Plant Circular RNA Database

Detail information of Os06g0298400_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os06g0298400_circ_g.4
					
						ID in PlantcircBase
						osa_circ_030596
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr6: 11087240-11089137  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							Os06g0298400						
					
						Parent gene annotation
						
							WW/Rsp5/WWP domain containing protein. (Os06t0298400-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os06g0298400_circ_g.1 Os06g0298400_circ_g.2 Os06g0298400_circ_g.3 Os06g0298400_circ_g.5 Os06g0298400_circ_g.6 Os06g0298400_circ_g.7 Os06g0298400_circ_g.8 Os06g0298400_circ_g.9 						
					
						Support reads
						2
					
						Tissues
						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
						Os06t0298400-01:3

General Information
CircRNA Name	Os06g0298400_circ_g.4
ID in PlantcircBase	osa_circ_030596
Alias	NA
Organism	Oryza sativa
Position	chr6: 11087240-11089137 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	Os06g0298400
Parent gene annotation	WW/Rsp5/WWP domain containing protein. (Os06t0298400-01)
Parent gene strand	+
Alternative splicing	Os06g0298400_circ_g.1 Os06g0298400_circ_g.2 Os06g0298400_circ_g.3 Os06g0298400_circ_g.5 Os06g0298400_circ_g.6 Os06g0298400_circ_g.7 Os06g0298400_circ_g.8 Os06g0298400_circ_g.9
Support reads	2
Tissues	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	Os06t0298400-01:3

			
						 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  
						
							ATGCTGGAGCTGTCACTAGTCATGAATCGATGGACATTGATCCTTTGCAGCTTGCAAGATATGG
CGAGGAATTGCTGCAAAGATTGAAGCCGCTAGAAAGggggaacaccttcgaaagagggagagcg
aggggaaaaccatgaccaacaaactggggttcccacttcaccatcttcttcaggtgggtttcat
cagtttcc

									
								

					

						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: 820
Transcript exons: 11087240-11087320,11087810-11087928,11088518-11089137
GGGGAACACCTTCGAAAGAGGGAGAGCGAGGGGAAAACCATGACCAACAAACTGGGGTTCCCAC
TTCACCATCTTCTTCAGATAAGAAGGAGAATCCTCTAGCGTTGCTTGGGCAATATAGTGATGAT
GAAGAGGAAGAGGAAGCAGCAGATCAACCCAATGATGAAACAGAGGCTAATCCTGCAGATGCAG
GTGATAAGATTACTCATGAACGTGGGGACTTGACTAGGAATGAAGGTGATGCACAAAGTGATCT
GGCTGGTTCTGCTAATGTCCAACAAGAGTTAACTGAAGCTGATGATAAGAAGTGCACTGGAAAT
ATTGCTGAAGAAAATGTTGTTGCCATAAAGCCAACTCTGGAAGATGGGACTGCAACAGCAACTG
AAGCTATTCCTGACTCATCTGGGATGCAAATTGTTGGTGACATTGGTGGGAATTGGAAGACTAT
AATGCATGAGCAGAGCAACCAGTGTTACTATTGGAACACAGTTACTGGAGAAACCTCTTGGGAG
ATTCCTAATGTATTAGCTTCTGAAATTGCAGCTGACAGTGTCACTTCTGCATCTGCTCCTACTC
ATGTAGACTACTCTATGGAGGCCCAAGCACATGCCCTTACCCACAATGCCGTGGAAGCTTATCC
AAGTGATATATCTGTGCTAAATGGCTCAGTGGCTTATGCTACTTTGGGAATGGGACAGCCTACT
CATGATGCTTATGCTTATGCTGGAGCTGTCACTAGTCATGAATCGATGGACATTGATCCTTTGC
AGCTTGCAAGATATGGCGAGGAATTGCTGCAAAGATTGAAGCCGCTAGAAAG
						
					

