Plant Circular RNA Database

Detail information of Os01g0503400_circ_g.6

			
						 General Information
					
						CircRNA Name
						Os01g0503400_circ_g.6
					
						ID in PlantcircBase
						osa_circ_001853
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 17461188-17462988  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0503400						
					
						Parent gene annotation
						
							Similar to (Rice Genome Annotation Project) metal transporter Nr
amp6. (Os01t0503400-01);Similar to cDNA clone:J013164K10, full i
nsert sequence. (Os01t0503400-02);Similar to OsNramp1 (Integral 
membrane protein). (Os01t0503400-03);Similar to (Rice Genome Ann
otation Project) metal transporter Nramp6. (Os01t0503400-04);Sim
ilar to cDNA clone:J013164K10, full insert sequence. (Os01t05034
00-05)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0503400_circ_g.7 						
					
						Support reads
						1
					
						Tissues
						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  
						
							CT-AC							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
						Os01t0503400-04:5
Os01t0503400-01:4
Os01t0503400-03:5
Os01t0503400-05:5

General Information
CircRNA Name	Os01g0503400_circ_g.6
ID in PlantcircBase	osa_circ_001853
Alias	NA
Organism	Oryza sativa
Position	chr1: 17461188-17462988 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0503400
Parent gene annotation	Similar to (Rice Genome Annotation Project) metal transporter Nr amp6. (Os01t0503400-01);Similar to cDNA clone:J013164K10, full i nsert sequence. (Os01t0503400-02);Similar to OsNramp1 (Integral membrane protein). (Os01t0503400-03);Similar to (Rice Genome Ann otation Project) metal transporter Nramp6. (Os01t0503400-04);Sim ilar to cDNA clone:J013164K10, full insert sequence. (Os01t05034 00-05)
Parent gene strand	-
Alternative splicing	Os01g0503400_circ_g.7
Support reads	1
Tissues	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	CT-AC 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	Os01t0503400-04:5 Os01t0503400-01:4 Os01t0503400-03:5 Os01t0503400-05:5

			
						 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  
						
							TGAAGGACAAAGGGGACTTACAGTTACTAGGATCAAGGTATGCGATGGAGATAACAAATCCAGG
ACCAACATGTGCAAGAAATCTCTTCCAAGTGGGTGCcccatatccttgtaacccgagaattagg
aaagtgcatgccccacatgctaggacaccggcccagaaagggatgtggagtagcatgttgtagg
ctaaagca

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							CCCATATCCTTGTAACCCGAGAATTAGGAAAGTGCATGCCCCACATGCTAGGACACCGGCCCAG
AAAGGGATGTGGAGTAGCATGTTGTAGGCTAAAGCAGTTCCTAAAACTGCACAAAGACCACAGA
AAGCACCATGAACCTTGAAGAATTTAAATACAGAAGATAAAACTGTAAAGTTCTGTAAGATTTA
TAAAGGAGAACTGTAGTGTATAGTGCAGATCTTGTAAGCCTATGTCAAGAAATAGATTATAAAA
AATGTGATCAAGATAGATAAGTTAACTGGCACACAAGAAAATAACTCCCACCAGTTACATAAAC
ATGTTATCTTGGACATTGACATGGTCTCCATAGTGCAACATTAGATGGTAATTTCTAATACAAT
ATATTTATTATAAACCAGCAATATAATACTATAAGGAACTTTCCACAACAAATCTATTTAGAAA
GAAATATGACAATTTAAAGTTTTGAAAGTTTGACTTAGCACATGTCCAAATTGATTTATGTGAC
CAGTGGGAGTATTTGATTAAGAAATAAAGCAAGATAAACACATGGAAACCCTATACCGTGAGAG
TAACATTCTCATAAACCACACTATTGGTGTTTCTATCTTCAAAATATAATTAGAGTTATATGCA
ATAATCATCAATATTTTAGATAATGGAATATTTTATTATCCCGGCCACTGCACCCAGAGATGGA
CAAAGCCATGATCACTTATTTACAAGTTTTCCATGCCAAGAAGAATAAACCAAACATAAAGCAA
CATGCTACAGATGTTGATGAAACACAAAATTTCAGTTCGCTTACAACCTATTGCTCAACCACCA
GCCGTAGTTATTGAATAGCTCTATTAAATTTATAATTCAATAAAACAAACTCTGCACAAGGAAG
TTCATTCAAAATATTAACCTAATTTATGGATTACCCCCATGGTTTATACATGGACAACAAATAT
GCTGTAAAAGAGGATACTATTTTTCCAAGTAACAAGTAAAAATAGTATTTCAACTTTTATAGAA
AGCAAAGACAAACAACAAATACTGATACATACCTCCTGGTATAGTGGCAGCAATAACACCAAGC
TCTGCTAGTAACCATAGGCAGTACTTGACATACTTTGGATATTCACCCATGCACAACTCAGCGA
GGTGCCTTCCTACAATATATTTATATGGTAAGTTTCATAGAACATGTATTTTTGTCACCAGCTT
GATAATATGGGTAGTTAGTTTCACCTGTAATGATACCCAAATTTGCTGCCAATGATTGTACAGT
CAACACAAATATGAACCCAAATAGGAGTACCCATAGCAACTGAAAATTTTAAAAATGAATGAAG
GAGAAGTGAGATGGCAAATCTACAATCAATTGACAAAAATGTATAACATAATATTCCACAGAAA
TTTTGAGAGCTTTATACCGAATATCTGTGGCTGGATCCAGCTACCAAATCAGTCTGCACTGTTC
CAATTTTCAAAGTGAAGTAGTTCAATATATTAGTACTAGAAAAAGAAAACGGTGGTATATGAGC
ATGTCCTGCCTAGGAATTCTAGTGGTATCCATCCATGTTCCTTGATCCTATTGTTGAATTTACC
AAAGCCATTTATGACTTAAAAATGTCTTTTTCTCACCATGCATGGATGGATGGACACAAACTGG
TGAGCAGAGACAGGCATAGTTCTAGTCCAAGGAAGATTGAAGGACAAAGGGGACTTACAGTTAC
TAGGATCAAGGTATGCGATGGAGATAACAAATCCAGGACCAACATGTGCAAGAAATCTCTTCCA
AGTGGGTGC
						
