGGTAGGATGGCCACCAATCCGCAGCTACAGGAAGAACACCATGGCGATGAGCCAG
CCTGCTCTGAAAGGCAAAGACGACGGCGAGGCGAAGCAGGCTCCGGCATCCGGTTGCCTCTATG
TCAAGGTGAGCATGGATGGTGCTCCTTACCTCAGGAAGGTGGACCTCAAGATGTACAAGAACTA
CAAGGAGCTCTCTTTGGCTCTGGAGAAGATGTTCAGCTGCTTTACCGTCGGTCATGGTGAATCA
AATGGGAAGTCAGGGAGAGATGGATTATCTGATTGCCGCCTGATGGATCTTAAAAATGGAACAG
AACTTGTGCTCACTTATGAGGACAAGGATGAAGATTGGATGCTTGTTGGTGATGTTCCGTGGCG
AATGTTCACAGACAGCTGTAGGAGGCTGAGGATTATGAAGGGGTCAGATGCAGTGGGCCTTG
						
					

						Genomic sequence
						
							GGCACAGGTGGTAGGATGGCCACCAATCCGCAGCTACAGGAAGAACACCATGGCGATGAGCCAG
CCTGCTCTGAAAGGCAAAGACGACGGCGAGGCGAAGCAGGCTCCGGCATCCGGTTGCCTCTATG
TCAAGGTGAGCATGGATGGTGCTCCTTACCTCAGGAAGGTGGACCTCAAGATGTACAAGAACTA
CAAGGAGCTCTCTTTGGCTCTGGAGAAGATGTTCAGCTGCTTTACCGTCGGTGAGCTCTCGTTT
TTGCGCCTAATTTTTTCATTTCCTTGTTGCTGTTGTGAGGTAGTAGTTCTTTCTTTAACTGATG
CTGTTCTTACCATATCGAGGTAGATCTAGTTTCCTTGGACTTGGAGACCAGACAATTCTCCATG
CCATTTATATTAATTAAATGTGGATTTGTCACATTTGGCATTCTACATACTGTAGTCATGTAGT
GTAACTGTTGGTTCAGTGCATAAAGAACTAGGGCCTGATGCTGTTGTTTGTTAAATATTAATGG
TTTGCTGGATTACTTCTCATCCAATCATTTACATTACTGTGATCCTTGGAACTATTGTTCTACT
TCTCTTATTATCTTCCATGGCAAGTAACGTTGCTGTGCAAGTGAAGCTTTCGGTTTTAGATTGT
TCTGCCTTCCTATTCTAGAACTGAAATTTTAGTTTACGTGTACGGTGTTATGTCATGCTGTTTG
TGCTGAACTGTAGCCTTCTACAAATGCCCTTGCTCTTGCTTCTAAGTCTAAGAATACGTAAATG
AAGCAGTGATGACAGTATTGTTGTTTGATTCATAAATTTTAGTTACTGCATAATTTGGATTTTT
CCCATCAATTGATTGGTCTCTGTTAACGCCATCTATTGTTCAGCTTTATTGGAAATGTTCCTGA
ACAGGGTTTACTTTCATATTTTGGGCTCCTGCAGGTCATGGTGAATCAAATGGGAAGTCAGGGA
GAGATGGATTATCTGATTGCCGCCTGATGGATCTTAAAAATGGAACAGAACTTGTGCTCACTTA
TGAGGACAAGGATGAAGATTGGATGCTTGTTGGTGATGTTCCGTGGCGGTGAGTAATGCTTATA
CCGCAAAATTTGTTTCCTACAATCGTAAGCAATGATGATGTTTTAATCCGTATCAGTGTATCTG
CAAATATCAAACTAGCTAGTGAAGTTTTAGTGACTTCTATATTTCCATCTTCGCATGACCTTAT
GCCTTGCTTGTTTGATGGATTGACTTGTTCTGGTAGGATGCAAAGTTTACTATATTGTTTTCTA
CTTGTATATGAAATCTAAAAAGGCCTGATACTATGGTTCCTGACAAGTCACGTCCCATTTATAG
TGAATACTTTATCTTTCATTAGAACACCATATAGCTGTTAGTCAAAGAAAGTAGTGAAGTTGAG
AAATATTTGGGTTATGGTAACAAATGTCTAATTGCAATCCTTGTGTCATATTCACCTATATTAG
TGGTGGGTCCTATATTTCGTCTCCTTACTTGAACAGCCTTTATTTTAGGTTATTTCCTGAAATT
TCATGGTCTGCAGTTCTGCGCTGCATTTCACTTCCTGGCCCACCAAGTTTACACACATTCCAAT
GAGTTCTTGGCTTGAGACCAGAACATGCTATTCTTAAAAGGCCACTTGACGTCTATTTTTTTTT
ATTTGTTGTATTGCAGAATGTTCACAGACAGCTGTAGGAGGCTGAGGATTATGAAGGGGTCAGA
TGCAGTGGGCCTTG
						