						Genomic sequence
						
							GGGGAACACCTTCGAAAGAGGGAGAGCGAGGGGAAAACCATGACCAACAAACTGGGGTTCCCAC
TTCACCATCTTCTTCAGGTGGGTTTCATCAGTTTCCTTCCAAGGGATTTGTAAAGAAGACATGC
CTGTGGAACCTAAATTTGGTGGAAATTTGGAATTTTTGTACAAGCATATATATGCTCCACATAT
ATGGTTGAGGCACATGTAGGGTTCCGGCCTGCAAGGAACATTGAGTAAATTCTTCAAACCGGGC
TGCTACTGTCAAAATTGAGTAAATGCCTATGGGTAATTTCTCTTTTGGCAGCCTCTAAGCGTGC
GGATCAGAATGTGATTGTTGCCTCCTCGGTTCGTATGTCTCTTTCTCTATAATTCATCTCCTAA
CCTGGTTGTTATATTATTGCCAGGCTGATATACTGCATGTAACATAGTTTTAACCTATATATAC
CACTTGTTTGACTTCTATTATACTCGAATACTGTGTATCTTCATATATACTTCAGAATAAAGTG
CAATGCAGATTGCCACATGCAAGCTATTGCAATTTTACTGATCCATTCTTATTTCCAGATAAGA
AGGAGAATCCTCTAGCGTTGCTTGGGCAATATAGTGATGATGAAGAGGAAGAGGAAGCAGCAGA
TCAACCCAATGATGAAACAGAGGCTAATCCTGCAGATGCAGGTGATAAGGTAATTCTACCTTTC
ATTTTGGCTTCTCTTTATCCATTTCTTTGGGTCGATCTACAGCTTTGGTTTATCTTATGGGCTC
TTGAACTTAAGCTTATGCTAGTTTTGTACTATATAAAGCAACAAATAAGCTGGAGCCTATGAAA
TGGCTTATAATAAGCTAGCTTTTGTTGTGTGTGTGTGTTGTTGGGGGGGGGGGGGGCTTGCTTG
GCCAACAAGCCGCCCTGTTTGGTACAGCTACTCTCTAGTATTGTTGGAGACTTGGAGTTCGATA
TCTCTAGCTCCAACAAATCTTGGAGTTGGAGCTGGGCCCAAATGCTGTTAGGGCGAGACATTTT
GTTCACACATTTGAGTCTACCGTTGGATGATTAAATTACATTGTTCAGTTTGCAAACTCTATTT
TCCGCAAGAATCCAGGAGAAGCCATGCCAAACAGGCCCTTGGCCTATTCTTAGCAATATTGTTT
TCCTGTACACTAGCCACTATAGGAAGCAATGTTGTCAACTATATCTCTTTGGCTTGAGAATTGA
TTTTATTATTGAAGAGTTTGAACACACCTGGCCTCATGGTAACACTACTTTGCTTGTTTCAGAT
TACTCATGAACGTGGGGACTTGACTAGGAATGAAGGTGATGCACAAAGTGATCTGGCTGGTTCT
GCTAATGTCCAACAAGAGTTAACTGAAGCTGATGATAAGAAGTGCACTGGAAATATTGCTGAAG
AAAATGTTGTTGCCATAAAGCCAACTCTGGAAGATGGGACTGCAACAGCAACTGAAGCTATTCC
TGACTCATCTGGGATGCAAATTGTTGGTGACATTGGTGGGAATTGGAAGACTATAATGCATGAG
CAGAGCAACCAGTGTTACTATTGGAACACAGTTACTGGAGAAACCTCTTGGGAGATTCCTAATG
TATTAGCTTCTGAAATTGCAGCTGACAGTGTCACTTCTGCATCTGCTCCTACTCATGTAGACTA
CTCTATGGAGGCCCAAGCACATGCCCTTACCCACAATGCCGTGGAAGCTTATCCAAGTGATATA
TCTGTGCTAAATGGCTCAGTGGCTTATGCTACTTTGGGAATGGGACAGCCTACTCATGATGCTT
ATGCTTATGCTGGAGCTGTCACTAGTCATGAATCGATGGACATTGATCCTTTGCAGCTTGCAAG
ATATGGCGAGGAATTGCTGCAAAGATTGAAGCCGCTAGAAAG
						
