Plant Circular RNA Database

Detail information of Os09g0475400_circ_g.6

			
						 General Information
					
						CircRNA Name
						Os09g0475400_circ_g.6
					
						ID in PlantcircBase
						osa_circ_039563
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 18211985-18214058  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							Os09g0475400						
					
						Parent gene annotation
						
							Helix-loop-helix DNA-binding domain containing protein. (Os09t04
75400-01);Similar to cDNA clone:J023084K14, full insert sequence
. (Os09t0475400-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os09g0475400_circ_g.1 Os09g0475400_circ_g.2 Os09g0475400_circ_g.3 Os09g0475400_circ_g.4 Os09g0475400_circ_g.5 Os09g0475400_circ_g.7 Os09g0475400_circ_g.8 Os09g0475400_circ_g.9 Os09g0475400_circ_g.10 						
					
						Support reads
						2
					
						Tissues
						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
						Os09t0475400-02:7
Os09t0475400-01:7

General Information
CircRNA Name	Os09g0475400_circ_g.6
ID in PlantcircBase	osa_circ_039563
Alias	NA
Organism	Oryza sativa
Position	chr9: 18211985-18214058 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	Os09g0475400
Parent gene annotation	Helix-loop-helix DNA-binding domain containing protein. (Os09t04 75400-01);Similar to cDNA clone:J023084K14, full insert sequence . (Os09t0475400-02)
Parent gene strand	+
Alternative splicing	Os09g0475400_circ_g.1 Os09g0475400_circ_g.2 Os09g0475400_circ_g.3 Os09g0475400_circ_g.4 Os09g0475400_circ_g.5 Os09g0475400_circ_g.7 Os09g0475400_circ_g.8 Os09g0475400_circ_g.9 Os09g0475400_circ_g.10
Support reads	2
Tissues	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	Os09t0475400-02:7 Os09t0475400-01:7

			
						 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  
						
							CTCAGGTGTTGATCTGTCCCAATCCAGCATATCTGTGCAGATCAACCTTGGCAAGCGAGCTGTT
AAGAGACCTGGTGCTGATGGATCCTCCAGTTCTAAGagttgacagtgagggtggatgggaaggg
tgggagctgcagtggaagtggtactgatcagcggcccagctcaccacgttcaaagcactctgct
accgagca

									
								

					

						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: 172
Transcript exons: 18211985-18212035,18213938-18214058
AGTTGACAGTGAGGGTGGATGGGAAGGGTGGGAGCTGCAGTGGAAGTGGTAGTTGACTCATGCC
CTTGAAAGCTCAGGTGTTGATCTGTCCCAATCCAGCATATCTGTGCAGATCAACCTTGGCAAGC
GAGCTGTTAAGAGACCTGGTGCTGATGGATCCTCCAGTTCTAAG
Transcript length: 818
Transcript exons: 18211985-18212111,18212873-18212942,18213031-18213126,18
213234-18213272,18213365-18213575,18213688-18213829,1821
3926-18214058
AGTTGACAGTGAGGGTGGATGGGAAGGGTGGGAGCTGCAGTGGAAGTGGTACTGATCAGCGGCC
CAGCTCACCACGTTCAAAGCACTCTGCTACCGAGCAGCGTCGGCGCAGCAAGATCAATGACAGG
TTTCAGATACTTAGGGAGCTGTTACCTCATAGCGACCAAAAGAGAGACAAAGCAACATTTCTGT
TAGAGGTTATTGAATACATACGCTTTTTGCAAGAGAAAGTGCAGAAGTTTGAAGCTTCAGTCCC
TGAATGGAACCAAGAAAATGCAAAGATACTTCCATGGTCAAACATATATTTTAGATCGTTCTGG
AAAAATTCACAAAGTAAAGGTCAGAACCCTGGAGATGATTTGCCTGATCCTTCACAGTTCATCC
GGAATGGGTCCTCTTCTGGGTATAATTTCACTGGCAAACCTGATGATAACCACAACATGGTGAC
ATCAGCAGCTGCCTCAGGGGCACAAGAACTGGTGGAAACTGACCATGCAGCTAGCGTGTCCTAC
AGATCAGCAGAAACTCCGACAAACATTACCAACAATGTTACATCCCAAGCCCAAGCCCAGTGGG
CTAGTCCGGCTGGTGTGGATGACTGTGCAATGAACAGCGAAATGTTAAATAACCAACAGTTGGC
AATTGATGAAGGAACAATAAGCTTGTCAAGCCAATATTCCCAACAGCTACTTGGTACGTTGACT
CATGCCCTTGAAAGCTCAGGTGTTGATCTGTCCCAATCCAGCATATCTGTGCAGATCAACCTTG
GCAAGCGAGCTGTTAAGAGACCTGGTGCTGATGGATCCTCCAGTTCTAAG
						