					

			
		

Sequences
Splice junction sequence	TGAAGGACAAAGGGGACTTACAGTTACTAGGATCAAGGTATGCGATGGAGATAACAAATCCAGG ACCAACATGTGCAAGAAATCTCTTCCAAGTGGGTGCcccatatccttgtaacccgagaattagg aaagtgcatgccccacatgctaggacaccggcccagaaagggatgtggagtagcatgttgtagg ctaaagca
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CCCATATCCTTGTAACCCGAGAATTAGGAAAGTGCATGCCCCACATGCTAGGACACCGGCCCAG AAAGGGATGTGGAGTAGCATGTTGTAGGCTAAAGCAGTTCCTAAAACTGCACAAAGACCACAGA AAGCACCATGAACCTTGAAGAATTTAAATACAGAAGATAAAACTGTAAAGTTCTGTAAGATTTA TAAAGGAGAACTGTAGTGTATAGTGCAGATCTTGTAAGCCTATGTCAAGAAATAGATTATAAAA AATGTGATCAAGATAGATAAGTTAACTGGCACACAAGAAAATAACTCCCACCAGTTACATAAAC ATGTTATCTTGGACATTGACATGGTCTCCATAGTGCAACATTAGATGGTAATTTCTAATACAAT ATATTTATTATAAACCAGCAATATAATACTATAAGGAACTTTCCACAACAAATCTATTTAGAAA GAAATATGACAATTTAAAGTTTTGAAAGTTTGACTTAGCACATGTCCAAATTGATTTATGTGAC CAGTGGGAGTATTTGATTAAGAAATAAAGCAAGATAAACACATGGAAACCCTATACCGTGAGAG TAACATTCTCATAAACCACACTATTGGTGTTTCTATCTTCAAAATATAATTAGAGTTATATGCA ATAATCATCAATATTTTAGATAATGGAATATTTTATTATCCCGGCCACTGCACCCAGAGATGGA CAAAGCCATGATCACTTATTTACAAGTTTTCCATGCCAAGAAGAATAAACCAAACATAAAGCAA CATGCTACAGATGTTGATGAAACACAAAATTTCAGTTCGCTTACAACCTATTGCTCAACCACCA GCCGTAGTTATTGAATAGCTCTATTAAATTTATAATTCAATAAAACAAACTCTGCACAAGGAAG TTCATTCAAAATATTAACCTAATTTATGGATTACCCCCATGGTTTATACATGGACAACAAATAT GCTGTAAAAGAGGATACTATTTTTCCAAGTAACAAGTAAAAATAGTATTTCAACTTTTATAGAA AGCAAAGACAAACAACAAATACTGATACATACCTCCTGGTATAGTGGCAGCAATAACACCAAGC TCTGCTAGTAACCATAGGCAGTACTTGACATACTTTGGATATTCACCCATGCACAACTCAGCGA GGTGCCTTCCTACAATATATTTATATGGTAAGTTTCATAGAACATGTATTTTTGTCACCAGCTT GATAATATGGGTAGTTAGTTTCACCTGTAATGATACCCAAATTTGCTGCCAATGATTGTACAGT CAACACAAATATGAACCCAAATAGGAGTACCCATAGCAACTGAAAATTTTAAAAATGAATGAAG GAGAAGTGAGATGGCAAATCTACAATCAATTGACAAAAATGTATAACATAATATTCCACAGAAA TTTTGAGAGCTTTATACCGAATATCTGTGGCTGGATCCAGCTACCAAATCAGTCTGCACTGTTC CAATTTTCAAAGTGAAGTAGTTCAATATATTAGTACTAGAAAAAGAAAACGGTGGTATATGAGC ATGTCCTGCCTAGGAATTCTAGTGGTATCCATCCATGTTCCTTGATCCTATTGTTGAATTTACC AAAGCCATTTATGACTTAAAAATGTCTTTTTCTCACCATGCATGGATGGATGGACACAAACTGG TGAGCAGAGACAGGCATAGTTCTAGTCCAAGGAAGATTGAAGGACAAAGGGGACTTACAGTTAC TAGGATCAAGGTATGCGATGGAGATAACAAATCCAGGACCAACATGTGCAAGAAATCTCTTCCA AGTGGGTGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.104571081