					

			
		

Sequences
Splice junction sequence	ATGCTGGAGCTGTCACTAGTCATGAATCGATGGACATTGATCCTTTGCAGCTTGCAAGATATGG CGAGGAATTGCTGCAAAGATTGAAGCCGCTAGAAAGggggaacaccttcgaaagagggagagcg aggggaaaaccatgaccaacaaactggggttcccacttcaccatcttcttcaggtgggtttcat cagtttcc
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: 820 Transcript exons: 11087240-11087320,11087810-11087928,11088518-11089137 GGGGAACACCTTCGAAAGAGGGAGAGCGAGGGGAAAACCATGACCAACAAACTGGGGTTCCCAC TTCACCATCTTCTTCAGATAAGAAGGAGAATCCTCTAGCGTTGCTTGGGCAATATAGTGATGAT GAAGAGGAAGAGGAAGCAGCAGATCAACCCAATGATGAAACAGAGGCTAATCCTGCAGATGCAG GTGATAAGATTACTCATGAACGTGGGGACTTGACTAGGAATGAAGGTGATGCACAAAGTGATCT GGCTGGTTCTGCTAATGTCCAACAAGAGTTAACTGAAGCTGATGATAAGAAGTGCACTGGAAAT ATTGCTGAAGAAAATGTTGTTGCCATAAAGCCAACTCTGGAAGATGGGACTGCAACAGCAACTG AAGCTATTCCTGACTCATCTGGGATGCAAATTGTTGGTGACATTGGTGGGAATTGGAAGACTAT AATGCATGAGCAGAGCAACCAGTGTTACTATTGGAACACAGTTACTGGAGAAACCTCTTGGGAG ATTCCTAATGTATTAGCTTCTGAAATTGCAGCTGACAGTGTCACTTCTGCATCTGCTCCTACTC ATGTAGACTACTCTATGGAGGCCCAAGCACATGCCCTTACCCACAATGCCGTGGAAGCTTATCC AAGTGATATATCTGTGCTAAATGGCTCAGTGGCTTATGCTACTTTGGGAATGGGACAGCCTACT CATGATGCTTATGCTTATGCTGGAGCTGTCACTAGTCATGAATCGATGGACATTGATCCTTTGC AGCTTGCAAGATATGGCGAGGAATTGCTGCAAAGATTGAAGCCGCTAGAAAG
Genomic sequence	GGGGAACACCTTCGAAAGAGGGAGAGCGAGGGGAAAACCATGACCAACAAACTGGGGTTCCCAC TTCACCATCTTCTTCAGGTGGGTTTCATCAGTTTCCTTCCAAGGGATTTGTAAAGAAGACATGC CTGTGGAACCTAAATTTGGTGGAAATTTGGAATTTTTGTACAAGCATATATATGCTCCACATAT ATGGTTGAGGCACATGTAGGGTTCCGGCCTGCAAGGAACATTGAGTAAATTCTTCAAACCGGGC TGCTACTGTCAAAATTGAGTAAATGCCTATGGGTAATTTCTCTTTTGGCAGCCTCTAAGCGTGC GGATCAGAATGTGATTGTTGCCTCCTCGGTTCGTATGTCTCTTTCTCTATAATTCATCTCCTAA CCTGGTTGTTATATTATTGCCAGGCTGATATACTGCATGTAACATAGTTTTAACCTATATATAC CACTTGTTTGACTTCTATTATACTCGAATACTGTGTATCTTCATATATACTTCAGAATAAAGTG CAATGCAGATTGCCACATGCAAGCTATTGCAATTTTACTGATCCATTCTTATTTCCAGATAAGA AGGAGAATCCTCTAGCGTTGCTTGGGCAATATAGTGATGATGAAGAGGAAGAGGAAGCAGCAGA TCAACCCAATGATGAAACAGAGGCTAATCCTGCAGATGCAGGTGATAAGGTAATTCTACCTTTC ATTTTGGCTTCTCTTTATCCATTTCTTTGGGTCGATCTACAGCTTTGGTTTATCTTATGGGCTC TTGAACTTAAGCTTATGCTAGTTTTGTACTATATAAAGCAACAAATAAGCTGGAGCCTATGAAA TGGCTTATAATAAGCTAGCTTTTGTTGTGTGTGTGTGTTGTTGGGGGGGGGGGGGGCTTGCTTG GCCAACAAGCCGCCCTGTTTGGTACAGCTACTCTCTAGTATTGTTGGAGACTTGGAGTTCGATA TCTCTAGCTCCAACAAATCTTGGAGTTGGAGCTGGGCCCAAATGCTGTTAGGGCGAGACATTTT GTTCACACATTTGAGTCTACCGTTGGATGATTAAATTACATTGTTCAGTTTGCAAACTCTATTT TCCGCAAGAATCCAGGAGAAGCCATGCCAAACAGGCCCTTGGCCTATTCTTAGCAATATTGTTT TCCTGTACACTAGCCACTATAGGAAGCAATGTTGTCAACTATATCTCTTTGGCTTGAGAATTGA TTTTATTATTGAAGAGTTTGAACACACCTGGCCTCATGGTAACACTACTTTGCTTGTTTCAGAT TACTCATGAACGTGGGGACTTGACTAGGAATGAAGGTGATGCACAAAGTGATCTGGCTGGTTCT GCTAATGTCCAACAAGAGTTAACTGAAGCTGATGATAAGAAGTGCACTGGAAATATTGCTGAAG AAAATGTTGTTGCCATAAAGCCAACTCTGGAAGATGGGACTGCAACAGCAACTGAAGCTATTCC TGACTCATCTGGGATGCAAATTGTTGGTGACATTGGTGGGAATTGGAAGACTATAATGCATGAG CAGAGCAACCAGTGTTACTATTGGAACACAGTTACTGGAGAAACCTCTTGGGAGATTCCTAATG TATTAGCTTCTGAAATTGCAGCTGACAGTGTCACTTCTGCATCTGCTCCTACTCATGTAGACTA CTCTATGGAGGCCCAAGCACATGCCCTTACCCACAATGCCGTGGAAGCTTATCCAAGTGATATA TCTGTGCTAAATGGCTCAGTGGCTTATGCTACTTTGGGAATGGGACAGCCTACTCATGATGCTT ATGCTTATGCTGGAGCTGTCACTAGTCATGAATCGATGGACATTGATCCTTTGCAGCTTGCAAG ATATGGCGAGGAATTGCTGCAAAGATTGAAGCCGCTAGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.256360015