					

						Genomic sequence
						
							AGTTGACAGTGAGGGTGGATGGGAAGGGTGGGAGCTGCAGTGGAAGTGGTACTGATCAGCGGCC
CAGCTCACCACGTTCAAAGCACTCTGCTACCGAGCAGCGTCGGCGCAGCAAGATCAATGACAGG
TAACATTTCCTGTATCCGGAGTTTCTGAACCATAGAAATGGCTATTACAGTATGATTGTCTGCA
GGACCTTTGGTGCTGTAGATTATGTTTGACCACATGTTATGTTCCCTGGATGAAGAGAATATAC
TGCAGGAATAGAGTGCCTGGTTATAAAGTATTGCAAAAATTTCTGGTGTATTTGTACATATTGA
GGCAATGTTTGTACCTATTAAATACAGTGAATTTGAAAAGAAATCCCAAATCAGTTTTTTAAAC
AAAAATCACAAAAGGGTATAAAGTGCACTTTACTGAGTTATGCAAGAGCACATTGGCACAAAAC
TACAAATCCTCTCCATCCAAAAAAACCCTGAAGTTCTCTTTTTTAATCTTGCAATCTGGAAAAT
CGAAGACATGAGTACTAATGCTTGTTGAAGACTAAGCAGGTGTCTAGAGGATGCATTGTCTAAA
TAACTTTTGGACATGTAATTGGTCGGGCTTCCCTTTTGTATACTGACAGGAAAAAAATGTCTTT
GTGAAGTCTCTTAAGTCTAGTATTATGAGTAAATTGTCATATTTTGTTCATGATAAACAACTGG
AACCACATTCAATCGTCAAAACCATATGAATTTCTGAGATCATAAAGGTTATGCATGTAACGCT
ACCAAATATTTACTTTGAAAGATCGTAGGTATATGTTCATGTGGAACGGAATGGGTCGCTTATA
TGAAGTTGAGCAAACACTTGTGTAACTGTTTCCTTTACTCTGCATCATTTCCACAGGTTTCAGA
TACTTAGGGAGCTGTTACCTCATAGCGACCAAAAGAGAGACAAAGCAACATTTCTGTTAGAGGT
ATGCTCGTAGCAGCAGCCTATTTGATCCAATTAGTCTCTCCGAGGTAATCAGCTTGGTTATTTT
TTTAACACCCTTTCTAATGCAGGTTATTGAATACATACGCTTTTTGCAAGAGAAAGTGCAGAAG
TTTGAAGCTTCAGTCCCTGAATGGAACCAAGAAAATGCAAAGATACTTCCATGGGTAATTACTA
CTCATTTTTATCCTCCCAAGCCAGCGCTGCTTGATTAGCATTTTTATGAAGTCAAATTTTGGCT
GTCTGCGTCTGAACACAGTTTTGTATTTTGCAGTCAAACATATATTTTAGATCGTTCTGGAAAA
ATTCACAAGTAAGTTACTGTTGATATTATACCCTTTTCAAATAATTTCATTTTTCAATTGGTAT
TCTGACCAGCATCTTCCTCATGCTCTTGTGCTGCAGAGTAAAGGTCAGAACCCTGGAGATGATT
TGCCTGATCCTTCACAGTTCATCCGGAATGGGTCCTCTTCTGGGTATAATTTCACTGGCAAACC
TGATGATAACCACAACATGGTGACATCAGCAGCTGCCTCAGGGGCACAAGAACTGGTGGAAACT
GACCATGCAGCTAGCGTGTCCTACAGATCAGCAGAAACTCCGACAAACATTACCAGTATGATTG
CTAATCCACAATTGATTTAATTTTTAGAATAGTTTTCTCTGCTACCTTTCTGAGACCAGAAGCA
GGATTGGTTATTCACGAATAAATCTTTCTTTGAACGTAGACAATGTTACATCCCAAGCCCAAGC
CCAGTGGGCTAGTCCGGCTGGTGTGGATGACTGTGCAATGAACAGCGAAATGTTAAATAACCAA
CAGTTGGCAATTGATGAAGGAACAATAAGCTTGTCAAGCCAATATTCCCAACAGTACGTCTTTA
AAAATATAATTCCCAGTGTTATTTTGTTCCCCTTGCTGGGAAAAGTACATTGATGCATAGGTTT
GTTTTTGTTGACTTACTACAGGCTACTTGGTACGTTGACTCATGCCCTTGAAAGCTCAGGTGTT
GATCTGTCCCAATCCAGCATATCTGTGCAGATCAACCTTGGCAAGCGAGCTGTTAAGAGACCTG
GTGCTGATGGATCCTCCAGTTCTAAG
						