					

			
		

Sequences
Splice junction sequence	CACTTGACGTCTATTTTTTTTTATTTGTTGTATTGCAGAATGTTCACAGACAGCTGTAGGAGGC TGAGGATTATGAAGGGGTCAGATGCAGTGGGCCTTGggcacaggtggtaggatggccaccaatc cgcagctacaggaagaacaccatggcgatgagccagcctgctctgaaaggcaaagacgacggcg aggcgaag
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: 446 Transcript exons: 13346607-13346848,13347537-13347678,13348287-13348348 GGCACAGGTGGTAGGATGGCCACCAATCCGCAGCTACAGGAAGAACACCATGGCGATGAGCCAG CCTGCTCTGAAAGGCAAAGACGACGGCGAGGCGAAGCAGGCTCCGGCATCCGGTTGCCTCTATG TCAAGGTGAGCATGGATGGTGCTCCTTACCTCAGGAAGGTGGACCTCAAGATGTACAAGAACTA CAAGGAGCTCTCTTTGGCTCTGGAGAAGATGTTCAGCTGCTTTACCGTCGGTCATGGTGAATCA AATGGGAAGTCAGGGAGAGATGGATTATCTGATTGCCGCCTGATGGATCTTAAAAATGGAACAG AACTTGTGCTCACTTATGAGGACAAGGATGAAGATTGGATGCTTGTTGGTGATGTTCCGTGGCG AATGTTCACAGACAGCTGTAGGAGGCTGAGGATTATGAAGGGGTCAGATGCAGTGGGCCTTG
Genomic sequence	GGCACAGGTGGTAGGATGGCCACCAATCCGCAGCTACAGGAAGAACACCATGGCGATGAGCCAG CCTGCTCTGAAAGGCAAAGACGACGGCGAGGCGAAGCAGGCTCCGGCATCCGGTTGCCTCTATG TCAAGGTGAGCATGGATGGTGCTCCTTACCTCAGGAAGGTGGACCTCAAGATGTACAAGAACTA CAAGGAGCTCTCTTTGGCTCTGGAGAAGATGTTCAGCTGCTTTACCGTCGGTGAGCTCTCGTTT TTGCGCCTAATTTTTTCATTTCCTTGTTGCTGTTGTGAGGTAGTAGTTCTTTCTTTAACTGATG CTGTTCTTACCATATCGAGGTAGATCTAGTTTCCTTGGACTTGGAGACCAGACAATTCTCCATG CCATTTATATTAATTAAATGTGGATTTGTCACATTTGGCATTCTACATACTGTAGTCATGTAGT GTAACTGTTGGTTCAGTGCATAAAGAACTAGGGCCTGATGCTGTTGTTTGTTAAATATTAATGG TTTGCTGGATTACTTCTCATCCAATCATTTACATTACTGTGATCCTTGGAACTATTGTTCTACT TCTCTTATTATCTTCCATGGCAAGTAACGTTGCTGTGCAAGTGAAGCTTTCGGTTTTAGATTGT TCTGCCTTCCTATTCTAGAACTGAAATTTTAGTTTACGTGTACGGTGTTATGTCATGCTGTTTG TGCTGAACTGTAGCCTTCTACAAATGCCCTTGCTCTTGCTTCTAAGTCTAAGAATACGTAAATG AAGCAGTGATGACAGTATTGTTGTTTGATTCATAAATTTTAGTTACTGCATAATTTGGATTTTT CCCATCAATTGATTGGTCTCTGTTAACGCCATCTATTGTTCAGCTTTATTGGAAATGTTCCTGA ACAGGGTTTACTTTCATATTTTGGGCTCCTGCAGGTCATGGTGAATCAAATGGGAAGTCAGGGA GAGATGGATTATCTGATTGCCGCCTGATGGATCTTAAAAATGGAACAGAACTTGTGCTCACTTA TGAGGACAAGGATGAAGATTGGATGCTTGTTGGTGATGTTCCGTGGCGGTGAGTAATGCTTATA CCGCAAAATTTGTTTCCTACAATCGTAAGCAATGATGATGTTTTAATCCGTATCAGTGTATCTG CAAATATCAAACTAGCTAGTGAAGTTTTAGTGACTTCTATATTTCCATCTTCGCATGACCTTAT GCCTTGCTTGTTTGATGGATTGACTTGTTCTGGTAGGATGCAAAGTTTACTATATTGTTTTCTA CTTGTATATGAAATCTAAAAAGGCCTGATACTATGGTTCCTGACAAGTCACGTCCCATTTATAG TGAATACTTTATCTTTCATTAGAACACCATATAGCTGTTAGTCAAAGAAAGTAGTGAAGTTGAG AAATATTTGGGTTATGGTAACAAATGTCTAATTGCAATCCTTGTGTCATATTCACCTATATTAG TGGTGGGTCCTATATTTCGTCTCCTTACTTGAACAGCCTTTATTTTAGGTTATTTCCTGAAATT TCATGGTCTGCAGTTCTGCGCTGCATTTCACTTCCTGGCCCACCAAGTTTACACACATTCCAAT GAGTTCTTGGCTTGAGACCAGAACATGCTATTCTTAAAAGGCCACTTGACGTCTATTTTTTTTT ATTTGTTGTATTGCAGAATGTTCACAGACAGCTGTAGGAGGCTGAGGATTATGAAGGGGTCAGA TGCAGTGGGCCTTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_016153 						
					