Conservation Information
Conserved circRNAs	NA
PMCS	0.104571081

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							17462325-17461275(+)
17462327-17461190(-)
17461194-17462638(-)
17462292-17462923(-)
						
						Potential amino acid sequence
						
							MHNSARCLPVMIPKFAANDCTVNTNMNPNRSTHSNEYLWLDPATKSVCKLLGSRYAMEITNPGP
TCARNLFQVGAPYPCNPRIRKVHAPHARTPAQKGMWSSML*(+)
MGEYPKYVKYCLWLLAELGVIAATIPGVLGTALAYNMLLHIPFWAGVLACGACTFLILGLQGYG
APTWKRFLAHVGPGFVISIAYLDPSNLQTDLVAGSSHRYSLLWVLLFGFIFVLTVQSLAANLGI
ITGRHLAELCMGEYPKYVKYCLWLLAELGVIAATIPGVLGTALAYNMLLHIPFWAGVLACGACT
FLILGLQGYGAPTWKRFLAHVGPGFVISIAYLDPSNLQTDLVAGSSHRYSLLWVLLFGFIFVLT
VQSLAANLGIITGRHLAELCMGEYPKYVKYCLWLLAELGVIAATIPGVLGTALAYNMLLHIPFW
AGVLACGACTFLILGLQGYGAPTWKRFLAHVGPGFVISIAYLDPSNLQTDLVAGSSHRYSLLWV
LLFGFIFVLTVQSLAANLGIITGRHLAELCMGEYPKYVKYCLWLLAELGVIAATIPGVLGTALA
YNMLLHIPFWAGVLACGACTFLILGLQGYG(-)
MGHPLGRDFLHMLVLDLLSPSHTLILVTCRLIW*(-)
MVTSRAWCYCCHYTRSFRNCFSLQHATPHPFLGRCPSMWGMHFPNSRVTRIWGTHLEEISCTCW
SWICYLHRIP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	17462325-17461275(+) 17462327-17461190(-) 17461194-17462638(-) 17462292-17462923(-)
Potential amino acid sequence	MHNSARCLPVMIPKFAANDCTVNTNMNPNRSTHSNEYLWLDPATKSVCKLLGSRYAMEITNPGP TCARNLFQVGAPYPCNPRIRKVHAPHARTPAQKGMWSSML(+) MGEYPKYVKYCLWLLAELGVIAATIPGVLGTALAYNMLLHIPFWAGVLACGACTFLILGLQGYG APTWKRFLAHVGPGFVISIAYLDPSNLQTDLVAGSSHRYSLLWVLLFGFIFVLTVQSLAANLGI ITGRHLAELCMGEYPKYVKYCLWLLAELGVIAATIPGVLGTALAYNMLLHIPFWAGVLACGACT FLILGLQGYGAPTWKRFLAHVGPGFVISIAYLDPSNLQTDLVAGSSHRYSLLWVLLFGFIFVLT VQSLAANLGIITGRHLAELCMGEYPKYVKYCLWLLAELGVIAATIPGVLGTALAYNMLLHIPFW AGVLACGACTFLILGLQGYGAPTWKRFLAHVGPGFVISIAYLDPSNLQTDLVAGSSHRYSLLWV LLFGFIFVLTVQSLAANLGIITGRHLAELCMGEYPKYVKYCLWLLAELGVIAATIPGVLGTALA YNMLLHIPFWAGVLACGACTFLILGLQGYG(-) MGHPLGRDFLHMLVLDLLSPSHTLILVTCRLIW(-) MVTSRAWCYCCHYTRSFRNCFSLQHATPHPFLGRCPSMWGMHFPNSRVTRIWGTHLEEISCTCW SWICYLHRIP*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0503400_circ_g.6

Address

Any questions?

Supported by