					

			
		

Sequences
Splice junction sequence	CTCAGGTGTTGATCTGTCCCAATCCAGCATATCTGTGCAGATCAACCTTGGCAAGCGAGCTGTT AAGAGACCTGGTGCTGATGGATCCTCCAGTTCTAAGagttgacagtgagggtggatgggaaggg tgggagctgcagtggaagtggtactgatcagcggcccagctcaccacgttcaaagcactctgct accgagca
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: 172 Transcript exons: 18211985-18212035,18213938-18214058 AGTTGACAGTGAGGGTGGATGGGAAGGGTGGGAGCTGCAGTGGAAGTGGTAGTTGACTCATGCC CTTGAAAGCTCAGGTGTTGATCTGTCCCAATCCAGCATATCTGTGCAGATCAACCTTGGCAAGC GAGCTGTTAAGAGACCTGGTGCTGATGGATCCTCCAGTTCTAAG Transcript length: 818 Transcript exons: 18211985-18212111,18212873-18212942,18213031-18213126,18 213234-18213272,18213365-18213575,18213688-18213829,1821 3926-18214058 AGTTGACAGTGAGGGTGGATGGGAAGGGTGGGAGCTGCAGTGGAAGTGGTACTGATCAGCGGCC CAGCTCACCACGTTCAAAGCACTCTGCTACCGAGCAGCGTCGGCGCAGCAAGATCAATGACAGG TTTCAGATACTTAGGGAGCTGTTACCTCATAGCGACCAAAAGAGAGACAAAGCAACATTTCTGT TAGAGGTTATTGAATACATACGCTTTTTGCAAGAGAAAGTGCAGAAGTTTGAAGCTTCAGTCCC TGAATGGAACCAAGAAAATGCAAAGATACTTCCATGGTCAAACATATATTTTAGATCGTTCTGG AAAAATTCACAAAGTAAAGGTCAGAACCCTGGAGATGATTTGCCTGATCCTTCACAGTTCATCC GGAATGGGTCCTCTTCTGGGTATAATTTCACTGGCAAACCTGATGATAACCACAACATGGTGAC ATCAGCAGCTGCCTCAGGGGCACAAGAACTGGTGGAAACTGACCATGCAGCTAGCGTGTCCTAC AGATCAGCAGAAACTCCGACAAACATTACCAACAATGTTACATCCCAAGCCCAAGCCCAGTGGG CTAGTCCGGCTGGTGTGGATGACTGTGCAATGAACAGCGAAATGTTAAATAACCAACAGTTGGC AATTGATGAAGGAACAATAAGCTTGTCAAGCCAATATTCCCAACAGCTACTTGGTACGTTGACT CATGCCCTTGAAAGCTCAGGTGTTGATCTGTCCCAATCCAGCATATCTGTGCAGATCAACCTTG GCAAGCGAGCTGTTAAGAGACCTGGTGCTGATGGATCCTCCAGTTCTAAG
Genomic sequence	AGTTGACAGTGAGGGTGGATGGGAAGGGTGGGAGCTGCAGTGGAAGTGGTACTGATCAGCGGCC CAGCTCACCACGTTCAAAGCACTCTGCTACCGAGCAGCGTCGGCGCAGCAAGATCAATGACAGG TAACATTTCCTGTATCCGGAGTTTCTGAACCATAGAAATGGCTATTACAGTATGATTGTCTGCA GGACCTTTGGTGCTGTAGATTATGTTTGACCACATGTTATGTTCCCTGGATGAAGAGAATATAC TGCAGGAATAGAGTGCCTGGTTATAAAGTATTGCAAAAATTTCTGGTGTATTTGTACATATTGA GGCAATGTTTGTACCTATTAAATACAGTGAATTTGAAAAGAAATCCCAAATCAGTTTTTTAAAC AAAAATCACAAAAGGGTATAAAGTGCACTTTACTGAGTTATGCAAGAGCACATTGGCACAAAAC TACAAATCCTCTCCATCCAAAAAAACCCTGAAGTTCTCTTTTTTAATCTTGCAATCTGGAAAAT CGAAGACATGAGTACTAATGCTTGTTGAAGACTAAGCAGGTGTCTAGAGGATGCATTGTCTAAA TAACTTTTGGACATGTAATTGGTCGGGCTTCCCTTTTGTATACTGACAGGAAAAAAATGTCTTT GTGAAGTCTCTTAAGTCTAGTATTATGAGTAAATTGTCATATTTTGTTCATGATAAACAACTGG AACCACATTCAATCGTCAAAACCATATGAATTTCTGAGATCATAAAGGTTATGCATGTAACGCT