						PMCS
						0.24450033

Conservation Information
Conserved circRNAs	osi_circ_016153
PMCS	0.24450033

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							13346657-13346617(+)
13348335-13347543(+)
13346721-13348332(-)
13347543-13347630(-)
						
						Potential amino acid sequence
						
							MAMSQPALKGKDDGEAKQAPASGCLYVKVSMDGAPYLRKVDLKMYKNYKELSLALEKMFSCFTV
GHGESNGKSGRDGLSDCRLMDLKNGTELVLTYEDKDEDWMLVGDVPWRMFTDSCRRLRIMKGSD
AVGLGHRW*(+)
MQWALGTGGRMATNPQLQEEHHGDEPACSERQRRRRGEAGSGIRLPLCQGEHGWCSLPQEGGPQ
DVQELQGALFGSGEDVQLLYRRSW*(+)
MPEPASPRRRLCLSEQAGSSPWCSSCSCGLVAILPPVPKAHCI*(-)
MTDGKAAEHLLQSQRELLVVLVHLEVHLPEVRSTIHAHLDIEATGCRSLLRLAVVFAFQSRLAH
RHGVLPVAADWWPSYHLCPRPTASDPFIILSLLQLSVNIRHGTSPTSIQSSSLSS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	13346657-13346617(+) 13348335-13347543(+) 13346721-13348332(-) 13347543-13347630(-)
Potential amino acid sequence	MAMSQPALKGKDDGEAKQAPASGCLYVKVSMDGAPYLRKVDLKMYKNYKELSLALEKMFSCFTV GHGESNGKSGRDGLSDCRLMDLKNGTELVLTYEDKDEDWMLVGDVPWRMFTDSCRRLRIMKGSD AVGLGHRW(+) MQWALGTGGRMATNPQLQEEHHGDEPACSERQRRRRGEAGSGIRLPLCQGEHGWCSLPQEGGPQ DVQELQGALFGSGEDVQLLYRRSW(+) MPEPASPRRRLCLSEQAGSSPWCSSCSCGLVAILPPVPKAHCI(-) MTDGKAAEHLLQSQRELLVVLVHLEVHLPEVRSTIHAHLDIEATGCRSLLRLAVVFAFQSRLAH RHGVLPVAADWWPSYHLCPRPTASDPFIILSLLQLSVNIRHGTSPTSIQSSSLSS(-)
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 Os06g0335500_circ_g.4

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