Conservation Information
Conserved circRNAs	NA
PMCS	0.256360015

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11088726-11087279(+)
11087313-11089059(-)
11087282-11089055(-)
						
						Potential amino acid sequence
						
							MQIVGDIGGNWKTIMHEQSNQCYYWNTVTGETSWEIPNVLASEIAADSVTSASAPTHVDYSMEA
QAHALTHNAVEAYPSDISVLNGSVAYATLGMGQPTHDAYAYAGAVTSHESMDIDPLQLARYGEE
LLQRLKPLERGNTFERGRARGKP*(+)
MVKWEPQFVGHGFPLALPLSKVFPLSSGFNLCSNSSPYLASCKGSMSIDS*(-)
MVFPSLSLFRRCSPFLAASIFAAIPRHILQAAKDQCPSIHD*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11088726-11087279(+) 11087313-11089059(-) 11087282-11089055(-)
Potential amino acid sequence	MQIVGDIGGNWKTIMHEQSNQCYYWNTVTGETSWEIPNVLASEIAADSVTSASAPTHVDYSMEA QAHALTHNAVEAYPSDISVLNGSVAYATLGMGQPTHDAYAYAGAVTSHESMDIDPLQLARYGEE LLQRLKPLERGNTFERGRARGKP(+) MVKWEPQFVGHGFPLALPLSKVFPLSSGFNLCSNSSPYLASCKGSMSIDS(-) MVFPSLSLFRRCSPFLAASIFAAIPRHILQAAKDQCPSIHD*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os06g0298400_circ_g.4

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