ACCAAATATTTACTTTGAAAGATCGTAGGTATATGTTCATGTGGAACGGAATGGGTCGCTTATA TGAAGTTGAGCAAACACTTGTGTAACTGTTTCCTTTACTCTGCATCATTTCCACAGGTTTCAGA TACTTAGGGAGCTGTTACCTCATAGCGACCAAAAGAGAGACAAAGCAACATTTCTGTTAGAGGT ATGCTCGTAGCAGCAGCCTATTTGATCCAATTAGTCTCTCCGAGGTAATCAGCTTGGTTATTTT TTTAACACCCTTTCTAATGCAGGTTATTGAATACATACGCTTTTTGCAAGAGAAAGTGCAGAAG TTTGAAGCTTCAGTCCCTGAATGGAACCAAGAAAATGCAAAGATACTTCCATGGGTAATTACTA CTCATTTTTATCCTCCCAAGCCAGCGCTGCTTGATTAGCATTTTTATGAAGTCAAATTTTGGCT GTCTGCGTCTGAACACAGTTTTGTATTTTGCAGTCAAACATATATTTTAGATCGTTCTGGAAAA ATTCACAAGTAAGTTACTGTTGATATTATACCCTTTTCAAATAATTTCATTTTTCAATTGGTAT TCTGACCAGCATCTTCCTCATGCTCTTGTGCTGCAGAGTAAAGGTCAGAACCCTGGAGATGATT TGCCTGATCCTTCACAGTTCATCCGGAATGGGTCCTCTTCTGGGTATAATTTCACTGGCAAACC TGATGATAACCACAACATGGTGACATCAGCAGCTGCCTCAGGGGCACAAGAACTGGTGGAAACT GACCATGCAGCTAGCGTGTCCTACAGATCAGCAGAAACTCCGACAAACATTACCAGTATGATTG CTAATCCACAATTGATTTAATTTTTAGAATAGTTTTCTCTGCTACCTTTCTGAGACCAGAAGCA GGATTGGTTATTCACGAATAAATCTTTCTTTGAACGTAGACAATGTTACATCCCAAGCCCAAGC CCAGTGGGCTAGTCCGGCTGGTGTGGATGACTGTGCAATGAACAGCGAAATGTTAAATAACCAA CAGTTGGCAATTGATGAAGGAACAATAAGCTTGTCAAGCCAATATTCCCAACAGTACGTCTTTA AAAATATAATTCCCAGTGTTATTTTGTTCCCCTTGCTGGGAAAAGTACATTGATGCATAGGTTT GTTTTTGTTGACTTACTACAGGCTACTTGGTACGTTGACTCATGCCCTTGAAAGCTCAGGTGTT GATCTGTCCCAATCCAGCATATCTGTGCAGATCAACCTTGGCAAGCGAGCTGTTAAGAGACCTG GTGCTGATGGATCCTCCAGTTCTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_018564 						
					
						PMCS
						0.220997019

Conservation Information
Conserved circRNAs	osi_circ_018564
PMCS	0.220997019

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							18213947-18212036(+)
18213474-18211987(+)
						
						Potential amino acid sequence
						
							MPLKAQVLICPNPAYLCRSTLASELLRDLVLMDPPVLRVDSEGGWEGWELQWKWY*(+)
MVTSAAASGAQELVETDHAASVSYRSAETPTNITNNVTSQAQAQWASPAGVDDCAMNSEMLNNQ
QLAIDEGTISLSSQYSQQLLGTLTHALESSGVDLSQSSISVQINLGKRAVKRPGADGSSSSKS*
(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	18213947-18212036(+) 18213474-18211987(+)
Potential amino acid sequence	MPLKAQVLICPNPAYLCRSTLASELLRDLVLMDPPVLRVDSEGGWEGWELQWKWY(+) MVTSAAASGAQELVETDHAASVSYRSAETPTNITNNVTSQAQAQWASPAGVDDCAMNSEMLNNQ QLAIDEGTISLSSQYSQQLLGTLTHALESSGVDLSQSSISVQINLGKRAVKRPGADGSSSSKS (+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os09g0475400_circ_g.6

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